package com.cipres.mrBayesPlugin.ui;

import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import javax.swing.JFileChooser;
import javax.swing.JLabel;

import org.json.simple.JSONObject;
import org.virion.jam.util.SimpleListener;

import com.biomatters.geneious.publicapi.components.Dialogs;
import com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument;
import com.biomatters.geneious.publicapi.documents.DocumentField;
import com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument;
import com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument;
import com.biomatters.geneious.publicapi.plugin.DocumentOperationException;
import com.biomatters.geneious.publicapi.plugin.Options;
import com.biomatters.geneious.publicapi.plugin.Options.BooleanOption;
import com.biomatters.geneious.publicapi.plugin.Options.ButtonOption;
import com.biomatters.geneious.publicapi.plugin.Options.Option;
import com.biomatters.geneious.publicapi.plugin.Options.OptionValue;
import com.biomatters.geneious.publicapi.plugin.Options.StringOption;
import com.biomatters.geneious.publicapi.utilities.FileUtilities;
import com.cipres.mrBayesPlugin.ui.CipresOptions.ParamType;
import com.cipres.mrBayesPlugin.utilities.MrBayesUtilities;

import jebl.util.SafePrintWriter;

public class IQTREEXSEDE_1_01_01Options extends CipresOptions {

	private static final String ESTIMATE="estimate";
	private static final String AUTO="auto";
	
	//Simple Parameters
	private static DoubleOption runtime_; 
	private static ComboBoxOption which_iqtree_; 
	private static IntegerOption specify_numpatterns_; 
	private static BooleanOption more_memory_;
	private static BooleanOption more_memory2_;
	private static BooleanOption specify_safe_;
	//private static BooleanOption specify_autocores_;
	private static ComboBoxOption specify_runtype_;
	private static ComboBoxOption sequence_type_;
	private static ComboBoxOption codon_type_;
	private static ComboBoxOption nt2aa_type_;
    private static StringOption starting_tree_File;
    private static ButtonOption starting_tree_FileBrowse;	 
	private static BooleanOption use_nj_; 
	private static BooleanOption use_random_; 
	private static StringOption specify_outgroup_;
	private static StringOption specify_prefix_;
	private static StringOption specify_seed_;
	//private static StringOption specify_quartets_;
	
	//Advanced Parameters
	private static ComboBoxOption specify_quartets_;
	private static IntegerOption specify_quartetnum_;
	private static StringOption specify_quartetset_file_;
	private static ButtonOption specify_quartetset_file_Browse;
	private static BooleanOption write_quartets_;
	
	private static Option partition_type_;
	private static StringOption partition_file_;
	private static BooleanOption mixed_sequence_;
	private static ComboBoxOption num_mixedsequences_;
	private static ButtonOption partition_file_Browse;
	private static StringOption datatype2_file_;
	private static ButtonOption datatype2_file_Browse;
	private static StringOption datatype3_file_;
	private static ButtonOption datatype3_file_Browse;
	private static StringOption datatype4_file_;
	private static ButtonOption datatype4_file_Browse;
	private static StringOption datatype5_file_;
	private static ButtonOption datatype5_file_Browse;
	
	private static ComboBoxOption specify_model_;
	private static ComboBoxOption specify_liemarkov_;
	private static ComboBoxOption select_rcluster_;
	private static StringOption specify_rclusterval_;
	private static StringOption specify_basemodels_;
	private static ComboBoxOption specify_aamodels_;
	private static StringOption specify_freqtypes_;
	private static StringOption specify_ratehettypes_;
	private static IntegerOption specify_mincat_;
	private static IntegerOption specify_maxcat_;
	private static StringOption specify_merit_;
	private static BooleanOption specify_fulltreesearch_;
	private static StringOption specify_addlmodels_;
	private static StringOption specify_nexusmodelfile_file_;
	private static ButtonOption specify_nexusmodelfile_file_Browse;
	
	
	private static StringOption freetextmodel_;
	private static ComboBoxOption specify_dnamodel_;
	private static ComboBoxOption specify_protmodel_;
	private static ComboBoxOption specify_protmixture_;
	private static StringOption guide_tree_file;
	private static ButtonOption guide_tree_file_Browse;
	private static StringOption frequency_file_file;
	private static ButtonOption frequency_file_file_Browse;	
	private static BooleanOption max_posteriormode_;
	private static ComboBoxOption specify_binmodel_;
	private static ComboBoxOption specify_codonmodel_;
	private static ComboBoxOption specify_modelfreq_;
	private static BooleanOption optimize_weights_;
	private static ComboBoxOption specify_modelrate_;
	private static ComboBoxOption asc_bias_;
	private static StringOption gamma_shape_;
	private static BooleanOption median_approximation_;
	private static IntegerOption invariable_sites_;
	private static BooleanOption thorough_estimation_;
	
	private static IntegerOption num_parstrees_;
	private static IntegerOption num_topparstrees_;
	private static IntegerOption num_besttrees_;
	private static IntegerOption num_unsucctostop_;
	private static StringOption num_tostop_;
	private static IntegerOption specify_radius_;
	private static DoubleOption perturb_strength_;
	private static BooleanOption slower_NNI_;
	private static BooleanOption no_mlpairwise_;
	private static BooleanOption use_fasttreesearch_;
	private static StringOption constraint_file_;
	private static ButtonOption constraint_file_Browse;

	private static ComboBoxOption bootstrap_type_;
	private static BooleanOption use_bnni_;
	private static IntegerOption num_bootreps_;
	private static BooleanOption write_boottrees_;
	private static BooleanOption write_boottrees1_;
	private static IntegerOption max_iters_;
	private static DoubleOption cc_ufboot_;
	private static IntegerOption iter_interval_;
	private static DoubleOption specify_tiebreaker_;
	private static ComboBoxOption part_resample_;
	
	private static BooleanOption use_symmtest_;
	private static ComboBoxOption specify_symtest_;
	private static ComboBoxOption specify_symtype_;
	private static DoubleOption specify_pval_;
	
	
	private static BooleanOption sh_test_;
	private static BooleanOption parametrical_test_;
	private static BooleanOption abayes_test_;
	private static BooleanOption lbp_test_;
	private static IntegerOption num_replicates_;
	
	private static BooleanOption write_ancestralseqs_;
	private static StringOption specify_ancestralthresh_;
	private static StringOption specify_ancestraltree_file_;
	private static ButtonOption specify_ancestraltree_file_Browse;
	
	private static StringOption specify_treefile_;
	private static ButtonOption specify_treefile_Browse;
	private static IntegerOption num_rell_;
	private static BooleanOption weighted_tests_;
	private static BooleanOption unbiased_test_;
	private static BooleanOption estimate_parsetreeonly_;
	private static StringOption fixed_usertree_file;
	private static ButtonOption fixed_usertree_file_Browse;
	
	private static StringOption tree_file1_;
	private static ButtonOption tree_file1_Browse;
	private static BooleanOption compute_consensustree_;
	private static BooleanOption compute_consensusnetwork_;
	private static DoubleOption min_threshold_;
	private static DoubleOption burnin_value_;
	private static StringOption target_treefile_;
	private static ButtonOption target_treefile_Browse;
	private static StringOption set_scalefactor_;
	private static StringOption set_precision_;	
	private static StringOption nodetarget_treefile_;
	
	private static StringOption tree_file2_;
	private static ButtonOption tree_file2_Browse;
	private static BooleanOption compute_rfdistances_all_;
	private static BooleanOption compute_rfdistances_adj_;
	private static StringOption specify_rfdistancestree_file_;
	private static ButtonOption specify_rfdistancestree_file_Browse;
	
	//private static BooleanOption generate_randomtrees_;
	private static StringOption num_taxa_;
	private static ComboBoxOption choose_randomtype_;
	private static StringOption specify_brlengths_;
	private static StringOption specify_treefilename_;
	
	//Concordance Factor Options
	//private static StringOption partition_modelfile_file_;
	//private static ButtonOption partition_modelfile_file_Browse;
	private static StringOption partition_modelfile2_file_;
	private static ButtonOption partition_modelfile2_file_Browse;	
	private static StringOption partition_tfile_file_;
	private static ButtonOption partition_tfile_file_Browse;
	private static StringOption setoftrees_file_file_;
	private static ButtonOption setoftrees_file_file_Browse;
	private static StringOption name_outfiles_;
	private static IntegerOption specify_numquartets_;
	
	
	//Dating Options
	private static StringOption specify_datefile_file_;
	private static ButtonOption specify_datefile_file_Browse;
	private static BooleanOption extract_datefile_;
	private static StringOption specify_datetip_;
	private static StringOption specify_rootdate_;
	private static StringOption specify_datetreefile_file_;
	private static ButtonOption specify_datetreefile_file_Browse;
	//private static StringOption specify_resampleint_; 
	private static IntegerOption specify_resampleint_; 
	private static StringOption specify_outlierthresh_;
	
	
	
	private static BooleanOption print_sitestats_;
	private static BooleanOption fix_branchlengths_;
	private static StringOption branchlengths_tree_file_;
	private static ButtonOption branchlengths_tree_file_Browse;
	private static StringOption specify_minbranchlength_;
	private static StringOption specify_maxbranchlength_;
	private static BooleanOption write_locally_optimal_;
	private static BooleanOption fix_brlengths_;
	private static BooleanOption per_sitefile_;
	private static BooleanOption per_sitewslfile_;
	private static BooleanOption per_sitewslmrfile_;
	private static BooleanOption per_sitewslrfile_;
	private static BooleanOption per_sitewslmfile_;
	private static BooleanOption per_sitewspmfile_;
	private static BooleanOption per_sitewsprfile_;
	private static BooleanOption per_sitewspmrfile_;
	private static BooleanOption per_sitewplfile_;
	private static BooleanOption write_sitelikelihoods_;
	private static BooleanOption write_loglikelihoods_;
	private static StringOption list_csintegers_file;
	private static ButtonOption list_csintegers_file_Browse;
	
	/*
	private static Option abayes_test_ = 0; 
	private static Option bootstrap_type_ = bb;
	private static Option choose_randomtype_ = -r; 
	private static Option lbp_test_ = 0; 
	private static Option mixed_sequence_ = 1; 
	private static Option num_bootreps_ = 1000; 
	private static Option num_mixedsequences_ = 2; 
	private static Option part_resample_ = GENE; 
	private static Option partition_type_ = -q; 
	private static Option sh_test_ = 0; 
	private static Option use_bnni_ = 1; 
	private static Option write_boottrees1_ = 0; 
	private static Option write_boottrees_ = 0; 
	private static Option write_locally_optimal_ = 0; 
	private static Option write_loglikelihoods_ = 0; 
	private static Option write_sitelikelihoods_ = 0; 
	*/
    protected static NameAndLabel[] nameAndLabels;	
    private Options simpleOptions;
    private Options advancedOptions;
    private Options advancedOptions2;
    private Options advancedOptions3;
    private Options advancedOptions4;
    
    private enum OptionIndex
    {
		RUNTIME_, 
		WHICH_IQTREE_,
		SPECIFY_NUMPATTERNS_, 
		MORE_MEMORY_,
		MORE_MEMORY2_,
		SPECIFY_SAFE_,
		//SPECIFY_AUTOCORES_,
		SPECIFY_RUNTYPE_,
		SEQUENCE_TYPE_,
		CODON_TYPE_,
		NT2AA_TYPE_,
	    STARTING_TREE_FILE,
		USE_NJ_, 
		USE_RANDOM_, 
		SPECIFY_OUTGROUP_,
		SPECIFY_SEED_,
		SPECIFY_PREFIX_,
		
		SPECIFY_QUARTETS_,
		SPECIFY_QUARTETNUM_,
		SPECIFY_QUARTETSET_FILE_,
		WRITE_QUARTETS_,		
		
		PARTITION_TYPE_,
		PARTITION_FILE_,
		MIXED_SEQUENCE_,
		NUM_MIXEDSEQUENCES_,
		DATATYPE2_FILE_,
		DATATYPE3_FILE_,
		DATATYPE4_FILE_,
		DATATYPE5_FILE_,
		
		SPECIFY_MODEL_,
		SPECIFY_LIEMARKOV_,
		SELECT_RCLUSTER_,
		SPECIFY_RCLUSTERVAL_,
		SPECIFY_BASEMODELS_,
		SPECIFY_AAMODELS_,
		SPECIFY_FREQTYPES_,
		SPECIFY_RATEHETTYPES_,
		SPECIFY_MINCAT_,
		SPECIFY_MAXCAT_,
		SPECIFY_MERIT_,
		SPECIFY_FULLTREESEARCH_,
		SPECIFY_ADDLMODELS_,
		SPECIFY_NEXUSMODELFILE_FILE_,
		
		FREETEXTMODEL_,
		SPECIFY_DNAMODEL_,
		SPECIFY_PROTMODEL_,
		SPECIFY_PROTMIXTURE_,
		GUIDE_TREE_,
		FREQUENCY_FILE_FILE_,
		MAX_POSTERIORMODE_,
		SPECIFY_BINMODEL_,
		SPECIFY_CODONMODEL_,
		SPECIFY_MODELFREQ_,
		OPTIMIZE_WEIGHTS_,
		SPECIFY_MODELRATE_,
		ASC_BIAS_,
		GAMMA_SHAPE_,
		MEDIAN_APPROXIMATION_,
		INVARIABLE_SITES_,
		THOROUGH_ESTIMATION_,
		
		NUM_PARSTREES_,
		NUM_TOPPARSTREES_,
		NUM_BESTTREES_,
		NUM_UNSUCCTOSTOP_,
		NUM_TOSTOP_,
		SPECIFY_RADIUS_,
		PERTURB_STRENGTH_,
		SLOWER_NNI_,
		NO_MLPAIRWISE_,
		USE_FASTTREESEARCH_,
		CONSTRAINT_FILE_,
		
		BOOTSTRAP_TYPE_,
		USE_BNNI_,
		NUM_BOOTREPS_,
		WRITE_BOOTTREES_,
		WRITE_BOOTTREES1_,
		MAX_ITERS_,
		CC_UFBOOT_,
		ITER_INTERVAL_,
		SPECIFY_TIEBREAKER_,
		PART_RESAMPLE_,
		
		USE_SYMMTEST_,
		SPECIFY_SYMTEST_,
		SPECIFY_SYMTYPE_,
		SPECIFY_PVAL_,	
		
		SH_TEST_,
		PARAMETRICAL_TEST_,
		ABAYES_TEST_,
		LBP_TEST_,
		NUM_REPLICATES_,
		
		WRITE_ANCESTRALSEQS_,
		SPECIFY_ANCESTRALTHRESH_,
		SPECIFY_ANCESTRALTREE_FILE_,
		
		SPECIFY_TREEFILE_,
		NUM_RELL_,
		WEIGHTED_TESTS_,
		UNBIASED_TEST_,
		ESTIMATE_PARSETREEONLY_,
		FIXED_USERTREE_FILE,
		
		TREE_FILE1_,
		COMPUTE_CONSENSUSTREE_,
		COMPUTE_CONSENSUSNETWORK_,
		MIN_THRESHOLD_,
		BURNIN_VALUE_,
		TARGET_TREEFILE_,
		SET_SCALEFACTOR_,
		SET_PRECISION_,
		NODETARGET_TREEFILE_,
		
		TREE_FILE2_,
		COMPUTE_RFDISTANCES_ALL_,
		COMPUTE_RFDISTANCES_ADJ_,
		SPECIFY_RFDISTANCESTREE_FILE_,
	
		//GENERATE_RANDOMTREES_,
		NUM_TAXA_,
		CHOOSE_RANDOMTYPE_,
		SPECIFY_BRLENGTHS_,
		SPECIFY_TREEFILENAME_,

		//PARTITION_MODELFILE_FILE_,
		PARTITION_MODELFILE2_FILE_,
		PARTITION_TFILE_FILE_,
		SETOFTREES_FILE_FILE_,
		NAME_OUTFILES_,
		SPECIFY_NUMQUARTETS_,
		
		SPECIFY_DATEFILE_FILE_,
		EXTRACT_DATEFILE_,
		SPECIFY_DATETIP_,
		SPECIFY_ROOTDATE_,
		SPECIFY_DATETREEFILE_FILE_,
		SPECIFY_RESAMPLEINT_, 
		SPECIFY_OUTLIERTHRESH_,
				
		
		PRINT_STTESTATS_,
		FIX_BRANCHLENGTHS,
		BRANCHLENGTHS_TREE_FILE_,
		SPECIFY_MINBRANCHLENGTH_,
		SPECIFY_MAXBRANCHLENGTH_,		
		WRITE_LOCALLY_OPTIMAL_,
		FIX_BRLENGTHS_,
		PER_SITEFILE_,
		PER_SITEWSLFILE_,
		PER_SITEWSLMRFILE_,
		PER_SITEWSLRFILE_,
		PER_SITEWSLMFILE_,
		PER_SITEWSPMFILE_,
		PER_SITEWSPRFILE_,
		PER_SITEWSPMRFILE_,
		PER_SITEWPLFILE_,
		WRITE_SITELIKELIHOODS_,
		WRITE_LOGLIKELIHOODS_,
		LIST_CSINTEGERS_FILE
		
    }
    
	static
    {
    	GENEIOUS_FORMAT = "geneious.iqtree.rest";
  
		nameAndLabels = new NameAndLabel[OptionIndex.values().length];
		
    	nameAndLabels[OptionIndex.RUNTIME_.ordinal()] = new NameAndLabel("runtime_", "Maximum Hours to Run (up to 168 hours)", "runtime_",
    			"<html>Estimate the maximum time your job will need to run.<br>" + 
    			"We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the \"debug\" queue.<br>" +
    		    "Once you are sure the configuration is correct, you then increase the time.<br>" +
    			"The reason is that jobs > 0.5 h are submitted to the \"normal\" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours.</html>");
    	nameAndLabels[OptionIndex.WHICH_IQTREE_.ordinal()] = new NameAndLabel("which_iqtree_", "Which version do you want to run", "which_iqtree_", "");
    	nameAndLabels[OptionIndex.SPECIFY_NUMPATTERNS_.ordinal()] = new NameAndLabel("specify_numpatterns_", "How many patterns does your data set have", "specify_numpatterns_", "");
    	nameAndLabels[OptionIndex.MORE_MEMORY_.ordinal()] = new NameAndLabel("more_memory_", "I need more memory", "more_memory_", "This option should only be used if analysis has run out of memmory");
    	nameAndLabels[OptionIndex.MORE_MEMORY2_.ordinal()] = new NameAndLabel("more_memory2_", "I need still more memory", "more_memory2_", "This option should only be used if analysis set with more memory of has run out of memmory");
    	nameAndLabels[OptionIndex.SPECIFY_SAFE_.ordinal()] = new NameAndLabel("specify_safe_", "Safe likelihood kernel to avoid numerical underflow (-safe)", "specify_safe_", "");
    	//nameAndLabels[OptionIndex.SPECIFY_AUTOCORES_.ordinal()] = new NameAndLabel("specify_autocores_", "Automatically select number of threads", "specify_autocores_", "");
    	nameAndLabels[OptionIndex.SPECIFY_RUNTYPE_.ordinal()] = new NameAndLabel("specify_runtype_", "Select the kind of run you need", "specify_runtype_", "");
    	nameAndLabels[OptionIndex.SEQUENCE_TYPE_.ordinal()] = new NameAndLabel("sequence_type_", "Specify your sequence type (-st)", "sequence_type_", "");
    	nameAndLabels[OptionIndex.CODON_TYPE_.ordinal()] = new NameAndLabel("codon_type_", "Specify your Codon type", "codon_type_", "");
    	nameAndLabels[OptionIndex.NT2AA_TYPE_.ordinal()] = new NameAndLabel("nt2aa_type_", "Specify your translation table", "nt2aa_type_", "");
    	nameAndLabels[OptionIndex.STARTING_TREE_FILE.ordinal()] = new NameAndLabel("starting_tree_", "Specify a starting (or other) tree file (-t)", "starting_tree_", "", true);
    	nameAndLabels[OptionIndex.USE_NJ_.ordinal()] = new NameAndLabel("use_nj_", "Use a NJ starting tree (-t BIONJ)", "use_nj_", "");
    	nameAndLabels[OptionIndex.USE_RANDOM_.ordinal()] = new NameAndLabel("use_random_", "Use a Random starting tree (-t RANDOM)", "use_random_", "");
    	nameAndLabels[OptionIndex.SPECIFY_OUTGROUP_.ordinal()] = new NameAndLabel("specify_outgroup_", "Specify the outgroup (-o)", "specify_outgroup_", "");
    	nameAndLabels[OptionIndex.SPECIFY_PREFIX_.ordinal()] = new NameAndLabel("specify_prefix_", "Specify the prefix for output files (-pre'/--prefix)", "specify_prefix_", "");
    	nameAndLabels[OptionIndex.SPECIFY_SEED_.ordinal()] = new NameAndLabel("specify_seed_", "Specify the seed (-seed)", "specify_seed_", "");
    	
    	nameAndLabels[OptionIndex.SPECIFY_QUARTETS_.ordinal()] = new NameAndLabel("specify_quartets_", "Quartets to be randomly drawn (-lmap)", "specify_quartets_", "");
    	nameAndLabels[OptionIndex.SPECIFY_QUARTETNUM_.ordinal()]= new NameAndLabel("specify_quartetnum_", "Specify number of quartets (-lmap)", "specify_quartetnum_", "");
        nameAndLabels[OptionIndex.SPECIFY_QUARTETSET_FILE_.ordinal()]= new NameAndLabel("specify_quartetset_file_", "Specify a NEXUS file specifying taxon clusters (-lmclust clusters.nex)", "specify_quartetset_file_", "");
        nameAndLabels[OptionIndex.WRITE_QUARTETS_.ordinal()] = new NameAndLabel("write_quartets_", "Write quartets to a file", "write_quartets_", "");
    	
        nameAndLabels[OptionIndex.PARTITION_TYPE_.ordinal()] = new NameAndLabel("partition_type_", "Please specify your partition type", "partition_type_", "");
    	nameAndLabels[OptionIndex.PARTITION_FILE_.ordinal()] = new NameAndLabel("partition_file_", "Please select your partition file", "partition_file_", "");
    	nameAndLabels[OptionIndex.MIXED_SEQUENCE_.ordinal()] = new NameAndLabel("mixed_sequence_", "I want to mix data types in a partitioned analysis", "mixed_sequence_", "");
    	nameAndLabels[OptionIndex.NUM_MIXEDSEQUENCES_.ordinal()] = new NameAndLabel("num_mixedsequences_", "How many data types (files) in your partitioned analysis", "num_mixedsequences_", "");
    	nameAndLabels[OptionIndex.DATATYPE2_FILE_.ordinal()] = new NameAndLabel("datatype2_file_", "Select the file with your second datatype ~partition_datatype2.phy", "datatype2_file_", "");
    	nameAndLabels[OptionIndex.DATATYPE3_FILE_.ordinal()] = new NameAndLabel("datatype3_file_", "Select the file with your third datatype ~partition_datatype3.phy", "datatype3_file_", "");
    	nameAndLabels[OptionIndex.DATATYPE4_FILE_.ordinal()] = new NameAndLabel("datatype4_file_", "Select the file with your fourth datatype ~partition_datatype4.phy", "datatype4_file_", "");
    	nameAndLabels[OptionIndex.DATATYPE5_FILE_.ordinal()] = new NameAndLabel("datatype5_file_", "Select the file with your fifth datatype ~partition_datatype5.phy", "datatype5_file_", "");
    
    	nameAndLabels[OptionIndex.SPECIFY_MODEL_.ordinal()] = new NameAndLabel("specify_model_", "Test for the best model (-m TEST)", "specify_model_", "");
    	nameAndLabels[OptionIndex.SPECIFY_LIEMARKOV_.ordinal()] = new NameAndLabel("specify_liemarkov_", "Specify a Lie Markov Option", "specify_liemarkov_", "");
    	nameAndLabels[OptionIndex.SELECT_RCLUSTER_.ordinal()] = new NameAndLabel("select_rcluster_", "Specify the relaxed clustering algorithm to use (-rcluster)", "select_rcluster_", "");
    	nameAndLabels[OptionIndex.SPECIFY_RCLUSTERVAL_.ordinal()] = new NameAndLabel("specify_rclusterval_", "Specify the percentage or max partition pairs for relaxed clustering algorithm", "specify_rclusterval_", "Use this option to specify the percentage for the relaxed clustering algorithm (Lanfear et al.,2014). This is similar to -*rcluster-percent option of PartitionFinder" + 
    	" For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations.");
    	nameAndLabels[OptionIndex.SPECIFY_BASEMODELS_.ordinal()] = new NameAndLabel("specify_basemodels_", "Specify names of the base models or program (-mset)", "specify_basemodels_", 
    			"<html>For -mset, specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program.<br>" + 
    			"Alternatively, one can specify a comma-separated list of base models.<br>" +
    			"For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations.</html>");
    	nameAndLabels[OptionIndex.SPECIFY_AAMODELS_.ordinal()] = new NameAndLabel("specify_aamodels_", "Specify nuclear, mitochondrial, chloroplast or viral (-msub, protein)", "specify_aamodels_", "");
    	nameAndLabels[OptionIndex.SPECIFY_FREQTYPES_.ordinal()] = new NameAndLabel("specify_freqtypes_", "Specify a comma-separated list of frequency types for model selection (-mfreq)" + 
    			"", "pecify_freqtypes_", "");
    	nameAndLabels[OptionIndex.SPECIFY_RATEHETTYPES_.ordinal()] = new NameAndLabel("specify_ratehettypes_", "Specify a comma-separated list of rate heterogeneity types for model selection (-mrate)\r\n" + 
    			"", "specify_ratehettypes_", "");
    	nameAndLabels[OptionIndex.SPECIFY_MINCAT_.ordinal()] = new NameAndLabel("specify_mincat_", "Specify minimum number of categories for FreeRate model (-cmin)", "specify_mincat_", "");
    	nameAndLabels[OptionIndex.SPECIFY_MAXCAT_.ordinal()] = new NameAndLabel("specify_maxcat_", "Specify maximum number of categories for FreeRate model (-cmax)", "specify_maxcat_", "");
    	nameAndLabels[OptionIndex.SPECIFY_MERIT_.ordinal()] = new NameAndLabel("specify_merit_", "Specify either AIC, AICc or BIC for the optimality criterion (-merit)", "specify_merit_", "");
    	nameAndLabels[OptionIndex.SPECIFY_FULLTREESEARCH_.ordinal()] = new NameAndLabel("specify_fulltreesearch_", "Turn on full tree search for each model considered, to obtain more accurate result. (-mtree)", "specify_fulltreesearch_", "");
    	nameAndLabels[OptionIndex.SPECIFY_ADDLMODELS_.ordinal()] = new NameAndLabel("specify_addlmodels_", "Specify a comma-separated list of mixture models to additionally consider for model selection. (-madd)", "specify_addlmodels_", "");
    	nameAndLabels[OptionIndex.SPECIFY_NEXUSMODELFILE_FILE_.ordinal()] = new NameAndLabel("specify_nexusmodelfile_", "Specify a Nexus Model file. (-mdef)", "specify_nexusmodelfile_", "");
    	
    	nameAndLabels[OptionIndex.FREETEXTMODEL_.ordinal()] = new NameAndLabel("freetextmodel_", "Specify any model using free text (-m)", "freetextmodel_", "");
    	nameAndLabels[OptionIndex.SPECIFY_DNAMODEL_.ordinal()] = new NameAndLabel("specify_dnamodel_", "Specify a DNA model (-m )", "specify_dnamodel_", "");
    	nameAndLabels[OptionIndex.SPECIFY_PROTMODEL_.ordinal()] = new NameAndLabel("specify_protmodel_", "Specify a Protein model (-m )", "specify_protmodel_", "");
    	nameAndLabels[OptionIndex.SPECIFY_PROTMIXTURE_.ordinal()] = new NameAndLabel("specify_protmixture_", "Specify a Protein Profile mixture", "specify_protmixture_", "");
    	nameAndLabels[OptionIndex.GUIDE_TREE_.ordinal()] = new NameAndLabel("guide_tree_", "Specify a guide tree file for PMSF analysis (-ft)", "guide_tree_", "");
    	nameAndLabels[OptionIndex.FREQUENCY_FILE_FILE_.ordinal()] = new NameAndLabel("frequency_file_", "Specify a frequency file for PMSF analysis (-fs)", "frequency_file_", "");
    	nameAndLabels[OptionIndex.SPECIFY_BINMODEL_.ordinal()] = new NameAndLabel("specify_binmodel_", "Specify a Binary/Morphological model (-m )", "specify_binmodel_", "");
    	nameAndLabels[OptionIndex.MAX_POSTERIORMODE_.ordinal()] = new NameAndLabel("max_posteriormode_", "Switch to posterior maximum mode for obtaining site-specific profiles (-max )", "max_posteriormode_", "");
    	nameAndLabels[OptionIndex.SPECIFY_CODONMODEL_.ordinal()] = new NameAndLabel("specify_codonmodel_", "Specify a Codon model (-m )", "specify_codonmodel_", "");
    	nameAndLabels[OptionIndex.SPECIFY_MODELFREQ_.ordinal()] = new NameAndLabel("specify_modelfreq_", "Specify model frequency", "specify_modelfreq_", "");
    	nameAndLabels[OptionIndex.OPTIMIZE_WEIGHTS_.ordinal()] = new NameAndLabel("optimize_weights_", "Optimize weights of mixture models (-mwopt)", "optimize_weights_", "");
    	nameAndLabels[OptionIndex.SPECIFY_MODELRATE_.ordinal()] = new NameAndLabel("specify_modelrate_", "Specify rate heterogeneity", "specify_modelrate_", "");
    	nameAndLabels[OptionIndex.ASC_BIAS_.ordinal()] = new NameAndLabel("asc_bias_", "Correct for Ascertainment bias (+ASC)", "asc_bias_", 
    			"<html>This is useful for binary/morphological datasets that only contain variable sites (the identical morphological features are usually not included in the alignments,<br>" +
    			"hence you need to correct for this, see, e.g., http://sysbio.oxfordjournals.org/content/50/6/913.short).<br>" +
    			"For DNA data this option might be useful when you analyze alignments of SNPs that also don't contain constant sites.<br>" +
    			"Note that, for mathematical and numerical reasons you can not apply an ascertainment bias correction to datasets or partitions that contain constant sites.");
    	nameAndLabels[OptionIndex.GAMMA_SHAPE_.ordinal()] = new NameAndLabel("gamma_shape_", "Specify the Gamma shape parameter (-a)", "gamma_shape_", "");
    	nameAndLabels[OptionIndex.MEDIAN_APPROXIMATION_.ordinal()] = new NameAndLabel("median_approximation_", "Perform the median approximation for Gamma rate heterogeneity (-gmedian)", "median_approximation_", 
    			"Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)");
    	nameAndLabels[OptionIndex.INVARIABLE_SITES_.ordinal()] = new NameAndLabel("invariable_sites_", "Specify the proportion of invariable sites (-i)", "invariable_sites_", "");
    	nameAndLabels[OptionIndex.THOROUGH_ESTIMATION_.ordinal()] = new NameAndLabel("thorough_estimation_", "Perform more thorough estimation for +I+G model parameters (--opt-gamma-inv)", "thorough_estimation_", "");
    
    	nameAndLabels[OptionIndex.NUM_PARSTREES_.ordinal()]  = new NameAndLabel("num_parstrees_", "Specify number of initial parsimony trees (-ninit)", "num_parstrees_", 
    			"<html>Specify number of initial parsimony trees.<br>" + 
    			"DEFAULT: 100. Here the PLL library (Flouri et al., 2015) is used,<br>" + 
    			"which implements the randomized stepwise addition and parsimony subtree pruning and regafting (SPR).</html>");
    	nameAndLabels[OptionIndex.NUM_TOPPARSTREES_.ordinal()] = new NameAndLabel("num_topparstrees_", "Specify number of top initial parsimony trees (-ntop)", "num_topparstrees_", 
    			"<html>Specify number of top initial parsimony trees to optimize with ML nearest neighbor interchange (NNI) search to initialize the candidate set.<br>DEFAULT: 20</html>");
    	nameAndLabels[OptionIndex.NUM_BESTTREES_.ordinal()] = new NameAndLabel("num_besttrees_", "Number of trees in the candidate set to maintain (-nbest)", "num_besttrees_", 
    			"<html>Specify number of trees in the candidate set to maintain during ML tree search.<br>DEFAULT: 5</html>");
    	nameAndLabels[OptionIndex.NUM_UNSUCCTOSTOP_.ordinal()] = new NameAndLabel("num_unsucctostop_", "Number of unsuccessful iterations to stop (-nstop)", "num_unsucctostop_", 
    			"<html>Specify number of unsuccessful iterations to stop.<br>DEFAULT: 100</html>");
    	nameAndLabels[OptionIndex.NUM_TOSTOP_.ordinal()] = new NameAndLabel("num_tostop_", "Number of iterations to stop (-n)", "num_tostop_", 
    			"<html>Specify number of iterations to stop.<br>" +
    			"This option overrides -nstop criterion. Use -n 0 to only estimate model parameters on an initial parsimony tree and ignore a full tree search to save time</html>");
    	nameAndLabels[OptionIndex.SPECIFY_RADIUS_.ordinal()] = new NameAndLabel("specify_radius_", "SPR radius for the initial search (-sprrad)", "specify_radius_", 
    			"<html>Specify SPR radius for the initial parsimony tree search.<br>DEFAULT: 6</html>");
    	nameAndLabels[OptionIndex.PERTURB_STRENGTH_.ordinal()] = new NameAndLabel("perturb_strength_", "Perturbation strength (between 0 and 1) (-pers)", "perturb_strength_", 
    			"<htm>Specify SPR radius for the initial parsimony tree search.<br>DEFAULT: 6</html>");
    	nameAndLabels[OptionIndex.SLOWER_NNI_.ordinal()] = new NameAndLabel("slower_NNI_", "Turn on more thorough and slower NNI search (-allnni)", "slower_NNI_", 
    			"<html>Turn on more thorough and slower NNI search.<br>It means that IQ-TREE will consider all possible NNIs instead of only those in the vicinity of previously applied NNIs.<br>DEFAULT: OFF</html>");
    	nameAndLabels[OptionIndex.NO_MLPAIRWISE_.ordinal()] = new NameAndLabel("no_mlpairwise_", "Avoid computing ML pairwise distances and BIONJ tree (-djc)", "no_mlpairwise_", 
    			"Avoid computing ML pairwise distances and BIONJ tree.");
    	nameAndLabels[OptionIndex.USE_FASTTREESEARCH_.ordinal()] = new NameAndLabel("use_fasttreesearch_", "Turn on the fast tree search mode (-fast)", "use_fasttreesearch_", "");
    	nameAndLabels[OptionIndex.CONSTRAINT_FILE_.ordinal()] = new NameAndLabel("constraint_file_", "Specify a topological constraint tree file in NEWICK format (-g)", "constraint_file_", 
    			"<html>Specify a topological constraint tree file in NEWICK format.<br>The constraint tree can be a multifurcating tree and need not to include all taxa.</html>");
    
    	nameAndLabels[OptionIndex.BOOTSTRAP_TYPE_.ordinal()] = new NameAndLabel("bootstrap_type_", "Bootstrap Type", "bootstrap_type_", "");
    	nameAndLabels[OptionIndex.USE_BNNI_.ordinal()] = new NameAndLabel("use_bnni_", "Use bnni to reduce overestimating support (-bnni)", "use_bnni_", "");
    	nameAndLabels[OptionIndex.NUM_BOOTREPS_.ordinal()] = new NameAndLabel("num_bootreps_", "Specify number of bootstrap replicates (>=1000 for ultrafast)", "num_bootreps_", 
    			"<html>-bb: Specify number of bootstrap replicates (>=1000)<br>" +
    			"-b: Specify number of bootstrap replicates (recommended >=100).<br>" + 
    			"This will perform both bootstrap and analysis on original alignment and provide a consensus tree.<br>" +
    			"-bc Like -b but omit analysis on original alignment.<br>" + 
    			"-bo Like -b but only perform bootstrap analysis (no analysis on original alignment and no consensus tree).</html>");
    	nameAndLabels[OptionIndex.WRITE_BOOTTREES_.ordinal()] = new NameAndLabel("write_boottrees_", "Turn on writing bootstrap trees to .ufboot file (-wbt)", "write_boottrees_", 
    			"Turn on writing bootstrap trees to .ufboot file. DEFAULT: OFF");
    	nameAndLabels[OptionIndex.WRITE_BOOTTREES1_.ordinal()] = new NameAndLabel("write_boottrees1_", "Turn on writing bootstrap trees with branch lengths (-wbtl)", "write_boottrees1_", 
    			"Turn on writing bootstrap trees with branch lengths (-wbt1) DEFAULT: OFF");
    	nameAndLabels[OptionIndex.MAX_ITERS_.ordinal()] = new NameAndLabel("max_iters_", "Specify maximum number of iterations to stop. (-nm)", "max_iters_", 
    			"Specify maximum number of iterations to stop. DEFAULT: 1000");
    	nameAndLabels[OptionIndex.CC_UFBOOT_.ordinal()] = new NameAndLabel("cc_ufboot_", "Minimum correlation coefficient for UFBoot convergence criterion (-bcor)", "cc_ufboot_",
    			"<html>Specify minimum correlation coefficient for UFBoot convergence criterion.<br>DEFAULT: 0.99</html>");
    	nameAndLabels[OptionIndex.ITER_INTERVAL_.ordinal()] = new NameAndLabel("iter_interval_", "Iteration interval checking for UFBoot convergence (-nstep)", "iter_interval_", 
    			"<html>Specify iteration interval checking for UFBoot convergence.<br>" +
    	        "DEFAULT: every 100 iterations</html>");
    	nameAndLabels[OptionIndex.SPECIFY_TIEBREAKER_.ordinal()] = new NameAndLabel("specify_tiebreaker_", "SPR radius for the initial search (-beps)", "specify_tiebreaker_", 
    			"<html>Specify a small epsilon to break tie in RELL evaluation for bootstrap trees.<br>DEFAULT: 0.5</html>");
    	nameAndLabels[OptionIndex.PART_RESAMPLE_.ordinal()] = new NameAndLabel("part_resample_", "Resampling strategies for partitioned analysis (-bspec)", "part_resample_", 
    			"<html>Specify the resampling strategies for partitioned analysis.<br>" +
    			"By default, IQ-TREE resamples alignment sites within partitions.<br>" + 
    			"With -bspec GENE IQ-TREE will resample partitions.<br>" +
    			"With -bspec GENESITE IQ-TREE will resample partitions and then resample sites within resampled partitions (Gadagkar et al., 2005).</html?");
   
    	nameAndLabels[OptionIndex.USE_SYMMTEST_.ordinal()] = new NameAndLabel("use_symmtest_", "Run symmetry test(s)", "use_symmtest_", "");
    	nameAndLabels[OptionIndex.SPECIFY_SYMTEST_.ordinal()] = new NameAndLabel("specify_symtest_", "Symmetry Test (--symtest)", "specify_symtest_", "");
    	nameAndLabels[OptionIndex.SPECIFY_SYMTYPE_.ordinal()] = new NameAndLabel("specify_symtype_", "When removing partitions, use", "specify_symtype_", "");
    	nameAndLabels[OptionIndex.SPECIFY_PVAL_.ordinal()] = new NameAndLabel("specify_pval_", "Specify a Symmetry p-value other than 0.05", "specify_pval_", "");
  
    	nameAndLabels[OptionIndex.SH_TEST_.ordinal()] = new NameAndLabel("sh_test_", "SH-Like Test (-alrt)", "sh_test_", "");
    	nameAndLabels[OptionIndex.PARAMETRICAL_TEST_.ordinal()] = new NameAndLabel("parametrical_test_", "Run the parametricaLRT test (-alrt 0)", "parametrical_test_", "");
    	nameAndLabels[OptionIndex.ABAYES_TEST_.ordinal()] = new NameAndLabel("abayes_test_", "Approximate Bayes test (-abayes)", "abayes_test_", "Perform approximate Bayes test ");
    	nameAndLabels[OptionIndex.LBP_TEST_.ordinal()] = new NameAndLabel("lbp_test_", "Fast local bootstrap probability (-lbp)", "lbp_test_", "");
    	nameAndLabels[OptionIndex.NUM_REPLICATES_.ordinal()] = new NameAndLabel("num_replicates_", "Specify number of replicates (1000 or more)", "num_replicates_", 
    			"<htmL>-alrt Specify number of replicates (>=1000) to perform SH-like approximate likelihood ratio test (SH-aLRT)<br>" +  
    			"-lbp Specify number of replicates (>=1000) to perform fast local bootstrap probability method<br>" + 
    			"</html>");
    
    	nameAndLabels[OptionIndex.SPECIFY_TREEFILE_.ordinal()] = new NameAndLabel("specify_treefile_", "Specify a file containing a set of trees (-z)", "specify_treefile_", "");
    	nameAndLabels[OptionIndex.NUM_RELL_.ordinal()] = new NameAndLabel("num_rell_", "Specify the number of RELL replicates (-zb)", "num_rell_", 
    			"<html>-zb Specify the number of RELL (Kishino et al., 1990) replicates (>=1000) to perform several tree topology tests for all trees passed via<br>" +
    			"-z. The tests include bootstrap proportion (BP), KH test (Kishino and Hasegawa, 1989), SH test (Shimodaira and Hasegawa, 1999) and expected likelihood weights (ELW) (Strimmer and Rambaut, 2002).</html>");
    	nameAndLabels[OptionIndex.WEIGHTED_TESTS_.ordinal()] = new NameAndLabel("weighted_tests_", "Perform the weighted-KH and weighted-SH test", "weighted_tests_", "");
    	nameAndLabels[OptionIndex.UNBIASED_TEST_.ordinal()] = new NameAndLabel("unbiased_test_", "Perform the approximately unbiased (AU) test", "unbiased_test_", "");
    	nameAndLabels[OptionIndex.ESTIMATE_PARSETREEONLY_.ordinal()] = new NameAndLabel("estimate_parsetreeonly_", "Only estimate model parameters on an initial parsimonly tree (-n 0)", "estimate_parsetreeonly_", "");
    	nameAndLabels[OptionIndex.FIXED_USERTREE_FILE.ordinal()] = new NameAndLabel("fixed_usertree_", "Specify a fixed user tree to estimate model parameters (-te)", "fixed_usertree_", 
    			"<html>-te Specify a fixed user tree to estimate model parameters.<br>" + 
    			"Thus it behaves like -n 0 but uses a user-defined tree instead of parsimony tree.</html>", true);
   
    	nameAndLabels[OptionIndex.WRITE_ANCESTRALSEQS_.ordinal()] = new NameAndLabel("write_ancestralseqs_", "Write ancestral sequences to .statefile (-asr)", "write_ancestralseqs_", "");
    	nameAndLabels[OptionIndex.SPECIFY_ANCESTRALTHRESH_.ordinal()] = new NameAndLabel("specify_ancestralthresh_", "Specify minimum threshold of posterior probability for best ancestral state (-asr-min)", "specify_ancestralthresh_", "");
    	nameAndLabels[OptionIndex.SPECIFY_ANCESTRALTREE_FILE_.ordinal()] = new NameAndLabel("specify_ancestraltree_", "Specify a user-defined tree to determine ancestral sequences (-te)", "specify_ancestraltree_", "", true);
    	
    	nameAndLabels[OptionIndex.TREE_FILE1_.ordinal()] = new NameAndLabel("tree_file1_", "Specify a file containing a set of trees", "tree_file1_", "");
    	nameAndLabels[OptionIndex.COMPUTE_CONSENSUSTREE_.ordinal()] = new NameAndLabel("compute_consensustree_", "Compute consensus tree of the trees passed via -t (-con)", "compute_consensustree_", 
    			"<html>-con Compute consensus tree of the trees passed via -t.<br>Resulting consensus tree is written to .contree file.</html>");
    	nameAndLabels[OptionIndex.COMPUTE_CONSENSUSNETWORK_.ordinal()] = new NameAndLabel("compute_consensusnetwork_", "Compute consensus network of the trees passed via -t (-net)", "compute_consensusnetwork_", "");
    	nameAndLabels[OptionIndex.MIN_THRESHOLD_.ordinal()] = new NameAndLabel("min_threshold_", "Specify a minimum threshold between 0 and 1 (-minsup)", "min_threshold_", "");
    	nameAndLabels[OptionIndex.BURNIN_VALUE_.ordinal()] = new NameAndLabel("burnin_value_", "Specify a burn-in (-bi)", "burnin_value_", "");
    	nameAndLabels[OptionIndex.TARGET_TREEFILE_.ordinal()] = new NameAndLabel("target_treefile_", "Specify an input “target” tree file (-sup)", "target_treefile_", 
    			"<html>-sup Specify an input “target” tree file.<br>" + 
    			"That means, support values are first extracted from the trees passed via -t,<br>" +
    			"and then mapped onto the target tree.<br>" + 
    			"Resulting tree with assigned support values is written to .suptree file.<br>" + 
    			"This option is useful to map and compare support values from different approaches onto a single tree.</html>");
    	nameAndLabels[OptionIndex.SET_SCALEFACTOR_.ordinal()] = new NameAndLabel("set_scalefactor_", "Set the scaling factor of support values for -sup option (-scale)", "set_scalefactor_", "-suptag Specify name of a node in -sup target tree. The corresponding node of .suptree will then be assinged with IDs of trees where this node appears. Special option -suptag ALL will assign such IDs fo all nodes of the target tree");
    	nameAndLabels[OptionIndex.SET_PRECISION_.ordinal()] = new NameAndLabel("set_precision_", "Set the precision of support values for -sup option (-prec)", "set_precision_", "");
    	nameAndLabels[OptionIndex.NODETARGET_TREEFILE_.ordinal()] = new NameAndLabel("nodetarget_treefile_", "Specify name of a node in -sup target tree (-suptag)", "nodetarget_treefile_", 
    			"<html>-suptag Specify name of a node in -sup target tree.<br>" + 
    			"The corresponding node of .suptree will then be assigned with IDs of trees where this node appears.<br>" + 
    			"Special option -suptag ALL will assign such IDs for all nodes of the target tree.</html>", false);
    
    	nameAndLabels[OptionIndex.TREE_FILE2_.ordinal()] = new NameAndLabel("tree_file2_", "Specify a second set of trees", "tree_file2_", "");
    	nameAndLabels[OptionIndex.COMPUTE_RFDISTANCES_ALL_.ordinal()] = new NameAndLabel("compute_rfdistances_all_", "Compute all-to-all RF distances between all trees passed via -t (-rf_all)", "compute_rfdistances_all_", "");
    	nameAndLabels[OptionIndex.COMPUTE_RFDISTANCES_ADJ_.ordinal()] = new NameAndLabel("compute_rfdistances_adj_", "Compute RF distances between adjacent trees passed via -t (-rf_adj)", "compute_rfdistances_adj_", "");
    	nameAndLabels[OptionIndex.SPECIFY_RFDISTANCESTREE_FILE_.ordinal()] = new NameAndLabel("specify_rfdistancestree_", "Select file of adjacent trees to pass via -t)", "specify_rfdistancestree_", "", true);
    
    	
    	//nameAndLabels[OptionIndex.GENERATE_RANDOMTREES_.ordinal()] = new NameAndLabel("generate_randomtrees_", "Generate random trees", "generate_randomtrees_", "");
    	nameAndLabels[OptionIndex.NUM_TAXA_.ordinal()] = new NameAndLabel("num_taxa_", "Specify number of taxa for the tree (-r)", "num_taxa_", "");
    	nameAndLabels[OptionIndex.CHOOSE_RANDOMTYPE_.ordinal()] = new NameAndLabel("choose_randomtype_", "Specify a model for the random trees", "choose_randomtype_", "");
    	nameAndLabels[OptionIndex.SPECIFY_BRLENGTHS_.ordinal()] = new NameAndLabel("specify_brlengths_", "Specify minimum, mean and maximum branch lengths of the random tree DEFAULT: -rlen 0.001 0.1 0.999", "specify_brlengths_", "Specify three numbers: minimum, mean and maximum branch lengths of the random tree.");
    	nameAndLabels[OptionIndex.SPECIFY_TREEFILENAME_.ordinal()] = new NameAndLabel("specify_treefilename_", "Specify a name for your random tree file (we recommend a name with .tree)", "specify_treefilename_", "Specify a name for the random tree output. Consider adding the .tree extension", false);
    	
    	//nameAndLabels[OptionIndex.PARTITION_MODELFILE_FILE_.ordinal()] = new NameAndLabel("partition_modelfile_", "Choose file that specifies the partition model (-p)", "partition_modelfile_", "");
    	nameAndLabels[OptionIndex.PARTITION_MODELFILE2_FILE_.ordinal()] = new NameAndLabel("partition_modelfile2_", "Choose file that specifies the model selection (-S)", "partition_modelfile2_", "");;
    	nameAndLabels[OptionIndex.PARTITION_TFILE_FILE_.ordinal()] = new NameAndLabel("partition_tfile_", "Choose a reference tree file for gcf (-t)", "partition_tfile_", "");;
    	nameAndLabels[OptionIndex.SETOFTREES_FILE_FILE_.ordinal()] = new NameAndLabel("setoftrees_file_", "Choose a set of trees for gcf (-gcf)", "setoftrees_file_", "");
    	nameAndLabels[OptionIndex.NAME_OUTFILES_.ordinal()] = new NameAndLabel("name_outfiles_", "Specify a prefix for the output files (--prefix)", "name_outfiles_", "", false);
    	nameAndLabels[OptionIndex.SPECIFY_NUMQUARTETS_.ordinal()] = new NameAndLabel("specify_numquartets_", "Specify number of quartets (--scf)", "specify_numquartets_", "");
		
    	nameAndLabels[OptionIndex.SPECIFY_DATEFILE_FILE_.ordinal()] = new NameAndLabel("specify_datefile_", "Choose a file that specifies dates (--date)", "specify_datefile_", "");
    	nameAndLabels[OptionIndex.EXTRACT_DATEFILE_.ordinal()] = new NameAndLabel("extract_datefile_", "Automatically extract dates from taxon names (--date TAXNAME)", "extract_datefile_", "", false);
    	nameAndLabels[OptionIndex.SPECIFY_DATETIP_.ordinal()] = new NameAndLabel("specify_datetip_", "Specify tip dates as a real number or YYYY-MM-DD (--date-tip)", "specify_datetip_", "");
    	nameAndLabels[OptionIndex.SPECIFY_ROOTDATE_.ordinal()] = new NameAndLabel("specify_rootdate_", "Specify root date as a real number or YYYY-MM-DD (--date-root)", "specify_rootdate_", "");
    	nameAndLabels[OptionIndex.SPECIFY_DATETREEFILE_FILE_.ordinal()] = new NameAndLabel("specify_datetreefile_", "Load and fix this topology (--te)","specify_datetreefile_", "");
    	nameAndLabels[OptionIndex.SPECIFY_RESAMPLEINT_.ordinal()] = new NameAndLabel("specify_resampleint_", "Resample branch lengths to infer the confidence interval (--date-ci)", "specify_resampleint_", ""); 
    	nameAndLabels[OptionIndex.SPECIFY_OUTLIERTHRESH_.ordinal()] = new NameAndLabel("specify_outlierthresh_", "z-score threshold to detect outliers", "specify_outlierthresh_", "");
    	
    	nameAndLabels[OptionIndex.PRINT_STTESTATS_.ordinal()] = new NameAndLabel("print_sitestats_", "Print alignment site statistics to .alninfo file (-alninfo)", "print_sitestats_", "");
    	nameAndLabels[OptionIndex.FIX_BRANCHLENGTHS.ordinal()] = new NameAndLabel("fix_branchlength_", "Fix branch lengths of tree passed via -te (-blfix)", "fix_branchlengths_", "");
    	nameAndLabels[OptionIndex.BRANCHLENGTHS_TREE_FILE_.ordinal()] = new NameAndLabel("branchlengths_tree_", "Provide a tree to fix branch lengths (-te)", "branchlengths_tree_", "", true);
    	nameAndLabels[OptionIndex.SPECIFY_MINBRANCHLENGTH_.ordinal()] = new NameAndLabel("specify_minbranchlength_", "Specify minimum branch length (-blmin)", "specify_minbranchlength_", "");
    	nameAndLabels[OptionIndex.SPECIFY_MAXBRANCHLENGTH_.ordinal()] = new NameAndLabel("specify_maxbranchlength_", "Specify maximum branch length (-blmax)", "specify_maxbranchlength_", "");
    	nameAndLabels[OptionIndex.WRITE_LOCALLY_OPTIMAL_.ordinal()] = new NameAndLabel("write_locally_optimal_", "Turn on writing all locally optimal trees (-wt)", "write_locally_optimal_", "");
    	nameAndLabels[OptionIndex.FIX_BRLENGTHS_.ordinal()] = new NameAndLabel("fix_brlengths_", "Turn on fixing branch lengths of tree passed via -t or -te (-fixbr)", "fix_brlengths_", "");
    	nameAndLabels[OptionIndex.PER_SITEFILE_.ordinal()] = new NameAndLabel("per_sitefile_", "Write per-site rates to .rate file (-wsr)", "per_sitefile_", "", false);
    	nameAndLabels[OptionIndex.PER_SITEWSLFILE_.ordinal()] = new NameAndLabel("per_sitewslfile_", "Write site log-liklihoods to .sitelh file (-wsl)", "per_sitewslfile_", "", false);
    	
    	nameAndLabels[OptionIndex.PER_SITEWSLRFILE_.ordinal()] = new NameAndLabel("per_sitewslrfile_", "Write site log-likelihoods per rate category (-wslr)", "per_sitewslrfile_", "", false);
    	nameAndLabels[OptionIndex.PER_SITEWSLMFILE_.ordinal()] = new NameAndLabel("per_sitewslmfile_", "Write site log-likelihoods per mixture class (-wslm)", "per_sitewslmfile_", "", false);
    	nameAndLabels[OptionIndex.PER_SITEWSLMRFILE_.ordinal()] = new NameAndLabel("per_sitewslmrfile_", "Write site log-liklihoods per mixture+rate class (-wslmr)", "per_sitewslmrfile_", "", false);
    	
    	nameAndLabels[OptionIndex.PER_SITEWSPMFILE_.ordinal()] = new NameAndLabel("per_sitewspmfile_", "Write site probabilities per mixture class (-wspm)", "per_sitewspmfile_", "", false);
   
    	nameAndLabels[OptionIndex.PER_SITEWSPRFILE_.ordinal()] = new NameAndLabel("per_sitewsprfile_", "Write site probabilities per rate category (-wspr)", "per_sitewsprfile_", "", false);
    	nameAndLabels[OptionIndex.PER_SITEWSPMRFILE_.ordinal()] = new NameAndLabel("per_sitewspmrfile_", "Write site probabilities per rate category (-wspmr)", "per_sitewspmrfile_", "", false);
    	nameAndLabels[OptionIndex.PER_SITEWPLFILE_.ordinal()] = new NameAndLabel("per_sitewplfile_", "Write partition log-likelihoods to .partlh file (-wpl)", "per_sitewplfile_", "", false);
    	nameAndLabels[OptionIndex.WRITE_SITELIKELIHOODS_.ordinal()] = new NameAndLabel("write_sitelikelihoods_", "Write log-likelihoods in TREE-PUZZLE format (-wsl)", "write_sitelikelihoods_", "");
    	nameAndLabels[OptionIndex.WRITE_LOGLIKELIHOODS_.ordinal()] = new NameAndLabel("write_loglikelihoods_", "Write log-likelihoods per rate category (-wslg)", "write_loglikelihoods_", "");
    	nameAndLabels[OptionIndex.LIST_CSINTEGERS_FILE.ordinal()] = new NameAndLabel("list_csintegers_file", "Specify a list of comma-separated integer numbers (-fconst)", "list_csintegers_file", "");
    }

	//AnnotatedPluginDocument[] selectedDocuments = null;
	
    public IQTREEXSEDE_1_01_01Options(final AnnotatedPluginDocument[] selectedDocuments) throws DocumentOperationException {
    	//super(selectedDocuments);
    	
    	OPTION_NAME = "IQTree_CIPRES";
    	this.selectedDocuments = selectedDocuments;
    	jfc.setFileSelectionMode(JFileChooser.FILES_ONLY);
    	//Simple Options
	    simpleOptions = this.addChildOptions("simpleOptions", "Simple Parameters", "");
	    
	    addJobNameOption(simpleOptions, selectedDocuments, 3);
	    
	    simpleOptions.beginAlignHorizontally(null, false);
	    runtime_= simpleOptions.addDoubleOption(nameAndLabels[OptionIndex.RUNTIME_.ordinal()].name, nameAndLabels[OptionIndex.RUNTIME_.ordinal()].label, 0.5, 0.05, 168.00);
	    simpleOptions.addLabel("  ");	    
	    final OptionValue[] which_iqtree_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_VERSION_212, ComboBoxValueLabel.IQTREE_VERSION_2227);
        which_iqtree_ = simpleOptions.addComboBoxOption(nameAndLabels[OptionIndex.WHICH_IQTREE_.ordinal()].name, nameAndLabels[OptionIndex.WHICH_IQTREE_.ordinal()].label, which_iqtree_Choices, which_iqtree_Choices[2]);	    
        simpleOptions.addLabel("  ");
        specify_numpatterns_ = simpleOptions.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_NUMPATTERNS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_NUMPATTERNS_.ordinal()].label, 1000, 1, Integer.MAX_VALUE);
        addBuffer(simpleOptions);
        simpleOptions.endAlignHorizontally();
	    
	    simpleOptions.beginAlignHorizontally(null, false);
	    //specify_numpatterns_ = simpleOptions.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_NUMPATTERNS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_NUMPATTERNS_.ordinal()].label, 0, 0, Integer.MAX_VALUE);
	    //simpleOptions.addLabel("  ");
	    more_memory_= simpleOptions.addBooleanOption(nameAndLabels[OptionIndex.MORE_MEMORY_.ordinal()].name, nameAndLabels[OptionIndex.MORE_MEMORY_.ordinal()].label, false);
	    more_memory2_= simpleOptions.addBooleanOption(nameAndLabels[OptionIndex.MORE_MEMORY2_.ordinal()].name, nameAndLabels[OptionIndex.MORE_MEMORY2_.ordinal()].label, false);
	    simpleOptions.addLabel("  ");
	    specify_safe_ = simpleOptions.addBooleanOption(nameAndLabels[OptionIndex.SPECIFY_SAFE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_SAFE_.ordinal()].label, false);	    
	    //specify_autocores_ = simpleOptions.addBooleanOption(nameAndLabels[OptionIndex.SPECIFY_AUTOCORES_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_AUTOCORES_.ordinal()].label, false);
	    addBuffer(simpleOptions);
	    simpleOptions.endAlignHorizontally();	    
	    
	    simpleOptions.beginAlignHorizontally(null, false);
	    //specify_autocores_ = simpleOptions.addBooleanOption(nameAndLabels[OptionIndex.SPECIFY_AUTOCORES_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_AUTOCORES_.ordinal()].label, false);
	    final OptionValue[] specify_runtype_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_RUNTYPE_MODEL, ComboBoxValueLabel.IQTREE_RUNTYPE_INFERENCE);
	    specify_runtype_ = simpleOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_RUNTYPE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_RUNTYPE_.ordinal()].label, specify_runtype_Choices, specify_runtype_Choices[1]);	    
	    simpleOptions.addLabel("  ");
	    final OptionValue[] sequence_type_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_NO_SELECT, ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_NT2AA);
	    sequence_type_ = simpleOptions.addComboBoxOption(nameAndLabels[OptionIndex.SEQUENCE_TYPE_.ordinal()].name, nameAndLabels[OptionIndex.SEQUENCE_TYPE_.ordinal()].label, sequence_type_Choices, sequence_type_Choices[0]);	    
	    addBuffer(simpleOptions);
	    simpleOptions.endAlignHorizontally();
	    
	    simpleOptions.beginAlignHorizontally(null, false);
	    //final OptionValue[] sequence_type_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_DNA, ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_NT2AA);
	    //sequence_type_ = simpleOptions.addComboBoxOption(nameAndLabels[OptionIndex.SEQUENCE_TYPE_.ordinal()].name, nameAndLabels[OptionIndex.SEQUENCE_TYPE_.ordinal()].label, sequence_type_Choices, sequence_type_Choices[0]);	    
	    
	    final OptionValue[] codon_type_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_CODON1, ComboBoxValueLabel.IQTREE_CODON25);
	    codon_type_ = simpleOptions.addComboBoxOption(nameAndLabels[OptionIndex.CODON_TYPE_.ordinal()].name, nameAndLabels[OptionIndex.CODON_TYPE_.ordinal()].label, codon_type_Choices, codon_type_Choices[0]);	    
	    simpleOptions.addLabel("  ");
	    final OptionValue[] nt2aa_type_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_NT2AA1, ComboBoxValueLabel.IQTREE_NT2AA25);
	    nt2aa_type_ = simpleOptions.addComboBoxOption(nameAndLabels[OptionIndex.NT2AA_TYPE_.ordinal()].name, nameAndLabels[OptionIndex.NT2AA_TYPE_.ordinal()].label, nt2aa_type_Choices, nt2aa_type_Choices[0]);	    
	    addBuffer(simpleOptions);
	    simpleOptions.endAlignHorizontally();
	    
	    simpleOptions.beginAlignHorizontally(null, false);
	    //final OptionValue[] nt2aa_type_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_NT2AA1, ComboBoxValueLabel.IQTREE_NT2AA25);
	    //nt2aa_type_ = simpleOptions.addComboBoxOption(nameAndLabels[OptionIndex.NT2AA_TYPE_.ordinal()].name, nameAndLabels[OptionIndex.NT2AA_TYPE_.ordinal()].label, nt2aa_type_Choices, nt2aa_type_Choices[0]);	    
	    FileChooser fc1 = createFileChooser(simpleOptions, nameAndLabels[OptionIndex.STARTING_TREE_FILE.ordinal()].name, nameAndLabels[OptionIndex.STARTING_TREE_FILE.ordinal()].label, true);
	    starting_tree_File = fc1.selectedFile;
	    starting_tree_FileBrowse = fc1.selectedFileBrowse;
	    simpleOptions.endAlignHorizontally();
	    
	    simpleOptions.beginAlignHorizontally(null, false);
	    use_nj_ = simpleOptions.addBooleanOption(nameAndLabels[OptionIndex.USE_NJ_.ordinal()].name, nameAndLabels[OptionIndex.USE_NJ_.ordinal()].label, false);
	    use_random_ = simpleOptions.addBooleanOption(nameAndLabels[OptionIndex.USE_RANDOM_.ordinal()].name, nameAndLabels[OptionIndex.USE_RANDOM_.ordinal()].label, false);
		specify_seed_= simpleOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_SEED_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_SEED_.ordinal()].label, "");
		//simpleOptions.addLabel("  ");
		//specify_quartets_= simpleOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_QUARTETS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_QUARTETS_.ordinal()].label, "");
		//addBuffer(simpleOptions);
		simpleOptions.endAlignHorizontally();
	    
	    simpleOptions.beginAlignHorizontally(null, false);
	    specify_outgroup_ = simpleOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_OUTGROUP_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_OUTGROUP_.ordinal()].label, "");
	    specify_prefix_ = simpleOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_PREFIX_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_PREFIX_.ordinal()].label, "output");
	    simpleOptions.endAlignHorizontally();
	    
	    
	    //simpleOptions.beginAlignHorizontally(null, false);
		//specify_seed_= simpleOptions.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_SEED_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_SEED_.ordinal()].label, 12345, 0, Integer.MAX_VALUE);
		//specify_quartets_= simpleOptions.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_QUARTETS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_QUARTETS_.ordinal()].label, 1, 1, Integer.MAX_VALUE);
		//simpleOptions.endAlignHorizontally();
		
	    
	    //Advanced Options
	    advancedOptions = this.addChildOptions("advancedOptions", "Advanced Parameters (P1)     ", "");
	    addCipresDivider(advancedOptions, "Quartet Options");
	    
	    advancedOptions.beginAlignHorizontally(null, false);
	    final OptionValue[] specify_quartets_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_QUARTET_NO, ComboBoxValueLabel.IQTREE_QUARTET_SPECIFY);
	    specify_quartets_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_QUARTETS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_QUARTETS_.ordinal()].label, specify_quartets_Choices, specify_quartets_Choices[0]);	    	    
	    specify_quartetnum_ = advancedOptions.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_QUARTETNUM_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_QUARTETNUM_.ordinal()].label, 0, 0, Integer.MAX_VALUE);
	    addBuffer(advancedOptions);
	    advancedOptions.endAlignHorizontally();
	    
	    advancedOptions.beginAlignHorizontally(null, false);
	    FileChooser fc_quartet = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.SPECIFY_QUARTETSET_FILE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_QUARTETSET_FILE_.ordinal()].label, true);
	    specify_quartetset_file_ = fc_quartet.selectedFile;
	    specify_quartetset_file_Browse = fc_quartet.selectedFileBrowse;
	    write_quartets_ = advancedOptions.addBooleanOption(nameAndLabels[OptionIndex.WRITE_QUARTETS_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_QUARTETS_.ordinal()].label, false);
	    advancedOptions.endAlignHorizontally();
	    
	    addCipresDivider(advancedOptions, "Partition Options");
	    
	    advancedOptions.beginAlignHorizontally(null, false);

	    FileChooser fc2 = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.PARTITION_FILE_.ordinal()].name, nameAndLabels[OptionIndex.PARTITION_FILE_.ordinal()].label, true);
	    partition_file_ = fc2.selectedFile;
	    partition_file_Browse = fc2.selectedFileBrowse;
	    final OptionValue[] partition_type_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_PARTITION_TYPE_Q, ComboBoxValueLabel.IQTREE_PARTITION_TYPE_SP);
	    partition_type_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.PARTITION_TYPE_.ordinal()].name, nameAndLabels[OptionIndex.PARTITION_TYPE_.ordinal()].label, partition_type_Choices, partition_type_Choices[0]);	    
	    advancedOptions.endAlignHorizontally();

	    advancedOptions.beginAlignHorizontally(null, false);	    
		mixed_sequence_ = advancedOptions.addBooleanOption(nameAndLabels[OptionIndex.MIXED_SEQUENCE_.ordinal()].name, nameAndLabels[OptionIndex.MIXED_SEQUENCE_.ordinal()].label, false);
		advancedOptions.addLabel("  ");
		final OptionValue[] num_mixedsequences_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_PARTITION_0, ComboBoxValueLabel.IQTREE_PARTITION_5);
		num_mixedsequences_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.NUM_MIXEDSEQUENCES_.ordinal()].name, nameAndLabels[OptionIndex.NUM_MIXEDSEQUENCES_.ordinal()].label, num_mixedsequences_Choices, num_mixedsequences_Choices[0]);
		addBuffer(advancedOptions);
		advancedOptions.endAlignHorizontally();
		
	    advancedOptions.beginAlignHorizontally(null, false);
	    FileChooser fc3 = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.DATATYPE2_FILE_.ordinal()].name, nameAndLabels[OptionIndex.DATATYPE2_FILE_.ordinal()].label, false);
		datatype2_file_ = fc3.selectedFile;
		datatype2_file_Browse = fc3.selectedFileBrowse;
		FileChooser fc4 = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.DATATYPE3_FILE_.ordinal()].name, nameAndLabels[OptionIndex.DATATYPE3_FILE_.ordinal()].label, false);
		datatype3_file_= fc4.selectedFile;
		datatype3_file_Browse = fc4.selectedFileBrowse;
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		FileChooser fc5 = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.DATATYPE4_FILE_.ordinal()].name, nameAndLabels[OptionIndex.DATATYPE4_FILE_.ordinal()].label, false);
		datatype4_file_ = fc5.selectedFile;
		datatype4_file_Browse = fc5.selectedFileBrowse;
		FileChooser fc6 = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.DATATYPE5_FILE_.ordinal()].name, nameAndLabels[OptionIndex.DATATYPE5_FILE_.ordinal()].label, false);
		datatype5_file_ = fc6.selectedFile;
		datatype5_file_Browse = fc6.selectedFileBrowse;
		advancedOptions.endAlignHorizontally();
		
		addCipresDivider(advancedOptions, "Automatic Model Selection Parameters");
		
	    advancedOptions.beginAlignHorizontally(null, false);
	    //Map<String, String> extraValues = new HashMap<String, String>();
	    //extraValues.put("   ", "");
	    final OptionValue[] specify_model_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_TESTONLY, ComboBoxValueLabel.IQTREE_TESTNEWMERGE);		
		specify_model_= advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_MODEL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MODEL_.ordinal()].label, specify_model_Choices, specify_model_Choices[0]);
		advancedOptions.addLabel("  ");
	    final OptionValue[] specify_liemarkov_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_LM, ComboBoxValueLabel.IQTREE_LMSS);		
		specify_liemarkov_= advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_LIEMARKOV_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_LIEMARKOV_.ordinal()].label, specify_liemarkov_Choices, specify_liemarkov_Choices[0]);		
		final OptionValue[] select_rcluster_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_RCLUSTER, ComboBoxValueLabel.IQTREE_RCLUSTERMAX);		
		select_rcluster_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SELECT_RCLUSTER_.ordinal()].name, nameAndLabels[OptionIndex.SELECT_RCLUSTER_.ordinal()].label,select_rcluster_Choices, select_rcluster_Choices[0]);		
		//specify_rclusterval_ = advancedOptions.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_RCLUSTERVAL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_RCLUSTERVAL_.ordinal()].label, 0, 0, Integer.MAX_VALUE);
		addBuffer(advancedOptions);
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		specify_rclusterval_ = advancedOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_RCLUSTERVAL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_RCLUSTERVAL_.ordinal()].label, "");
	
		specify_basemodels_ = advancedOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_BASEMODELS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_BASEMODELS_.ordinal()].label, "");
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		final OptionValue[] specify_aamodels_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_NUCLEAR, ComboBoxValueLabel.IQTREE_VIRAL);
		specify_aamodels_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_AAMODELS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_AAMODELS_.ordinal()].label, specify_aamodels_Choices, specify_aamodels_Choices[0]);
		specify_freqtypes_ = advancedOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_FREQTYPES_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_FREQTYPES_.ordinal()].label, "");
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		specify_ratehettypes_ = advancedOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_RATEHETTYPES_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_RATEHETTYPES_.ordinal()].label, "");
		specify_mincat_ = advancedOptions.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_MINCAT_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MINCAT_.ordinal()].label, 2, 0, Integer.MAX_VALUE);
		//advancedOptions.addLabel("  ");
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);		
		specify_maxcat_ = advancedOptions.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_MAXCAT_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MAXCAT_.ordinal()].label, 10, 0, Integer.MAX_VALUE);
		//addBuffer(advancedOptions);
		specify_merit_ = advancedOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_MERIT_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MERIT_.ordinal()].label, "");
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);		
		specify_fulltreesearch_ = advancedOptions.addBooleanOption(nameAndLabels[OptionIndex.SPECIFY_FULLTREESEARCH_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_FULLTREESEARCH_.ordinal()].label, false);
		specify_addlmodels_ = advancedOptions.addStringOption(nameAndLabels[OptionIndex.SPECIFY_ADDLMODELS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_ADDLMODELS_.ordinal()].label, "");
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);				
		FileChooser specify_nexusmodelfile_fc = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.SPECIFY_NEXUSMODELFILE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_NEXUSMODELFILE_FILE_.ordinal()].label, false);
		specify_nexusmodelfile_file_ = specify_nexusmodelfile_fc.selectedFile;
		specify_nexusmodelfile_file_Browse = specify_nexusmodelfile_fc.selectedFileBrowse;
		addBuffer(advancedOptions);
		advancedOptions.endAlignHorizontally();
		
		addCipresDivider(advancedOptions, "Specify Substitution Models");
		
		advancedOptions.beginAlignHorizontally(null, false);
		freetextmodel_ = advancedOptions.addStringOption(nameAndLabels[OptionIndex.FREETEXTMODEL_.ordinal()].name, nameAndLabels[OptionIndex.FREETEXTMODEL_.ordinal()].label, "");
		//Map<String, String> extraValuesModel = new HashMap<String, String>();
		//extraValuesModel.put("  ", "");
		final OptionValue[] specify_dnamodel_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_JC69, ComboBoxValueLabel.IQTREE_GTR);
		specify_dnamodel_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_DNAMODEL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_DNAMODEL_.ordinal()].label, specify_dnamodel_Choices, specify_dnamodel_Choices[0]);
		max_posteriormode_ = advancedOptions.addBooleanOption(nameAndLabels[OptionIndex.MAX_POSTERIORMODE_.ordinal()].name, nameAndLabels[OptionIndex.MAX_POSTERIORMODE_.ordinal()].label, false);
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		final OptionValue[] specify_protmodel_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_BLOSUM62, ComboBoxValueLabel.IQTREE_CF4);
		specify_protmodel_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_PROTMODEL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_PROTMODEL_.ordinal()].label, specify_protmodel_Choices, specify_protmodel_Choices[0]);		
		final OptionValue[] specify_protmixture_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_PC10, ComboBoxValueLabel.IQTREE_PCF4);
		specify_protmixture_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_PROTMIXTURE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_PROTMIXTURE_.ordinal()].label, specify_protmixture_Choices, specify_protmixture_Choices[0]);		
		final OptionValue[] specify_binmodel_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_JC2, ComboBoxValueLabel.IQTREE_ORDERED);
		specify_binmodel_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_BINMODEL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_BINMODEL_.ordinal()].label, specify_binmodel_Choices, specify_binmodel_Choices[0]);
		final OptionValue[] specify_codonmodel_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_MG, ComboBoxValueLabel.IQTREE_SCHN05);
		specify_codonmodel_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_CODONMODEL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_CODONMODEL_.ordinal()].label, specify_codonmodel_Choices, specify_codonmodel_Choices[0]);
		addBuffer(advancedOptions);
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		FileChooser fc7 = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.GUIDE_TREE_.ordinal()].name, nameAndLabels[OptionIndex.GUIDE_TREE_.ordinal()].label, false);
		guide_tree_file = fc7.selectedFile;
		guide_tree_file_Browse = fc7.selectedFileBrowse;
		//advancedOptions.endAlignHorizontally();
		
		//advancedOptions.beginAlignHorizontally(null, false);
		FileChooser frequency_file_fc = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.FREQUENCY_FILE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.FREQUENCY_FILE_FILE_.ordinal()].label, false);
		frequency_file_file = frequency_file_fc.selectedFile;
		frequency_file_file_Browse = frequency_file_fc.selectedFileBrowse;
		advancedOptions.endAlignHorizontally();
		//advancedOptions.beginAlignHorizontally(null, false);
		//FileChooser fc7 = createFileChooser(advancedOptions, nameAndLabels[OptionIndex.GUIDE_TREE_.ordinal()].name, nameAndLabels[OptionIndex.GUIDE_TREE_.ordinal()].label, false);
		//guide_tree_file = fc7.selectedFile;
		//guide_tree_file_Browse = fc7.selectedFileBrowse;
		//final OptionValue[] specify_binmodel_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_JC2, ComboBoxValueLabel.IQTREE_ORDERED);
		//specify_binmodel_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_BINMODEL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_BINMODEL_.ordinal()].label, specify_binmodel_Choices, specify_binmodel_Choices[0]);
		//advancedOptions.endAlignHorizontally();
		
		//advancedOptions.beginAlignHorizontally(null, false);
		//final OptionValue[] specify_codonmodel_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_MG, ComboBoxValueLabel.IQTREE_SCHN05);
		//specify_codonmodel_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_CODONMODEL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_CODONMODEL_.ordinal()].label, specify_codonmodel_Choices, specify_codonmodel_Choices[0]);
		//final OptionValue[] specify_modelfreq_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_F, ComboBoxValueLabel.IQTREE_F3x4);
		//specify_modelfreq_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_MODELFREQ_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MODELFREQ_.ordinal()].label, specify_modelfreq_Choices, specify_modelfreq_Choices[0]);
		//advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		final OptionValue[] specify_modelfreq_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_F, ComboBoxValueLabel.IQTREE_F3x4);
		specify_modelfreq_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_MODELFREQ_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MODELFREQ_.ordinal()].label, specify_modelfreq_Choices, specify_modelfreq_Choices[0]);
		advancedOptions.addLabel("  ");
		optimize_weights_ = advancedOptions.addBooleanOption(nameAndLabels[OptionIndex.OPTIMIZE_WEIGHTS_.ordinal()].name, nameAndLabels[OptionIndex.OPTIMIZE_WEIGHTS_.ordinal()].label, false);
		
		final OptionValue[] specify_modelrate_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_I, ComboBoxValueLabel.IQTREE_IR);
		specify_modelrate_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_MODELRATE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MODELRATE_.ordinal()].label, specify_modelrate_Choices, specify_modelrate_Choices[0]);
		advancedOptions.addLabel("  ");
		final OptionValue[] asc_bias_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_YES, ComboBoxValueLabel.IQTREE_NO);
		asc_bias_ = advancedOptions.addComboBoxOption(nameAndLabels[OptionIndex.ASC_BIAS_.ordinal()].name, nameAndLabels[OptionIndex.ASC_BIAS_.ordinal()].label, asc_bias_Choices, asc_bias_Choices[1]);
		addBuffer(advancedOptions);
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		gamma_shape_ = advancedOptions.addStringOption(nameAndLabels[OptionIndex.GAMMA_SHAPE_.ordinal()].name, nameAndLabels[OptionIndex.GAMMA_SHAPE_.ordinal()].label, "");
		advancedOptions.addLabel("  ");
		median_approximation_ = advancedOptions.addBooleanOption(nameAndLabels[OptionIndex.MEDIAN_APPROXIMATION_.ordinal()].name, nameAndLabels[OptionIndex.MEDIAN_APPROXIMATION_.ordinal()].label, false);
		addBuffer(advancedOptions);
		advancedOptions.endAlignHorizontally();
		
		advancedOptions.beginAlignHorizontally(null, false);
		invariable_sites_ = advancedOptions.addIntegerOption(nameAndLabels[OptionIndex.INVARIABLE_SITES_.ordinal()].name, nameAndLabels[OptionIndex.INVARIABLE_SITES_.ordinal()].label, 0, 0, Integer.MAX_VALUE);
		advancedOptions.addLabel("  ");
		thorough_estimation_ = advancedOptions.addBooleanOption(nameAndLabels[OptionIndex.THOROUGH_ESTIMATION_.ordinal()].name, nameAndLabels[OptionIndex.THOROUGH_ESTIMATION_.ordinal()].label, false);
		addBuffer(advancedOptions);
		advancedOptions.endAlignHorizontally();
		
		advancedOptions2 = this.addChildOptions("advancedOptions2", "Advanced Parameters (P2)     ", "");
		
		addCipresDivider(advancedOptions2, "Tree Search Parameters");
		
		advancedOptions2.beginAlignHorizontally(null, false);
		num_parstrees_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.NUM_PARSTREES_.ordinal()].name, nameAndLabels[OptionIndex.NUM_PARSTREES_.ordinal()].label, 100, 1, Integer.MAX_VALUE);
		advancedOptions2.addLabel("  ");
		num_topparstrees_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.NUM_TOPPARSTREES_.ordinal()].name, nameAndLabels[OptionIndex.NUM_TOPPARSTREES_.ordinal()].label, 20, 1, Integer.MAX_VALUE);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		num_besttrees_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.NUM_BESTTREES_.ordinal()].name, nameAndLabels[OptionIndex.NUM_BESTTREES_.ordinal()].label, 5, 1, Integer.MAX_VALUE);
		advancedOptions2.addLabel("  ");
		num_unsucctostop_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.NUM_UNSUCCTOSTOP_.ordinal()].name, nameAndLabels[OptionIndex.NUM_UNSUCCTOSTOP_.ordinal()].label, 100, 1, Integer.MAX_VALUE);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		num_tostop_ = advancedOptions2.addStringOption(nameAndLabels[OptionIndex.NUM_TOSTOP_.ordinal()].name, nameAndLabels[OptionIndex.NUM_TOSTOP_.ordinal()].label, "");
		advancedOptions2.addLabel("  ");
		specify_radius_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_RADIUS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_RADIUS_.ordinal()].label, 6, 0, Integer.MAX_VALUE);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		perturb_strength_ = advancedOptions2.addDoubleOption(nameAndLabels[OptionIndex.PERTURB_STRENGTH_.ordinal()].name, nameAndLabels[OptionIndex.PERTURB_STRENGTH_.ordinal()].label, 0.5, 0.0, 1.0);
		advancedOptions2.addLabel("  ");
		slower_NNI_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.SLOWER_NNI_.ordinal()].name, nameAndLabels[OptionIndex.SLOWER_NNI_.ordinal()].label, false);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		no_mlpairwise_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.NO_MLPAIRWISE_.ordinal()].name, nameAndLabels[OptionIndex.NO_MLPAIRWISE_.ordinal()].label, false);
		use_fasttreesearch_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.USE_FASTTREESEARCH_.ordinal()].name, nameAndLabels[OptionIndex.USE_FASTTREESEARCH_.ordinal()].label, false);
		FileChooser fc8 = createFileChooser(advancedOptions2, nameAndLabels[OptionIndex.CONSTRAINT_FILE_.ordinal()].name, nameAndLabels[OptionIndex.CONSTRAINT_FILE_.ordinal()].label, true);
		constraint_file_ = fc8.selectedFile;
		constraint_file_Browse = fc8.selectedFileBrowse;
		advancedOptions2.endAlignHorizontally();
		
		addCipresDivider(advancedOptions2, "Bootstrap Search Parameters");
		
		advancedOptions2.beginAlignHorizontally(null, false);
		final OptionValue[] bootstrap_type_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_BB, ComboBoxValueLabel.IQTREE_BC);
		bootstrap_type_ = advancedOptions2.addComboBoxOption(nameAndLabels[OptionIndex.BOOTSTRAP_TYPE_.ordinal()].name, nameAndLabels[OptionIndex.BOOTSTRAP_TYPE_.ordinal()].label, bootstrap_type_Choices, bootstrap_type_Choices[0]);
		advancedOptions2.addLabel("  ");
		use_bnni_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.USE_BNNI_.ordinal()].name, nameAndLabels[OptionIndex.USE_BNNI_.ordinal()].label, true);
		advancedOptions2.addLabel("  ");
		num_bootreps_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.NUM_BOOTREPS_.ordinal()].name, nameAndLabels[OptionIndex.NUM_BOOTREPS_.ordinal()].label, 1000, 0, Integer.MAX_VALUE);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		//advancedOptions2.beginAlignHorizontally(null, false);
		//num_bootreps_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.NUM_BOOTREPS_.ordinal()].name, nameAndLabels[OptionIndex.NUM_BOOTREPS_.ordinal()].label, 1000, 1000, Integer.MAX_VALUE);
		//write_boottrees_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.WRITE_BOOTTREES_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_BOOTTREES_.ordinal()].label, false);
		//advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		write_boottrees_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.WRITE_BOOTTREES_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_BOOTTREES_.ordinal()].label, false);
		advancedOptions2.addLabel("  ");
		write_boottrees1_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.WRITE_BOOTTREES1_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_BOOTTREES1_.ordinal()].label, false);
		advancedOptions2.addLabel("  ");
		max_iters_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.MAX_ITERS_.ordinal()].name, nameAndLabels[OptionIndex.MAX_ITERS_.ordinal()].label, 1000, 0, Integer.MAX_VALUE);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		cc_ufboot_ = advancedOptions2.addDoubleOption(nameAndLabels[OptionIndex.CC_UFBOOT_.ordinal()].name, nameAndLabels[OptionIndex.CC_UFBOOT_.ordinal()].label, 0.99, 0.0, Double.MAX_VALUE);
		advancedOptions2.addLabel("  ");
		iter_interval_ = advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.ITER_INTERVAL_.ordinal()].name, nameAndLabels[OptionIndex.ITER_INTERVAL_.ordinal()].label, 100, 0, Integer.MAX_VALUE);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		specify_tiebreaker_ = advancedOptions2.addDoubleOption(nameAndLabels[OptionIndex.SPECIFY_TIEBREAKER_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_TIEBREAKER_.ordinal()].label, 0.5, 0.00, Double.MAX_VALUE);
		advancedOptions2.addLabel("  ");
		final OptionValue[] part_resample_Choices = ComboBoxValueLabel.fillOptionValues(extraValues, ComboBoxValueLabel.IQTREE_GENE, ComboBoxValueLabel.IQTREE_GENESITE);
		part_resample_ = advancedOptions2.addComboBoxOption(nameAndLabels[OptionIndex.PART_RESAMPLE_.ordinal()].name, nameAndLabels[OptionIndex.PART_RESAMPLE_.ordinal()].label, part_resample_Choices, part_resample_Choices[0]);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		addCipresDivider(advancedOptions2, "Symmetry Tests");
		
		advancedOptions2.beginAlignHorizontally(null, false);
		use_symmtest_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.USE_SYMMTEST_.ordinal()].name, nameAndLabels[OptionIndex.USE_SYMMTEST_.ordinal()].label, false);
		
	    final OptionValue[] specify_symtest_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_SYMTEST, ComboBoxValueLabel.IQTREE_SYMTEST_KEEP_ZERO);
        specify_symtest_ = advancedOptions2.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_SYMTEST_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_SYMTEST_.ordinal()].label, specify_symtest_Choices, specify_symtest_Choices[0]);	    
        addBuffer(advancedOptions2);
        advancedOptions2.endAlignHorizontally();
        
        advancedOptions2.beginAlignHorizontally(null, false);
        final OptionValue[] specify_symtype_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_SYMTYPE_PVAL, ComboBoxValueLabel.IQTREE_SYMTYPE_INT);
        specify_symtype_ = advancedOptions2.addComboBoxOption(nameAndLabels[OptionIndex.SPECIFY_SYMTYPE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_SYMTYPE_.ordinal()].label, specify_symtype_Choices, specify_symtype_Choices[0]);	    
		specify_pval_ = advancedOptions2.addDoubleOption(nameAndLabels[OptionIndex.SPECIFY_PVAL_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_PVAL_.ordinal()].label, 0.05, 0.00000000000000000000001, 0.999);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		addCipresDivider(advancedOptions2, "Single Branch Tests");
		
		advancedOptions2.beginAlignHorizontally(null, false);
		sh_test_= advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.SH_TEST_.ordinal()].name, nameAndLabels[OptionIndex.SH_TEST_.ordinal()].label, false);
		//abayes_test_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.ABAYES_TEST_.ordinal()].name, nameAndLabels[OptionIndex.ABAYES_TEST_.ordinal()].label, false);
		//advancedOptions2.endAlignHorizontally();
		
		//advancedOptions2.beginAlignHorizontally(null, false);
		lbp_test_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.LBP_TEST_.ordinal()].name, nameAndLabels[OptionIndex.LBP_TEST_.ordinal()].label, false);
		num_replicates_= advancedOptions2.addIntegerOption(nameAndLabels[OptionIndex.NUM_REPLICATES_.ordinal()].name, nameAndLabels[OptionIndex.NUM_REPLICATES_.ordinal()].label, 1000, 1000, Integer.MAX_VALUE);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		parametrical_test_= advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.PARAMETRICAL_TEST_.ordinal()].name, nameAndLabels[OptionIndex.PARAMETRICAL_TEST_.ordinal()].label, false);
		abayes_test_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.ABAYES_TEST_.ordinal()].name, nameAndLabels[OptionIndex.ABAYES_TEST_.ordinal()].label, false);
		addBuffer(advancedOptions2);
		advancedOptions2.endAlignHorizontally();
		
		addCipresDivider(advancedOptions2, "Ancestral State Reconstruction");
		advancedOptions2.beginAlignHorizontally(null, false);
		write_ancestralseqs_ = advancedOptions2.addBooleanOption(nameAndLabels[OptionIndex.WRITE_ANCESTRALSEQS_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_ANCESTRALSEQS_.ordinal()].label, false);
		specify_ancestralthresh_ = advancedOptions2.addStringOption(nameAndLabels[OptionIndex.SPECIFY_ANCESTRALTHRESH_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_ANCESTRALTHRESH_.ordinal()].label, "");
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions2.beginAlignHorizontally(null, false);
		FileChooser fcSpecifyAncestralTree = createFileChooser(advancedOptions2, nameAndLabels[OptionIndex.SPECIFY_ANCESTRALTREE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_ANCESTRALTREE_FILE_.ordinal()].label, true);
		specify_ancestraltree_file_ = fcSpecifyAncestralTree.selectedFile;
		specify_ancestraltree_file_Browse = fcSpecifyAncestralTree.selectedFileBrowse;
		advancedOptions2.endAlignHorizontally();
		
		advancedOptions3 = this.addChildOptions("advancedOptions3", "Advanced Parameters (P3)     ", "");
		
		addCipresDivider(advancedOptions3, "Tree Topology Tests");
		
		advancedOptions3.beginAlignHorizontally(null, false);
		FileChooser fc9 = createFileChooser(advancedOptions3, nameAndLabels[OptionIndex.SPECIFY_TREEFILE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_TREEFILE_.ordinal()].label, true);
		specify_treefile_ = fc9.selectedFile;
		specify_treefile_Browse = fc9.selectedFileBrowse;
		num_rell_ = advancedOptions3.addIntegerOption(nameAndLabels[OptionIndex.NUM_RELL_.ordinal()].name, nameAndLabels[OptionIndex.NUM_RELL_.ordinal()].label, 0, 0, Integer.MAX_VALUE);
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions3.beginAlignHorizontally(null, false);
		weighted_tests_ = advancedOptions3.addBooleanOption(nameAndLabels[OptionIndex.WEIGHTED_TESTS_.ordinal()].name, nameAndLabels[OptionIndex.WEIGHTED_TESTS_.ordinal()].label, false);
		unbiased_test_ = advancedOptions3.addBooleanOption(nameAndLabels[OptionIndex.UNBIASED_TEST_.ordinal()].name, nameAndLabels[OptionIndex.UNBIASED_TEST_.ordinal()].label, false);
		estimate_parsetreeonly_ = advancedOptions3.addBooleanOption(nameAndLabels[OptionIndex.ESTIMATE_PARSETREEONLY_.ordinal()].name, nameAndLabels[OptionIndex.ESTIMATE_PARSETREEONLY_.ordinal()].label, false);
		addBuffer(advancedOptions3);
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions3.beginAlignHorizontally(null, false);
		FileChooser fc10 = createFileChooser(advancedOptions3, nameAndLabels[OptionIndex.FIXED_USERTREE_FILE.ordinal()].name, nameAndLabels[OptionIndex.FIXED_USERTREE_FILE.ordinal()].label, true);
		fixed_usertree_file = fc10.selectedFile;
		fixed_usertree_file_Browse = fc10.selectedFileBrowse;
		advancedOptions3.endAlignHorizontally();
		
		//advancedOptions3 = this.addChildOptions("advancedOptions3", "Advanced Parameters (P3)     ", "");
		
		addCipresDivider(advancedOptions3, "Consesnsus Trees");
		
		advancedOptions3.beginAlignHorizontally(null, false);
		FileChooser fc11 = createFileChooser(advancedOptions3, nameAndLabels[OptionIndex.TREE_FILE1_.ordinal()].name, nameAndLabels[OptionIndex.TREE_FILE1_.ordinal()].label, true);
		tree_file1_ = fc11.selectedFile;
		tree_file1_Browse = fc11.selectedFileBrowse;		
		compute_consensustree_ =  advancedOptions3.addBooleanOption(nameAndLabels[OptionIndex.COMPUTE_CONSENSUSTREE_.ordinal()].name, nameAndLabels[OptionIndex.COMPUTE_CONSENSUSTREE_.ordinal()].label, false);
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions3.beginAlignHorizontally(null, false);
		compute_consensusnetwork_ = advancedOptions3.addBooleanOption(nameAndLabels[OptionIndex.COMPUTE_CONSENSUSNETWORK_.ordinal()].name, nameAndLabels[OptionIndex.COMPUTE_CONSENSUSNETWORK_.ordinal()].label, false);
		min_threshold_ = advancedOptions3.addDoubleOption(nameAndLabels[OptionIndex.MIN_THRESHOLD_.ordinal()].name, nameAndLabels[OptionIndex.MIN_THRESHOLD_.ordinal()].label, 0.0, 0.0, 1.0);
		advancedOptions3.addLabel("  ");
		burnin_value_ = advancedOptions3.addDoubleOption(nameAndLabels[OptionIndex.BURNIN_VALUE_.ordinal()].name, nameAndLabels[OptionIndex.BURNIN_VALUE_.ordinal()].label, 0.0, 0.0, Double.MAX_VALUE);
		addBuffer(advancedOptions3);
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions3.beginAlignHorizontally(null, false);
		FileChooser fc12 = createFileChooser(advancedOptions3, nameAndLabels[OptionIndex.TARGET_TREEFILE_.ordinal()].name, nameAndLabels[OptionIndex.TARGET_TREEFILE_.ordinal()].label, true);
		target_treefile_ = fc12.selectedFile;
		target_treefile_Browse = fc12.selectedFileBrowse;
		set_scalefactor_ = advancedOptions3.addStringOption(nameAndLabels[OptionIndex.SET_SCALEFACTOR_.ordinal()].name, nameAndLabels[OptionIndex.SET_SCALEFACTOR_.ordinal()].label, "");
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions3.beginAlignHorizontally(null, false);
		set_precision_ = advancedOptions3.addStringOption(nameAndLabels[OptionIndex.SET_PRECISION_.ordinal()].name, nameAndLabels[OptionIndex.SET_PRECISION_.ordinal()].label, "");
		nodetarget_treefile_ = advancedOptions3.addStringOption(nameAndLabels[OptionIndex.NODETARGET_TREEFILE_.ordinal()].name, nameAndLabels[OptionIndex.NODETARGET_TREEFILE_.ordinal()].label, "");
		advancedOptions3.endAlignHorizontally();
		
		addCipresDivider(advancedOptions3, "Computing Robinson's Foulds distances");
		
		advancedOptions3.beginAlignHorizontally(null, false);
		FileChooser fc13 = createFileChooser(advancedOptions3, nameAndLabels[OptionIndex.TREE_FILE2_.ordinal()].name, nameAndLabels[OptionIndex.TREE_FILE2_.ordinal()].label, true);
		tree_file2_ = fc13.selectedFile;
		tree_file2_Browse = fc13.selectedFileBrowse;
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions3.beginAlignHorizontally(null, false);
		compute_rfdistances_all_ = advancedOptions3.addBooleanOption(nameAndLabels[OptionIndex.COMPUTE_RFDISTANCES_ALL_.ordinal()].name, nameAndLabels[OptionIndex.COMPUTE_RFDISTANCES_ALL_.ordinal()].label, false);
		compute_rfdistances_adj_ = advancedOptions3.addBooleanOption(nameAndLabels[OptionIndex.COMPUTE_RFDISTANCES_ADJ_.ordinal()].name, nameAndLabels[OptionIndex.COMPUTE_RFDISTANCES_ADJ_.ordinal()].label, false);
		addBuffer(advancedOptions3);
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions3.beginAlignHorizontally(null, false);
		FileChooser specify_rfdistancestree_file_fc = createFileChooser(advancedOptions3, nameAndLabels[OptionIndex.SPECIFY_RFDISTANCESTREE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_RFDISTANCESTREE_FILE_.ordinal()].label, true);
		specify_rfdistancestree_file_ = specify_rfdistancestree_file_fc.selectedFile;
		specify_rfdistancestree_file_Browse = specify_rfdistancestree_file_fc.selectedFileBrowse;
		
		advancedOptions3.endAlignHorizontally();
		
		addCipresDivider(advancedOptions3, "Generate Random Trees Only (then quit)");
		
		advancedOptions3.beginAlignHorizontally(null, false);
		//generate_randomtrees_ = advancedOptions3.addBooleanOption(nameAndLabels[OptionIndex.GENERATE_RANDOMTREES_.ordinal()].name, nameAndLabels[OptionIndex.GENERATE_RANDOMTREES_.ordinal()].label, false);
		num_taxa_ = advancedOptions3.addStringOption(nameAndLabels[OptionIndex.NUM_TAXA_.ordinal()].name, nameAndLabels[OptionIndex.NUM_TAXA_.ordinal()].label, "");
		advancedOptions3.addLabel("  ");
		final OptionValue[] choose_randomtype_Choices = ComboBoxValueLabel.fillOptionValues(ComboBoxValueLabel.IQTREE_none, ComboBoxValueLabel.IQTREE_rcsg);
		choose_randomtype_ = advancedOptions3.addComboBoxOption(nameAndLabels[OptionIndex.CHOOSE_RANDOMTYPE_.ordinal()].name, nameAndLabels[OptionIndex.CHOOSE_RANDOMTYPE_.ordinal()].label, choose_randomtype_Choices, choose_randomtype_Choices[0]);
		//advancedOptions3.addLabel("  ");
		addBuffer(advancedOptions3);
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions3.beginAlignHorizontally(null, false);
		specify_brlengths_ = advancedOptions3.addStringOption(nameAndLabels[OptionIndex.SPECIFY_BRLENGTHS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_BRLENGTHS_.ordinal()].label, "");
		specify_treefilename_ = advancedOptions3.addStringOption(nameAndLabels[OptionIndex.SPECIFY_TREEFILENAME_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_TREEFILENAME_.ordinal()].label, "");
		addBuffer(advancedOptions3);
		advancedOptions3.endAlignHorizontally();
		
		advancedOptions4 = this.addChildOptions("advancedOptions4", "Advanced Parameters (P4)     ", "");
		
		addCipresDivider(advancedOptions4, "Concordance Factor Options");
		
		advancedOptions4.beginAlignHorizontally(null, false);
		//FileChooser partition_modelfile_file_fc = createFileChooser(advancedOptions4, nameAndLabels[OptionIndex.PARTITION_MODELFILE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.PARTITION_MODELFILE_FILE_.ordinal()].label, true);
		//partition_modelfile_file_ = partition_modelfile_file_fc.selectedFile;
		//partition_modelfile_file_Browse = partition_modelfile_file_fc.selectedFileBrowse;
		

		FileChooser partition_modelfile2_file_fc = createFileChooser(advancedOptions4, nameAndLabels[OptionIndex.PARTITION_MODELFILE2_FILE_.ordinal()].name, nameAndLabels[OptionIndex.PARTITION_MODELFILE2_FILE_.ordinal()].label, true);
		partition_modelfile2_file_ = partition_modelfile2_file_fc.selectedFile;
		partition_modelfile2_file_Browse = partition_modelfile2_file_fc.selectedFileBrowse;
		advancedOptions4.endAlignHorizontally();

		advancedOptions4.beginAlignHorizontally(null, false);
		FileChooser partition_tfile_file_fc = createFileChooser(advancedOptions4, nameAndLabels[OptionIndex.PARTITION_TFILE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.PARTITION_TFILE_FILE_.ordinal()].label, true);
		partition_tfile_file_ = partition_tfile_file_fc.selectedFile;
		partition_tfile_file_Browse = partition_tfile_file_fc.selectedFileBrowse;
				
		FileChooser setoftrees_file_file_fc = createFileChooser(advancedOptions4, nameAndLabels[OptionIndex.SETOFTREES_FILE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.SETOFTREES_FILE_FILE_.ordinal()].label, true);
		setoftrees_file_file_ = setoftrees_file_file_fc.selectedFile;
		setoftrees_file_file_Browse = setoftrees_file_file_fc.selectedFileBrowse;
		advancedOptions4.endAlignHorizontally();
		
		advancedOptions4.beginAlignHorizontally(null, false);
		specify_numquartets_ = advancedOptions4.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_NUMQUARTETS_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_NUMQUARTETS_.ordinal()].label, 0, 0, Integer.MAX_VALUE);
		//name_outfiles_ = advancedOptions4.addStringOption(nameAndLabels[OptionIndex.NAME_OUTFILES_.ordinal()].name, nameAndLabels[OptionIndex.NAME_OUTFILES_.ordinal()].label, "");
		//name_outfiles_.setHidden(true);
		addBuffer(advancedOptions4);
		advancedOptions4.endAlignHorizontally();
		
		addCipresDivider(advancedOptions4, "Dating Options");
		
		advancedOptions4.beginAlignHorizontally(null, false);
		FileChooser specify_datefile_file_fc = createFileChooser(advancedOptions4, nameAndLabels[OptionIndex.SPECIFY_DATEFILE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_DATEFILE_FILE_.ordinal()].label, true);
		specify_datefile_file_ = specify_datefile_file_fc.selectedFile;
		specify_datefile_file_Browse = specify_datefile_file_fc.selectedFileBrowse;
		
		extract_datefile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.EXTRACT_DATEFILE_.ordinal()].name, nameAndLabels[OptionIndex.EXTRACT_DATEFILE_.ordinal()].label, false);
		advancedOptions4.endAlignHorizontally();
		
		advancedOptions4.beginAlignHorizontally(null, false);
		specify_datetip_ = advancedOptions4.addStringOption(nameAndLabels[OptionIndex.SPECIFY_DATETIP_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_DATETIP_.ordinal()].label, "");
		specify_rootdate_ = advancedOptions4.addStringOption(nameAndLabels[OptionIndex.SPECIFY_ROOTDATE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_ROOTDATE_.ordinal()].label, "");
		advancedOptions4.endAlignHorizontally();
		
		advancedOptions4.beginAlignHorizontally(null, false);
		
		FileChooser specify_datetreefile_file_fc = createFileChooser(advancedOptions4, nameAndLabels[OptionIndex.SPECIFY_DATETREEFILE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_DATETREEFILE_FILE_.ordinal()].label, true);
		specify_datetreefile_file_ = specify_datetreefile_file_fc.selectedFile;
		specify_datetreefile_file_Browse = specify_datetreefile_file_fc.selectedFileBrowse;
		
		specify_resampleint_ = advancedOptions4.addIntegerOption(nameAndLabels[OptionIndex.SPECIFY_RESAMPLEINT_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_RESAMPLEINT_.ordinal()].label, 0, 0, Integer.MAX_VALUE);
		
		//specify_resampleint_ = advancedOptions4.addStringOption(nameAndLabels[OptionIndex.SPECIFY_RESAMPLEINT_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_RESAMPLEINT_.ordinal()].label, "100");
		//specify_outlierthresh_ = advancedOptions4.addDoubleOption(nameAndLabels[OptionIndex.SPECIFY_OUTLIERTHRESH_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_OUTLIERTHRESH_.ordinal()].label, 0.5, 0.05, 168.00);
		advancedOptions4.endAlignHorizontally();
		
		advancedOptions4.beginAlignHorizontally(null, false);
		specify_outlierthresh_ = advancedOptions4.addStringOption(nameAndLabels[OptionIndex.SPECIFY_OUTLIERTHRESH_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_OUTLIERTHRESH_.ordinal()].label, "");		
		advancedOptions4.endAlignHorizontally();
		
		
		addCipresDivider(advancedOptions4, "Miscellaneous Options");
		
		advancedOptions4.beginAlignHorizontally(null, false);
		print_sitestats_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PRINT_STTESTATS_.ordinal()].name, nameAndLabels[OptionIndex.PRINT_STTESTATS_.ordinal()].label, false);
		fix_branchlengths_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.FIX_BRANCHLENGTHS.ordinal()].name, nameAndLabels[OptionIndex.FIX_BRANCHLENGTHS.ordinal()].label, false);
		FileChooser branchlengths_tree_file_fc = createFileChooser(advancedOptions4, nameAndLabels[OptionIndex.BRANCHLENGTHS_TREE_FILE_.ordinal()].name, nameAndLabels[OptionIndex.BRANCHLENGTHS_TREE_FILE_.ordinal()].label, true);
		branchlengths_tree_file_ = branchlengths_tree_file_fc.selectedFile;
		branchlengths_tree_file_Browse = branchlengths_tree_file_fc.selectedFileBrowse;		
		advancedOptions4.endAlignHorizontally();
		
		advancedOptions4.beginAlignHorizontally(null, false);
		specify_minbranchlength_ = advancedOptions4.addStringOption(nameAndLabels[OptionIndex.SPECIFY_MINBRANCHLENGTH_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MINBRANCHLENGTH_.ordinal()].label, "");
		specify_maxbranchlength_ = advancedOptions4.addStringOption(nameAndLabels[OptionIndex.SPECIFY_MAXBRANCHLENGTH_.ordinal()].name, nameAndLabels[OptionIndex.SPECIFY_MAXBRANCHLENGTH_.ordinal()].label, "");
		advancedOptions4.endAlignHorizontally();
		
		advancedOptions4.beginAlignHorizontally(null, false);
    	write_locally_optimal_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.WRITE_LOCALLY_OPTIMAL_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_LOCALLY_OPTIMAL_.ordinal()].label, false);
    	fix_brlengths_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.FIX_BRLENGTHS_.ordinal()].name, nameAndLabels[OptionIndex.FIX_BRLENGTHS_.ordinal()].label, false);
    	per_sitefile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEFILE_.ordinal()].label, false);
    	addBuffer(advancedOptions4);
    	advancedOptions4.endAlignHorizontally();
    	
    	//advancedOptions4.beginAlignHorizontally(null, false);
    	//per_sitefile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEFILE_.ordinal()].label, false);
    	//per_sitewslfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSLFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSLFILE_.ordinal()].label, false);
    	//advancedOptions4.endAlignHorizontally();
    	
    	advancedOptions4.beginAlignHorizontally(null, false);
    	per_sitewslfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSLFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSLFILE_.ordinal()].label, false);
       	//per_sitewslmrfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSMRLFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSLMRFILE_.ordinal()].label, false);
    	per_sitewslrfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSLRFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSLRFILE_.ordinal()].label, false);
    	per_sitewslmfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSLMFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSLMFILE_.ordinal()].label, false);
    	addBuffer(advancedOptions4);
    	advancedOptions4.endAlignHorizontally();
    	
    	advancedOptions4.beginAlignHorizontally(null, false);
    	per_sitewslmrfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSLMRFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSLMRFILE_.ordinal()].label, false);
    	per_sitewspmfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSPMFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSPMFILE_.ordinal()].label, false);
    	per_sitewsprfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSPRFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSPRFILE_.ordinal()].label, false);
      	addBuffer(advancedOptions4);
    	advancedOptions4.endAlignHorizontally();
    	
    	//per_sitewspmrfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSPMRFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSPMRFILE_.ordinal()].label, false);

    	//addBuffer(advancedOptions4);
    	//advancedOptions4.endAlignHorizontally();
    	
    	//advancedOptions4.beginAlignHorizontally(null, false);
    	//per_sitewspmrfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSPMRFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSPMRFILE_.ordinal()].label, false);
    	//per_sitewplfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWPLFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWPLFILE_.ordinal()].label, false);
    	//advancedOptions4.endAlignHorizontally();
    	
    	advancedOptions4.beginAlignHorizontally(null, false);
    	per_sitewspmrfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWSPMRFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWSPMRFILE_.ordinal()].label, false);

    	per_sitewplfile_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.PER_SITEWPLFILE_.ordinal()].name, nameAndLabels[OptionIndex.PER_SITEWPLFILE_.ordinal()].label, false);
    	write_sitelikelihoods_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.WRITE_SITELIKELIHOODS_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_SITELIKELIHOODS_.ordinal()].label, false);
    	//write_loglikelihoods_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.WRITE_LOGLIKELIHOODS_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_LOGLIKELIHOODS_.ordinal()].label, false);
    	addBuffer(advancedOptions4);
    	advancedOptions4.endAlignHorizontally();
    	
    	advancedOptions4.beginAlignHorizontally(null, false);
    	write_loglikelihoods_ = advancedOptions4.addBooleanOption(nameAndLabels[OptionIndex.WRITE_LOGLIKELIHOODS_.ordinal()].name, nameAndLabels[OptionIndex.WRITE_LOGLIKELIHOODS_.ordinal()].label, false);
		FileChooser fc14 = createFileChooser(advancedOptions4, nameAndLabels[OptionIndex.LIST_CSINTEGERS_FILE.ordinal()].name, nameAndLabels[OptionIndex.LIST_CSINTEGERS_FILE.ordinal()].label, true);
		list_csintegers_file = fc14.selectedFile;
		list_csintegers_file_Browse = fc14.selectedFileBrowse;
    	advancedOptions4.endAlignHorizontally();
    	
	    /*Add tab***********************************/
	    Options.Option parameterChooser = addChildOptionsPageChooser("parameterChooser",
	                "Parameters",
	                null,
	                Options.PageChooserType.BUTTONS,
	                true);
		
        addLabel(" ");
        beginAlignHorizontally(null, false);
        addLabel(OPTION_NAME);
        endAlignHorizontally();
        
	    setInitialEnabledState();
	    noSavedValues();
	    setDescription();
	    buildRelationshipAmongOptions();
	    parameterChooser.setShouldSaveValue(false);
    }
    
    private void setInitialEnabledState()
    {
    	more_memory_.setEnabled(false);
    	more_memory2_.setEnabled(false);
    	codon_type_.setEnabled(false);
    	nt2aa_type_.setEnabled(false);
    	num_mixedsequences_.setEnabled(false);
    	datatype2_file_.setEnabled(false);
    	datatype3_file_.setEnabled(false);
    	datatype4_file_.setEnabled(false);
    	datatype5_file_.setEnabled(false);
    	specify_aamodels_.setEnabled(false);
    	
    	freetextmodel_.setEnabled(false);
    	specify_dnamodel_.setEnabled(false);
    	specify_protmodel_.setEnabled(false);
    	specify_protmixture_.setEnabled(false);
    	guide_tree_file.setEnabled(false);
    	guide_tree_file_Browse.setEnabled(false);
    	frequency_file_file.setEnabled(false);
    	frequency_file_file_Browse.setEnabled(false);    	
    	max_posteriormode_.setEnabled(false);
    	specify_binmodel_.setEnabled(false);
    	specify_codonmodel_.setEnabled(false);
    	specify_modelfreq_.setEnabled(false);
    	specify_modelrate_.setEnabled(false);
    	asc_bias_.setEnabled(false);
    	gamma_shape_.setEnabled(false);
    	median_approximation_.setEnabled(false);
    	invariable_sites_.setEnabled(false);
    	thorough_estimation_.setEnabled(false);
    	
    	num_parstrees_.setEnabled(false);
    	num_topparstrees_.setEnabled(false);
    	num_besttrees_.setEnabled(false);
    	num_unsucctostop_.setEnabled(false);
    	num_tostop_.setEnabled(false);
    	specify_radius_.setEnabled(false);
    	perturb_strength_.setEnabled(false);
    	slower_NNI_.setEnabled(false);
    	no_mlpairwise_.setEnabled(false);
    	use_fasttreesearch_.setEnabled(false);
    	constraint_file_.setEnabled(false);
    	constraint_file_Browse.setEnabled(false);
    	
    	num_replicates_.setEnabled(false);
    	weighted_tests_.setEnabled(false);
    	unbiased_test_.setEnabled(true);
    	estimate_parsetreeonly_.setEnabled(false);
    	
    	compute_consensustree_.setEnabled(false);
    	compute_consensusnetwork_.setEnabled(false);
    	min_threshold_.setEnabled(false);
    	burnin_value_.setEnabled(false);
    	
    	compute_rfdistances_all_.setEnabled(false);
    	compute_rfdistances_adj_.setEnabled(false);
    	
    	fix_brlengths_.setEnabled(false);
    	per_sitefile_.setEnabled(false);
    	per_sitewslfile_.setEnabled(false);
    	per_sitewslmrfile_.setEnabled(false);
    	per_sitewslrfile_.setEnabled(false);
    	per_sitewslmfile_.setEnabled(false);
    	per_sitewspmfile_.setEnabled(false);
    	per_sitewsprfile_.setEnabled(false);
    	per_sitewspmrfile_.setEnabled(false);
    	per_sitewplfile_.setEnabled(false);
    	
		//specify_rcluster_.setEnabled(false);
		specify_basemodels_.setEnabled(false);
		specify_freqtypes_.setEnabled(false);
		specify_ratehettypes_.setEnabled(false);
		specify_mincat_.setEnabled(false);
		specify_maxcat_.setEnabled(false);
		specify_merit_.setEnabled(false);
		specify_fulltreesearch_.setEnabled(false);
		specify_addlmodels_.setEnabled(false);
		bootstrap_type_.setEnabled(false);
		
		partition_modelfile2_file_.setEnabled(true);
		partition_tfile_file_.setEnabled(true);
		setoftrees_file_file_.setEnabled(true);
		specify_numquartets_.setEnabled(true);
		specify_datefile_file_.setEnabled(true);
		extract_datefile_.setEnabled(true);
		specify_datetip_.setEnabled(true);
		specify_rootdate_.setEnabled(true);
		specify_datetreefile_file_.setEnabled(true);
		specify_resampleint_.setEnabled(true);
		specify_outlierthresh_.setEnabled(true);
    	
    }
    
    private void noSavedValues()
    {    	
    	starting_tree_File.setShouldSaveValue(false);

    	partition_file_.setShouldSaveValue(false);
 
    	datatype2_file_.setShouldSaveValue(false);
 
    	datatype3_file_.setShouldSaveValue(false);
 
    	datatype4_file_.setShouldSaveValue(false);
   
    	datatype5_file_.setShouldSaveValue(false);

    	guide_tree_file.setShouldSaveValue(false);
    	
    	frequency_file_file.setShouldSaveValue(false);

    	constraint_file_.setShouldSaveValue(false);

    	specify_treefile_.setShouldSaveValue(false);

    	fixed_usertree_file.setShouldSaveValue(false);
    	
    	tree_file1_.setShouldSaveValue(false);

    	target_treefile_.setShouldSaveValue(false);

    	tree_file2_.setShouldSaveValue(false);
    	
    	list_csintegers_file.setShouldSaveValue(false);
    	
    	//partition_modelfile_file_.setShouldSaveValue(false);
    	
    	partition_modelfile2_file_.setShouldSaveValue(false);
    		
    	partition_tfile_file_.setShouldSaveValue(false);
    	
    	setoftrees_file_file_.setShouldSaveValue(false);    	

    	specify_datefile_file_.setShouldSaveValue(false);

    	specify_datetreefile_file_.setShouldSaveValue(false);

    	branchlengths_tree_file_.setShouldSaveValue(false);

    	list_csintegers_file.setShouldSaveValue(false);
    	
    	invariable_sites_.setShouldSaveValue(false);
    	num_tostop_.setShouldSaveValue(false);
    	specify_resampleint_.setShouldSaveValue(false);
    	
    	specify_mincat_.setShouldSaveValue(false);
    	specify_maxcat_.setShouldSaveValue(false);
    	num_topparstrees_.setShouldSaveValue(false);
    	max_iters_.setShouldSaveValue(false);
    	cc_ufboot_.setShouldSaveValue(false);
    	iter_interval_.setShouldSaveValue(false);
    	specify_tiebreaker_.setShouldSaveValue(false);
    	
    	
    }
    
    private void setDescription()
    {
    	for (OptionIndex index : OptionIndex.values())
    	{
        	Option opt = simpleOptions.getOption(nameAndLabels[index.ordinal()].name);
        	if (opt == null)
        		opt = advancedOptions.getOption(nameAndLabels[index.ordinal()].name);
        	if (opt == null)
        		opt = advancedOptions2.getOption(nameAndLabels[index.ordinal()].name);
        	if (opt == null)
        		opt = advancedOptions3.getOption(nameAndLabels[index.ordinal()].name);
        	if (opt == null)
        		opt = advancedOptions4.getOption(nameAndLabels[index.ordinal()].name);
        	if (opt == null || nameAndLabels[index.ordinal()].description == null || nameAndLabels[index.ordinal()].description.isBlank())
        		continue;
        	opt.setDescription(nameAndLabels[index.ordinal()].description);
    	}
    }
    
    private void buildRelationshipAmongOptions()
    {
        SimpleListener sl = new SimpleListener() {
    		@Override
    		public void objectChanged() {
    			doubleCheckRelationship();
    			
    			doubleCheckRelationship();
    		}
        };
        	specify_runtype_.addChangeListener(sl);
        	specify_numpatterns_.addChangeListener(sl);
        	mixed_sequence_.addChangeListener(sl);
        	sequence_type_.addChangeListener(sl);
        	partition_type_.addChangeListener(sl);
        	mixed_sequence_.addChangeListener(sl);
        	num_mixedsequences_.addChangeListener(sl);
        	starting_tree_File.addChangeListener(sl);
        	specify_protmodel_.addChangeListener(sl);
        	bootstrap_type_.addChangeListener(sl);
        	specify_symtest_.addChangeListener(sl);
        	use_symmtest_.addChangeListener(sl);
        	sh_test_.addChangeListener(sl);
        	parametrical_test_.addChangeListener(sl);
        	abayes_test_.addChangeListener(sl);
        	lbp_test_.addChangeListener(sl);
        	num_rell_.addChangeListener(sl);
        	tree_file1_.addChangeListener(sl);
        	fixed_usertree_file.addChangeListener(sl);
        	freetextmodel_.addChangeListener(sl);
        	specify_model_.addChangeListener(sl);
        	target_treefile_.addChangeListener(sl);
        	partition_file_.addChangeListener(sl);
        	//generate_randomtrees_.addChangeListener(sl);
        	select_rcluster_.addChangeListener(sl);
        	specify_quartetnum_.addChangeListener(sl);
        	specify_quartets_.addChangeListener(sl);
        	write_quartets_.addChangeListener(sl);
        	
        	partition_modelfile2_file_.addChangeListener(sl);
        	partition_tfile_file_.addChangeListener(sl);
    		setoftrees_file_file_.addChangeListener(sl);
    		specify_numquartets_.addChangeListener(sl);
    		specify_datefile_file_.addChangeListener(sl);
    		extract_datefile_.addChangeListener(sl);
    		specify_datetip_.addChangeListener(sl);
    		specify_rootdate_.addChangeListener(sl);
    		specify_datetreefile_file_.addChangeListener(sl);
    		specify_resampleint_.addChangeListener(sl);
    		specify_outlierthresh_.addChangeListener(sl);  
    		
    		more_memory_.addChangeListener(sl);
    		more_memory2_.addChangeListener(sl);
        	
        	doubleCheckRelationship();
        	
    }
    
    private void doubleCheckRelationship()
    {
    	String runType1 = ComboBoxValueLabel.IQTREE_RUNTYPE_MODEL.getValue();
    	String runType2 = ComboBoxValueLabel.IQTREE_RUNTYPE_INFERENCE.getValue();
    	
    	String specify_runtype_Value = getValueAsString(OptionIndex.SPECIFY_RUNTYPE_);
    	String specify_numpatterns_Value = getValueAsString(OptionIndex.SPECIFY_NUMPATTERNS_);
    	String sequence_type_Value = getValueAsString(OptionIndex.SEQUENCE_TYPE_);
    	
    	
    	//if (specify_runtype_Value != null && specify_runtype_Value.equals(runType2) && specify_numpatterns_Value != null && specify_numpatterns_Value.strip().equals("1"))  		
    	if (sequence_type_Value != null && !sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_AMINO.getValue()))
    	{
    		more_memory_.setEnabled(true);
    		more_memory2_.setEnabled(true);
    	}
    	else
    	{
    		more_memory_.setEnabled(false);
    		more_memory2_.setEnabled(false);
    	}
    	
    	if (specify_runtype_Value != null && specify_runtype_Value.equals(runType2))
    		bootstrap_type_.setEnabled(true);
    	else
    		bootstrap_type_.setEnabled(false);
    	
    	/*
    	if (specify_numpatterns_Value != null)
    	{
    		partition_type_.setEnabled(Integer.parseInt(specify_numpatterns_Value) > 1);
    	}*/
    	
    	if (specify_runtype_Value != null && specify_runtype_Value.equals(runType1))
    	{
    		//specify_autocores_.setEnabled(true);
    		setFileSelectorEnabled(OptionIndex.SPECIFY_NEXUSMODELFILE_FILE_, true);
    	}
    	else
    	{
    		//specify_autocores_.setEnabled(false);
    		setFileSelectorEnabled(OptionIndex.SPECIFY_NEXUSMODELFILE_FILE_, false);
    	}
    	
    	
    	//String sequence_type_Value = getValueAsString(OptionIndex.SEQUENCE_TYPE_);
    	if (sequence_type_Value != null && sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_CODON.getValue()))
    		codon_type_.setEnabled(true);
    	else
    		codon_type_.setEnabled(false);
    	
    	if (sequence_type_Value != null && sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_NT2AA.getValue()))
    		nt2aa_type_.setEnabled(true);
    	else
    		nt2aa_type_.setEnabled(false);
    	
    	String partition_type_Value = getValueAsString(OptionIndex.PARTITION_TYPE_);
    	if (partition_type_Value != null && !partition_type_Value.isBlank())
    	{
    		//setFileSelectorEnabled(OptionIndex.PARTITION_FILE_,true);
    		mixed_sequence_.setEnabled(true);
    		//part_resample_.setEnabled(true);
    	}
    	else
    	{
    		//setFileSelectorEnabled(OptionIndex.PARTITION_FILE_,false);
    		mixed_sequence_.setEnabled(false);
    		//part_resample_.setEnabled(false);
    	}
    	
    	String  partition_file_Value = getValueAsString(OptionIndex.PARTITION_FILE_);
    	if (partition_file_Value != null && !partition_file_Value.isBlank())
    	{
    		//more_memory_.setEnabled(true);
    		partition_type_.setEnabled(true);
    		part_resample_.setEnabled(true);
    	}
    	else
    	{
    		//more_memory_.setEnabled(false);
    		partition_type_.setEnabled(false);
    		part_resample_.setEnabled(false);
    	}
    	Boolean mixed_sequence_Value = getValueAsBoolean(OptionIndex.MIXED_SEQUENCE_);
    	sequence_type_.setEnabled(!mixed_sequence_Value);
    	num_mixedsequences_.setEnabled(mixed_sequence_Value);
    	
    	String num_mixedsequences_Value = getValueAsString(OptionIndex.NUM_MIXEDSEQUENCES_);
    	if (num_mixedsequences_Value != null && !num_mixedsequences_Value.isBlank())
    	{
    		try
    		{
	    		int num_mixedsequences = Integer.parseInt(num_mixedsequences_Value);
	    		setFileSelectorEnabled(OptionIndex.DATATYPE2_FILE_, num_mixedsequences > 1);
	    		setFileSelectorEnabled(OptionIndex.DATATYPE3_FILE_, num_mixedsequences > 2);
	    		setFileSelectorEnabled(OptionIndex.DATATYPE4_FILE_, num_mixedsequences > 3);
	    		setFileSelectorEnabled(OptionIndex.DATATYPE5_FILE_, num_mixedsequences > 4);
    		}
    		catch (NumberFormatException nfe)
    		{
        		setFileSelectorEnabled(OptionIndex.DATATYPE2_FILE_, false);
        		setFileSelectorEnabled(OptionIndex.DATATYPE3_FILE_, false);
        		setFileSelectorEnabled(OptionIndex.DATATYPE4_FILE_, false);
        		setFileSelectorEnabled(OptionIndex.DATATYPE5_FILE_, false);    	   			
    		}
    		
    	}
    	else
    	{
    		setFileSelectorEnabled(OptionIndex.DATATYPE2_FILE_, false);
    		setFileSelectorEnabled(OptionIndex.DATATYPE3_FILE_, false);
    		setFileSelectorEnabled(OptionIndex.DATATYPE4_FILE_, false);
    		setFileSelectorEnabled(OptionIndex.DATATYPE5_FILE_, false);    		
    	}
    	String starting_tree_File_Value = getValueAsString(OptionIndex.STARTING_TREE_FILE);
    	if  (starting_tree_File_Value != null && !starting_tree_File_Value.isBlank())
    	{
    		use_nj_.setEnabled(false);
    		use_random_.setEnabled(false);
    	}
    	else
    	{
    		use_nj_.setEnabled(true);
    		use_random_.setEnabled(true);
    	}
    	
    	String specify_model_Value = getValueAsString(OptionIndex.SPECIFY_MODEL_);
    	if ((specify_runtype_Value != null && specify_runtype_Value.equals(runType1)) && (specify_model_Value != null && !specify_model_Value.isBlank()))
    	{
    		//specify_rcluster_.setEnabled(true);
    		specify_basemodels_.setEnabled(true);
    		specify_freqtypes_.setEnabled(true);
    		specify_ratehettypes_.setEnabled(true);
    		specify_mincat_.setEnabled(true);
    		specify_maxcat_.setEnabled(true);
    		specify_merit_.setEnabled(true);
    		specify_fulltreesearch_.setEnabled(true);
    		specify_addlmodels_.setEnabled(true);
    	}
    	else
    	{
    		//specify_rcluster_.setEnabled(false);
    		specify_basemodels_.setEnabled(false);
    		specify_freqtypes_.setEnabled(false);
    		specify_ratehettypes_.setEnabled(false);
    		specify_mincat_.setEnabled(false);
    		specify_maxcat_.setEnabled(false);
    		specify_merit_.setEnabled(false);
    		specify_fulltreesearch_.setEnabled(false);
    		specify_addlmodels_.setEnabled(false);
    	}
    	
    	if (sequence_type_Value != null && sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_AMINO.getValue()) )
    	{
    		specify_aamodels_.setEnabled(true);
    	}
    	else
    		specify_aamodels_.setEnabled(false);
    	
    	if (specify_runtype_Value != null && specify_runtype_Value.equals(runType2) )
    	{
    		freetextmodel_.setEnabled(true);
    		specify_modelfreq_.setEnabled(true);
    		specify_modelrate_.setEnabled(true);
    		asc_bias_.setEnabled(true);
    		gamma_shape_.setEnabled(true);
    		median_approximation_.setEnabled(true);
    		invariable_sites_.setEnabled(true);
    		thorough_estimation_.setEnabled(true);
    		num_parstrees_.setEnabled(true);
    		num_topparstrees_.setEnabled(true);
    		num_besttrees_.setEnabled(true);
    		num_unsucctostop_.setEnabled(true);
    		specify_radius_.setEnabled(true);
    		perturb_strength_.setEnabled(true);
    		slower_NNI_.setEnabled(true);
    		no_mlpairwise_.setEnabled(true);
    		use_fasttreesearch_.setEnabled(true);
    		setFileSelectorEnabled(OptionIndex.CONSTRAINT_FILE_,true);
    		
    		per_sitefile_.setEnabled(true);
    		per_sitewslfile_.setEnabled(true);
    		per_sitewslmrfile_.setEnabled(true);
    		per_sitewslrfile_.setEnabled(true);
    		per_sitewslmfile_.setEnabled(true);
    		per_sitewspmfile_.setEnabled(true);
    		per_sitewsprfile_.setEnabled(true);
    		per_sitewspmrfile_.setEnabled(true);
    		per_sitewplfile_.setEnabled(true);
    		
    	}
    	else
    	{
    		freetextmodel_.setEnabled(false);
    		specify_modelfreq_.setEnabled(false);
    		specify_modelrate_.setEnabled(false);
    		asc_bias_.setEnabled(false);
    		gamma_shape_.setEnabled(false);
    		median_approximation_.setEnabled(false);
    		invariable_sites_.setEnabled(false);
    		thorough_estimation_.setEnabled(false);
    		num_parstrees_.setEnabled(false);
    		num_topparstrees_.setEnabled(false);
    		num_besttrees_.setEnabled(false);
    		num_unsucctostop_.setEnabled(false);
    		specify_radius_.setEnabled(false);
    		perturb_strength_.setEnabled(false);
    		slower_NNI_.setEnabled(false);
    		no_mlpairwise_.setEnabled(false);
    		use_fasttreesearch_.setEnabled(false);
    		setFileSelectorEnabled(OptionIndex.CONSTRAINT_FILE_,false);
    		
    		per_sitefile_.setEnabled(false);
    		per_sitewslfile_.setEnabled(false);
    		per_sitewslmrfile_.setEnabled(false);
    		per_sitewslrfile_.setEnabled(false);
    		per_sitewslmfile_.setEnabled(false);
    		per_sitewspmfile_.setEnabled(false);
    		per_sitewsprfile_.setEnabled(false);
    		per_sitewspmrfile_.setEnabled(false);
    		per_sitewplfile_.setEnabled(false);
    	}
    	
    	String freetextmodel_Value = getValueAsString(OptionIndex.FREETEXTMODEL_);
       	if (sequence_type_Value != null && sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_DNA.getValue())  && specify_runtype_Value != null && specify_runtype_Value.equals(runType2)  &&
       			(freetextmodel_Value == null || freetextmodel_Value.isBlank()))
    	{
       		specify_dnamodel_.setEnabled(true);
    	}
    	else
    		specify_dnamodel_.setEnabled(false);
       	
       	if (sequence_type_Value != null && (sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_AMINO.getValue()) ||
       			sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_NT2AA.getValue())) && specify_runtype_Value != null && specify_runtype_Value.equals(runType2) &&
       			(freetextmodel_Value == null || freetextmodel_Value.isBlank()))
    	{
       		specify_protmodel_.setEnabled(true);
       		//setFileSelectorEnabled(OptionIndex.GUIDE_TREE_,true);
    	}
    	else
    	{
    		specify_protmodel_.setEnabled(false);
    		//setFileSelectorEnabled(OptionIndex.GUIDE_TREE_,false);
    	}
       	
       	String specify_protmodel_Value = getValueAsString(OptionIndex.SPECIFY_PROTMODEL_);
       	if (sequence_type_Value != null && (sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_AMINO.getValue()) ||
       			sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_NT2AA.getValue())) && specify_runtype_Value != null && specify_runtype_Value.equals(runType2) &&
       			specify_protmodel_Value != null && !specify_protmodel_Value.isBlank())
       		specify_protmixture_.setEnabled(true);
       	else
       		specify_protmixture_.setEnabled(false);
       	
       	
       	/* String specify_protmixture_Value = getValueAsString(OptionIndex.SPECIFY_PROTMIXTURE_);
       	if (specify_protmixture_Value != null &&
       		(specify_protmixture_Value.equals(ComboBoxValueLabel.IQTREE_PC10.getValue()) ||
       		specify_protmixture_Value.equals(ComboBoxValueLabel.IQTREE_PC20.getValue()) ||
			specify_protmixture_Value.equals(ComboBoxValueLabel.IQTREE_PC30.getValue()) ||
			specify_protmixture_Value.equals(ComboBoxValueLabel.IQTREE_PC40.getValue()) ||
			specify_protmixture_Value.equals(ComboBoxValueLabel.IQTREE_PC50.getValue()) ||
			specify_protmixture_Value.equals(ComboBoxValueLabel.IQTREE_PC60.getValue()) || */
       	
       	if (specify_protmodel_Value != null &&
       		(specify_protmodel_Value.equals(ComboBoxValueLabel.IQTREE_C10.getValue()) ||
			specify_protmodel_Value.equals(ComboBoxValueLabel.IQTREE_C20.getValue()) ||
			specify_protmodel_Value.equals(ComboBoxValueLabel.IQTREE_C30.getValue()) ||
			specify_protmodel_Value.equals(ComboBoxValueLabel.IQTREE_C40.getValue()) ||
			specify_protmodel_Value.equals(ComboBoxValueLabel.IQTREE_C50.getValue()) ||
			specify_protmodel_Value.equals(ComboBoxValueLabel.IQTREE_C60.getValue())))
       	{
       		max_posteriormode_.setEnabled(true);
       		setFileSelectorEnabled(OptionIndex.GUIDE_TREE_,true);
       		setFileSelectorEnabled(OptionIndex.FREQUENCY_FILE_FILE_,true);
       	}
       	else
       
       	{
       		max_posteriormode_.setEnabled(false);
       		setFileSelectorEnabled(OptionIndex.GUIDE_TREE_,false);
       		setFileSelectorEnabled(OptionIndex.FREQUENCY_FILE_FILE_,false);
       	}
       	
       		

       	
    	if (sequence_type_Value != null && (sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_BINARY.getValue()) ||
       			sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_MORPH.getValue())) && specify_runtype_Value != null && specify_runtype_Value.equals(runType2) &&
       			(freetextmodel_Value == null || freetextmodel_Value.isBlank()))
    	{
    		//max_posteriormode_.setEnabled(true);		
    		specify_binmodel_.setEnabled(true);
    	}
    	else
    	{
    		//max_posteriormode_.setEnabled(false);
    		specify_binmodel_.setEnabled(false);
    	}
    	
       	if (sequence_type_Value != null && sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_CODON.getValue())  && specify_runtype_Value != null && specify_runtype_Value.equals(runType2) &&
       			(freetextmodel_Value == null || freetextmodel_Value.isBlank()))
    	{
       		specify_codonmodel_.setEnabled(true);
    	}
    	else
    		specify_codonmodel_.setEnabled(false);
       	
       	String bootstrap_type_Value = getValueAsString(OptionIndex.BOOTSTRAP_TYPE_);
    	if (specify_runtype_Value != null && specify_runtype_Value.equals(runType2) &&
    		(bootstrap_type_Value == null || (!bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_B.getValue()) && !bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_BB.getValue()))))
    	{
    		num_tostop_.setEnabled(true);
    	}
    	else
    		num_tostop_.setEnabled(false);
    	
    	if (bootstrap_type_Value != null && (bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_BB.getValue())))
    	{
    		use_bnni_.setEnabled(true);
    		String num_bootreps_Value = getValueAsString(OptionIndex.NUM_BOOTREPS_);
    		if (num_bootreps_Value !=  null && Integer.parseInt(num_bootreps_Value) < 1000)
    			num_bootreps_.setValue(1000);
    	}
    	else
    	{
    		use_bnni_.setEnabled(false);
    	}
    	
    	if (bootstrap_type_Value != null && !bootstrap_type_Value.isBlank())
    	{
    		num_bootreps_.setEnabled(true);
    		write_boottrees_.setEnabled(true);
    		write_boottrees1_.setEnabled(true);
    		max_iters_.setEnabled(true);
    		cc_ufboot_.setEnabled(true);
    		iter_interval_.setEnabled(true);
    		specify_tiebreaker_.setEnabled(true);
    	}
    	else
    	{
    		num_bootreps_.setEnabled(false);
    		write_boottrees_.setEnabled(false);
    		write_boottrees1_.setEnabled(false);
    		max_iters_.setEnabled(false);
    		cc_ufboot_.setEnabled(false);
    		iter_interval_.setEnabled(false);
    		specify_tiebreaker_.setEnabled(false);
    	} 
    	
    	Boolean use_symmtest_Value = getValueAsBoolean(OptionIndex.USE_SYMMTEST_);
    	specify_symtest_.setEnabled(use_symmtest_Value);
    	
    	if (bootstrap_type_Value == null || 
    		(!bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_B.getValue())  &&
    		 !bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_BO.getValue()) &&
    		 !bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_BC.getValue()) ))
    	{
    		sh_test_.setEnabled(true);
    		parametrical_test_.setEnabled(true);
    		abayes_test_.setEnabled(true);
    		lbp_test_.setEnabled(true);
    		
    	}
    	else
    	{
    		sh_test_.setEnabled(false);
    		parametrical_test_.setEnabled(false);
    		abayes_test_.setEnabled(false);
    		lbp_test_.setEnabled(false);
    	}
    	
    	Boolean sh_test_Value = getValueAsBoolean(OptionIndex.SH_TEST_);
    	//Boolean abayes_test_Value = getValueAsBoolean(OptionIndex.ABAYES_TEST_);
    	Boolean lbp_test_Value = getValueAsBoolean(OptionIndex.LBP_TEST_);
    	
    	if (sh_test_Value || lbp_test_Value)
    		num_replicates_.setEnabled(true);
    	else
    		num_replicates_.setEnabled(false);
    	
    	//Boolean parametrical_test_Value = getValueAsBoolean(OptionIndex.PARAMETRICAL_TEST_);
    	//parametrical_test_.setEnabled(!sh_test_Value);
    	//sh_test_.setEnabled(!parametrical_test_Value);
    	
    	String num_rell_Value = getValueAsString(OptionIndex.NUM_RELL_);
    	if (num_rell_Value != null && !num_rell_Value.isBlank())
    	{
    		weighted_tests_.setEnabled(true);
    		estimate_parsetreeonly_.setEnabled(true);
    	}
    	else
    	{
    		weighted_tests_.setEnabled(false);
    		estimate_parsetreeonly_.setEnabled(false);
    	}
    	
    	String tree_file1_Value = getValueAsString(OptionIndex.TREE_FILE1_);
    	if (tree_file1_Value != null && !tree_file1_Value.isBlank())
    	{
    		compute_consensustree_.setEnabled(true);
    		compute_consensusnetwork_.setEnabled(true);
    		min_threshold_.setEnabled(true);
    		burnin_value_.setEnabled(true);
    		compute_rfdistances_all_.setEnabled(true);
    		compute_rfdistances_adj_.setEnabled(true);
    	}
    	else
    	{
    		compute_consensustree_.setEnabled(false);
    		compute_consensusnetwork_.setEnabled(false);
    		min_threshold_.setEnabled(false);
    		burnin_value_.setEnabled(false);
    		compute_rfdistances_all_.setEnabled(false);
    		compute_rfdistances_adj_.setEnabled(false);
    	}
    	
    	String fixed_usertree_file_Value = getValueAsString(OptionIndex.FIXED_USERTREE_FILE);
    	if ((tree_file1_Value != null && !tree_file1_Value.isBlank()) ||
    		(fixed_usertree_file_Value != null && !fixed_usertree_file_Value.isBlank()))
    	{
    		fix_brlengths_.setEnabled(true);
    	}
    	else
    		fix_brlengths_.setEnabled(false);
    	
    	String target_treefile_Value = getValueAsString(OptionIndex.TARGET_TREEFILE_);
    	if (target_treefile_Value != null && !target_treefile_Value.isBlank())
    	{
    		set_precision_.setEnabled(true);
    		set_scalefactor_.setEnabled(true);
    	}
    	else
    	{
    		set_precision_.setEnabled(false);
    		set_scalefactor_.setEnabled(false);
    	}
    	
    	//Boolean generate_randomtrees_Value = getValueAsBoolean(OptionIndex.GENERATE_RANDOMTREES_);
    	//if (generate_randomtrees_Value)
    	{
    		choose_randomtype_.setEnabled(true);
    		num_taxa_.setEnabled(true);
    		specify_brlengths_.setEnabled(true);
    	}
    	/* else
    	{
    		choose_randomtype_.setEnabled(false);
    		num_taxa_.setEnabled(false);
    		specify_brlengths_.setEnabled(false);    		
    	} */
    	
    	
    	String select_rcluster_Value = getValueAsString(OptionIndex.SELECT_RCLUSTER_);
    	if (select_rcluster_Value == null || select_rcluster_Value.isBlank())
    		specify_rclusterval_.setEnabled(false);
    	else
    		specify_rclusterval_.setEnabled(true);
    	
    	String specify_quartets_Value = getValueAsString(OptionIndex.SPECIFY_QUARTETS_);
    	if (specify_quartets_Value != null && !specify_quartets_Value.isBlank() && specify_quartets_Value.equals("specify_quartet"))
    	{
    		specify_quartetnum_.setEnabled(true);
    	}
    	else
    	{
    		specify_quartetnum_.setEnabled(false);
    	}
    	if (specify_quartets_Value != null && !specify_quartets_Value.isBlank())
    	{
    		write_quartets_.setEnabled(true);
    	}
    	else
    	{
    		write_quartets_.setEnabled(false);
    	}    	
    	
    	String which_iqtree = getValueAsString(OptionIndex.WHICH_IQTREE_);
    	if (which_iqtree != null && Integer.parseInt(which_iqtree) > 200)
    	{
    		partition_modelfile2_file_.setEnabled(true);
    		partition_tfile_file_.setEnabled(true);
    		setoftrees_file_file_.setEnabled(true);
    		specify_numquartets_.setEnabled(true);
    		specify_datefile_file_.setEnabled(true);
    		extract_datefile_.setEnabled(true);
    		specify_datetip_.setEnabled(true);
    		specify_rootdate_.setEnabled(true);
    		specify_datetreefile_file_.setEnabled(true);
    		specify_resampleint_.setEnabled(true);
    		specify_outlierthresh_.setEnabled(true);   
    	
    	}
    	else
    	{
    		partition_modelfile2_file_.setEnabled(false);
    		partition_tfile_file_.setEnabled(false);
    		setoftrees_file_file_.setEnabled(false);
    		specify_numquartets_.setEnabled(false);
    		specify_datefile_file_.setEnabled(false);
    		extract_datefile_.setEnabled(false);
    		specify_datetip_.setEnabled(false);
    		specify_rootdate_.setEnabled(false);
    		specify_datetreefile_file_.setEnabled(false);
    		specify_resampleint_.setEnabled(false);
    		specify_outlierthresh_.setEnabled(false);       		
    	}
    	
		Boolean more_memory_Boolean =  getValueAsBoolean(OptionIndex.MORE_MEMORY_);
		Boolean more_memory2_Boolean =  getValueAsBoolean(OptionIndex.MORE_MEMORY2_);    	
    	if (more_memory_Boolean)
    		more_memory2_.setEnabled(false);
    	if (more_memory2_Boolean)
    		more_memory_.setEnabled(false);
    }   
    
    @Override
    //public String verifyOptionsAreValid()
    public boolean areValuesGoodEnoughToContinue()
    {
    	String runType1 = ComboBoxValueLabel.IQTREE_RUNTYPE_MODEL.getValue();
    	String runType2 = ComboBoxValueLabel.IQTREE_RUNTYPE_INFERENCE.getValue();
    	
    	StringBuilder sb = new StringBuilder();
    	
    	String specify_seed_Value = getValueAsString(OptionIndex.SPECIFY_SEED_);
    	
    	if (specify_seed_Value != null && !specify_seed_Value.isBlank())
    	{
    		try
    		{
    			Integer.parseInt(specify_seed_Value);
    		}
    		catch (NumberFormatException nfe)
    		{
    			sb.append("Specify the seed (-seed): must be an integer<br>");
    		}
    	}
    	
    	String specify_numpatterns_Value = getValueAsString(OptionIndex.SPECIFY_NUMPATTERNS_);
    	    	
    	if (specify_numpatterns_Value == null || (Integer.parseInt(specify_numpatterns_Value) <= 0))
    	{
    		sb.append("Please specify the number of patterns which must be greater than zero (on Simple Parameters page)<br>");
    	}
    	
    	String specify_runtype_Value = getValueAsString(OptionIndex.SPECIFY_RUNTYPE_);
    	/*String specify_mem_Value = getValueAsString(OptionIndex.SPECIFY_MEM_);
    	if (specify_runtype_Value  !=  null && specify_runtype_Value .equals(runType2) &&
    		specify_numparts_Value != null && Integer.parseInt(specify_numparts_Value) == 1 &&
    		specify_mem_Value != null && Double.parseDouble(specify_mem_Value) > 120)
    	{
    		sb.append("The run will not complete if -mem is greater than 120 GB, please contact us<br>");
    	}*/
    	
    	String partition_type = getValueAsString(OptionIndex.PARTITION_TYPE_);
    	String partition_file = getValueAsString(OptionIndex.PARTITION_FILE_);
    	if (partition_type != null && !partition_type.isBlank() && (partition_file == null || partition_file.isBlank()))
    		sb.append("Please select a partition file (on Advanced Parameters Page 1)<br>");
    	
    	if ((partition_type == null || partition_type.isBlank()) && (partition_file != null &&  !partition_file.isBlank()))
    		sb.append("Please specify your partition type<br>");
    	    	
    	String use_bnni = getValueAsString(OptionIndex.USE_BNNI_);
    	String which_iqtree = getValueAsString(OptionIndex.WHICH_IQTREE_);
    	if (partition_type != null && partition_type.equals(ComboBoxValueLabel.IQTREE_PARTITION_TYPE_SP.getValue()) && 
    		use_bnni != null && !use_bnni.isBlank() &&
    		which_iqtree != null && Integer.parseInt(which_iqtree) <= 9)
    	{
    		sb.append("Sorry, a bug in this version will prevent the use of -sp with a partiton file, please use the -spp option (on Advanced Parameters Page 1)<br>");
    	}
    	
    	String starting_tree_Value = getValueAsString(OptionIndex.STARTING_TREE_FILE);
    	Boolean use_nj_Value = getValueAsBoolean(OptionIndex.USE_NJ_);
    	Boolean use_random_Value = getValueAsBoolean(OptionIndex.USE_RANDOM_);
    	if (starting_tree_Value == null || starting_tree_Value.isBlank())
    	{
    		if (use_nj_Value && use_random_Value)
    			sb.append("Sorry, you cannot choose both a random and a NJ starting tree<br>");
    	}
    	
    	String freetextmodel_Value = getValueAsString(OptionIndex.FREETEXTMODEL_);
    	String specify_dnamodel_Value = getValueAsString(OptionIndex.SPECIFY_DNAMODEL_);
    	if (specify_runtype_Value != null && specify_runtype_Value.equals(runType2))
    	{
    		if (freetextmodel_Value != null && !freetextmodel_Value.isBlank() && specify_dnamodel_Value != null && !specify_dnamodel_Value.isBlank())
    			sb.append("Sorry, you can't specify a DNA model and use the free text entry<br>");
    	}
    	
    	String sequence_type_Value = getValueAsString(OptionIndex.SEQUENCE_TYPE_);
    	String specify_model_Value = getValueAsString(OptionIndex.SPECIFY_MODEL_);
    	
    	if (sequence_type_Value != null && sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_NO_SELECT.getValue()))
    	{
    		sb.append("Please select the sequence type<br>");
    	}
    	if (sequence_type_Value != null && sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_DNA.getValue()) && specify_runtype_Value != null && specify_runtype_Value.equals(runType2))
    	{
    		if (specify_model_Value != null && !specify_model_Value.isBlank() && specify_dnamodel_Value != null && !specify_dnamodel_Value.isBlank())
    			sb.append("Sorry, you can't specify a DNA model and run a model test<br>");
    	}
    	
    	String specify_protmodel_Value = getValueAsString(OptionIndex.SPECIFY_PROTMODEL_);
    	if (sequence_type_Value != null && 
    		(sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_AMINO.getValue()) || sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_NT2AA.getValue())) && 
    		specify_runtype_Value != null && specify_runtype_Value.equals(runType2))
    	{
    		if (freetextmodel_Value != null && !freetextmodel_Value.isBlank() && specify_protmodel_Value != null && !specify_protmodel_Value.isBlank())
    			sb.append("Sorry, you can't specify a protein model and use the free text entry<br>");
    	}
    	
    	String specify_binmodel_Value = getValueAsString(OptionIndex.SPECIFY_BINMODEL_);
    	if (sequence_type_Value != null && 
        		(sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_BINARY.getValue()) || sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_MORPH.getValue())) && 
        		specify_runtype_Value != null && specify_runtype_Value.equals(runType2))
        {
        	if (freetextmodel_Value != null && !freetextmodel_Value.isBlank() && specify_binmodel_Value != null && !specify_binmodel_Value.isBlank())
        		sb.append("Sorry, you can't specify a BIN model and use the free text entry<br>");
        }
    	
    	
    	String specify_codonmodel_Value = getValueAsString(OptionIndex.SPECIFY_CODONMODEL_);
    	if (sequence_type_Value != null && sequence_type_Value.equals(ComboBoxValueLabel.IQTREE_SEQUENCE_TYPE_CODON.getValue()) && 
    			specify_runtype_Value != null && specify_runtype_Value.equals(runType2))
    	{
    		if (freetextmodel_Value != null && !freetextmodel_Value.isBlank() && specify_codonmodel_Value != null && !specify_codonmodel_Value.isBlank())
    			sb.append("Sorry, you can't specify a CODON model and use the free text entry<br>");
    	}
    	
    	String bootstrap_type_Value = getValueAsString(OptionIndex.BOOTSTRAP_TYPE_);
    	String num_tostop_Value = getValueAsString(OptionIndex.NUM_TOSTOP_);
    	if (specify_runtype_Value != null && specify_runtype_Value.equals(runType2))
    	{
    		if (num_tostop_Value != null && !num_tostop_Value.isBlank() &&
    			bootstrap_type_Value != null && bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_BB.getValue()))
    			sb.append("Sorry, the -n parameter cannot be used with Ultrafast Bootstrapping<br>");
    	}
    	
    	String num_bootreps_Value = getValueAsString(OptionIndex.NUM_BOOTREPS_);
    	if (bootstrap_type_Value != null && bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_BB.getValue())
    		&& num_bootreps_Value != null)
    	{
    		if (Integer.parseInt(num_bootreps_Value) < 1000)
    			sb.append("The value of bootstraps must be greater than or equal to 1,000 for Ultrafast Bootstrapping<br>");
    	}
    	
    	String iter_interval_Value = getValueAsString(OptionIndex.ITER_INTERVAL_);
    	if (bootstrap_type_Value != null && !bootstrap_type_Value.isBlank())
    	{
    		if (iter_interval_Value != null && !iter_interval_Value.isBlank())
    		{
    			int iter_inter = Integer.parseInt(iter_interval_Value);
    			if (iter_inter % 2 != 0)
    				sb.append("Step size must be a multiple of 2 (on Advanced Page 2 under Bootstrap Search Parameters section)<br>");
    			if (iter_inter > 0 && iter_inter < 10)
    				sb.append("Step size must be at least 10 (on Advanced Page 2 under Bootstrap Search Parameters section)<br>");
    		}
    	}
    	
    	String specify_symtest_Value = getValueAsString(OptionIndex.SPECIFY_SYMTEST_);
    	if (specify_symtest_Value != null && specify_symtest_Value.equals("symtest-pval"))
    	{
    		String specify_pval_Value = getValueAsString(OptionIndex.SPECIFY_PVAL_);
    		try
    		{
    			double pval = Double.parseDouble(specify_pval_Value);
    			if (pval <= 0.0)
    				sb.append("Please enter a pval that is bigger than 0.0<br>");
    		}
   			catch (NumberFormatException nfe)
			{
				sb.append("A Symmetry p-value must be a float number<br>");
			}    		
    	}
    	String num_replicates_Value = getValueAsString(OptionIndex.NUM_REPLICATES_);
    	boolean sh_test_Value = getValueAsBoolean(OptionIndex.SH_TEST_);
    	boolean lbp_test_Value = getValueAsBoolean(OptionIndex.LBP_TEST_);
    	if (sh_test_Value || lbp_test_Value)
    		if (num_replicates_Value != null && !num_replicates_Value.isBlank())
    		{
    			try
    			{
    				if (Integer.parseInt(num_replicates_Value) < 1000 && lbp_test_Value)
    					sb.append("The value of replicates must be bigger or equal to 1,000<br>");
    				else if (Integer.parseInt(num_replicates_Value) < 1000 && sh_test_Value)
    					sb.append("The value of replicates must be bigger or equal to 1,000 for the SH- test<br>");
    			}
    			catch (NumberFormatException nfe)
    			{
    				sb.append("The value of replicates must be an integer<br>");
    			}
    		}
    		else
    		{
    			sb.append("Please enter a value of replicates<br>");
    		}
    	
    	String num_rell_Value = getValueAsString(OptionIndex.NUM_RELL_);
    	if (num_rell_Value != null && !num_rell_Value.isBlank())
    	{
    		int num_rell = Integer.parseInt(num_rell_Value);
    		if (num_rell < 1000)
    			sb.append("Sorry, the number of RELL replicates cannot be less than 1,000<br>");
    	}
    	
    	String specify_quartets_Value = getValueAsString(OptionIndex.SPECIFY_QUARTETS_);
    	if (specify_quartets_Value != null && !specify_quartets_Value.isBlank())
    	{
    		int specify_quartets = 0;
    		boolean exceptionHappened = false;
    		String specify_quartetnum_Value = getValueAsString(OptionIndex.SPECIFY_QUARTETNUM_);
    		if (specify_quartetnum_Value != null && !specify_quartetnum_Value.isBlank())
    		{
	    		try
	    		{
	    			specify_quartets = Integer.parseInt(specify_quartetnum_Value);  			
	    		}
	    		catch (NumberFormatException nfe)
	    		{
	    			sb.append("The value of quartets must be an integer<br>");
	    			exceptionHappened = true;
	    		}
	    		if (exceptionHappened == false && specify_quartets <= 0 )
	    			sb.append("The value of quartets must be bigger than zero<br>");
    		}
    	}
    	String specify_quartetset_file_Value = getValueAsString(OptionIndex.SPECIFY_QUARTETSET_FILE_);
    	if (specify_quartetset_file_Value != null && !specify_quartetset_file_Value.isBlank())
    	{
    		if (!specify_quartetset_file_Value.endsWith("\\partition_file.txt"))
    		{
    			sb.append("The partition file must be named partition_file.txt<br>");
    		}
    	}
    	String partiton_file_Value = getValueAsString(OptionIndex.PARTITION_FILE_);
    	if (partiton_file_Value != null && !partiton_file_Value.isBlank())
    	{
    		if (!partiton_file_Value.endsWith("\\clusters.nex"))
    		{
    			sb.append("The NEXUS file specifying taxon clusters must be named clusters.nex<br>");
    		}
    	}    	
    	String gamma_shape_Value = getValueAsString(OptionIndex.GAMMA_SHAPE_);
    	if (gamma_shape_Value != null && !gamma_shape_Value.isBlank())
    	{
    		double gamma_shape = 0.0;
    		boolean exceptionHappened = false;
    		try
    		{
    			gamma_shape = Double.parseDouble(gamma_shape_Value);
    		}
    		catch (NumberFormatException nfe)
    		{
    			sb.append("The value of gamma shape must be a float<br>");
    			exceptionHappened = true;
    		}
    		if (exceptionHappened == false && gamma_shape <= 0.0)
    			sb.append("The value of quartets must be bigger than 0.0<br>");
    	}
    	
    	String specify_outlierthresh_Value = getValueAsString(OptionIndex.SPECIFY_OUTLIERTHRESH_);
    	if (specify_outlierthresh_Value != null && !specify_outlierthresh_Value.isBlank())
    	{
    		try
    		{
    			Double.parseDouble(specify_outlierthresh_Value);
    		}
    		catch (NumberFormatException nfe)
    		{
    			sb.append("z-score threshold must be a number<br>");
    		}
    	}
    	
    	/*
    	String partition_type_Value = getValueAsString(OptionIndex.PARTITION_TYPE_);
    	if (specify_numparts_Value != null && (Integer.parseInt(specify_numparts_Value) > 1) && (partition_type_Value == null || partition_type_Value.isBlank()))
    	{
    		sb.append("Partition type must be specified when number of partions is greater than 1<br>");
    	}*/
    	
    	String specify_rclusterval_Value = getValueAsString(OptionIndex.SPECIFY_RCLUSTERVAL_);
    	String select_rcluster_Value = getValueAsString(OptionIndex.SELECT_RCLUSTER_);
    	if ((specify_rclusterval_Value != null && !specify_rclusterval_Value.isBlank()) && (select_rcluster_Value == null ||select_rcluster_Value.isBlank() ))
    		sb.append("Please specify the rcluster algorithm<br>");
    	if ((specify_rclusterval_Value == null || specify_rclusterval_Value.isBlank()) && (select_rcluster_Value != null && !select_rcluster_Value.isBlank()))
    		sb.append("Please specify the percentage or max partition pairs for the  rcluster algorithm<br>");
    	
    	String name_outfiles_Value = getValueAsString(OptionIndex.NAME_OUTFILES_);
    	String specify_prefix_Value = getValueAsString(OptionIndex.SPECIFY_PREFIX_);
    	
    	/*
    	if (name_outfiles_Value != null && !name_outfiles_Value.isBlank()
    			&& specify_prefix_Value != null && !specify_prefix_Value.isBlank())
    	{
    		sb.append("You have entered two different prefixes. Please remove one.<br>");
    	}*/
    	
    	
    	String partition_file_Value = getValueAsString(OptionIndex.PARTITION_FILE_);
    	/*
    	String partition_type_Value = getValueAsString(OptionIndex.PARTITION_TYPE_);
    	
    	if (partition_file_Value != null && !partition_file_Value.isBlank() && (partition_type_Value == null || partition_type_Value.isBlank()))
    		sb.append("Please specify your partition type");
    	*/
    	//String specify_model_Value = getValueAsString(OptionIndex.SPECIFY_MODEL_);
    	
    	if (specify_model_Value != null && 
    			(specify_model_Value.equals(ComboBoxValueLabel.IQTREE_TESTMERGEONLY.getValue()) ||
    			specify_model_Value.equals(ComboBoxValueLabel.IQTREE_TESTMERGE.getValue()) ||
    			specify_model_Value.equals(ComboBoxValueLabel.IQTREE_TESTNEWMERGEONLY.getValue()) ||		
    			specify_model_Value.equals(ComboBoxValueLabel.IQTREE_TESTNEWMERGE.getValue()))	
    		 && (partition_file_Value == null || partition_file_Value.isBlank()))
    	{
    		sb.append("You must specify a partition file to use the MERGE options<br>");
    	}
    	
    	Boolean fix_branchlengths_Boolean = getValueAsBoolean(OptionIndex.FIX_BRANCHLENGTHS);
    	String branchlengths_tree_Value = getValueAsString(OptionIndex.BRANCHLENGTHS_TREE_FILE_);
    	
    	if (fix_branchlengths_Boolean && (branchlengths_tree_Value == null || branchlengths_tree_Value.isBlank()))
    		sb.append("Please provide a tree for fixing branch lengths<br>");
    	
    	String specify_minbranchlength_Value = getValueAsString(OptionIndex.SPECIFY_MINBRANCHLENGTH_);
    	String specify_maxbranchlength_Value = getValueAsString(OptionIndex.SPECIFY_MINBRANCHLENGTH_);
    	
    	if (specify_minbranchlength_Value != null && !specify_minbranchlength_Value.isBlank())
    	{
    		try
    		{
    			Double.parseDouble(specify_minbranchlength_Value);
    		}
    		catch (NumberFormatException nfe)
    		{
    			sb.append("Minimum branch length must be a number<br>");
    		}
    	}
    	
    	if (specify_maxbranchlength_Value != null && !specify_maxbranchlength_Value.isBlank())
    	{
    		try
    		{
    			Double.parseDouble(specify_maxbranchlength_Value);
    		}
    		catch (NumberFormatException nfe)
    		{
    			sb.append("Maximum branch length must be a number<br>");
    		}
    	}
    	
    	String num_taxa_Value = getValueAsString(OptionIndex.NUM_TAXA_);
    	String choose_randomtype_Value = getValueAsString(OptionIndex.CHOOSE_RANDOMTYPE_);
    	String specify_treefilename_Value = getValueAsString(OptionIndex.SPECIFY_TREEFILENAME_);    	
    	String tree_file1_Value = getValueAsString(OptionIndex.TREE_FILE1_);
    	if (tree_file1_Value != null && !tree_file1_Value.isBlank() && specify_treefilename_Value != null && !specify_treefilename_Value.isBlank())
    	{
    		sb.append("Sorry, you cant specify random trees and provide a starting tree<br>");
    	}
    	
    	//Boolean generate_randomtrees_Value = getValueAsBoolean(OptionIndex.GENERATE_RANDOMTREES_);
    	
    	//if (generate_randomtrees_Value && (num_taxa_Value == null || num_taxa_Value.isBlank()) && (choose_randomtype_Value == null || choose_randomtype_Value.isBlank()) )
    	//{
    	//	sb.append("Please specify the number of taxa and choose a random tree model for your random tree<br>");
    	//}
    	
    	/*
    	if (generate_randomtrees_Value && (choose_randomtype_Value == null || choose_randomtype_Value.isBlank()))
    	{
    		sb.append("Please choose a random tree model<br>");
    	}*/
    	
    	if ((num_taxa_Value != null && !num_taxa_Value.isBlank()))
    	{
    		int taxa = 0;
    		try
    		{
    			taxa = Integer.parseInt(num_taxa_Value);
    		}
    		catch (Exception ex)
    		{
    			
    		}
    		if (taxa <= 0)
    			sb.append("Number of taxa must be an integer that is bigger than zero<br>");
    	}
    	if ((choose_randomtype_Value != null && !choose_randomtype_Value.isBlank()) &&
    		(num_taxa_Value == null || num_taxa_Value.isBlank()))
    	{
    		sb.append("Please specify the number of taxa for your random tree<br>");
    	}
    	if ((num_taxa_Value != null && !num_taxa_Value.isBlank()) &&
        		(choose_randomtype_Value == null || choose_randomtype_Value.isBlank()))
        {
        	sb.append("Please choose a random tree model<br>");
        }
      	if ((num_taxa_Value != null && !num_taxa_Value.isBlank()) &&
        		(specify_treefilename_Value == null || specify_treefilename_Value.isBlank()))
        {
        	sb.append("Please specify a name for your random tree file output<br>");
        }  	
        
      	String partition_modelfile2_file_Value = getValueAsString(OptionIndex.PARTITION_MODELFILE2_FILE_);
      	if (partition_modelfile2_file_Value != null && !partition_modelfile2_file_Value.isBlank() )
      	{
      		if (!partition_modelfile2_file_Value.endsWith("\\alignment_file.txt"))
      		{
      			sb.append("The file that specifies the model selection (-S) must be called alignment_file.txt");
      		}
      		if (partition_file_Value != null && !partition_file_Value.isBlank())
      			sb.append("You cannot specify a -S file and a -p partition file");
      	}
      	String specify_resampleint_Value = getValueAsString(OptionIndex.SPECIFY_RESAMPLEINT_);
      	if (specify_resampleint_Value != null && !specify_resampleint_Value.isBlank())
      	{
      		int resampleint = 0;
      		try
      		{
      			resampleint = Integer.parseInt(specify_resampleint_Value);
      		}
      		catch (Exception e)
      		{
      			//sb.append("Resample branch lengths must be an integer<br>");
      		}
      		//if (resampleint <= 0)
      		//	sb.append("Resample branch lengths must be an integer that is bigger than zero<br>");
      	}
      	
      	String invariable_sites_Value = getValueAsString(OptionIndex.INVARIABLE_SITES_);
      	if (invariable_sites_Value != null && !invariable_sites_Value.isBlank())
      	{
      		double invariable_sites_Double = -1.0;
      		if (!invariable_sites_Value.equals(ESTIMATE))
      		{
      			try
      			{
      				invariable_sites_Double = Double.parseDouble(invariable_sites_Value);
      			}
      			catch (Exception e)
      			{
      				
      			}
      			if (invariable_sites_Double < 0.0)
      			{
      				sb.append("The proportion of invariable sites should be either 'estimate' or a double that is not negative<br>");
      			}
      		}
      	}
    	if (bootstrap_type_Value != null && (bootstrap_type_Value.equals(ComboBoxValueLabel.IQTREE_BB.getValue())))
    	{
    		//use_bnni_.setEnabled(true);
    		//String num_bootreps_Value = getValueAsString(OptionIndex.NUM_BOOTREPS_);
    		if (num_bootreps_Value !=  null && Integer.parseInt(num_bootreps_Value) < 1000)
    			sb.append("For ultrafast, the value of bootstraps must be greater than or equal to 1000");
    	}      	
      	checkValueIsInteger(sb, getValueAsString(OptionIndex.SPECIFY_RCLUSTERVAL_), null, OptionIndex.SPECIFY_RCLUSTERVAL_);
      	//checkValueIsInteger(sb, getValueAsString(OptionIndex.NUM_TOSTOP_), AUTO, OptionIndex.NUM_TOSTOP_);
      	checkValueIsInteger(sb, getValueAsString(OptionIndex.NUM_TOSTOP_), null, OptionIndex.NUM_TOSTOP_);
      	
    	String jobName = getJobName();
    	if (jobName == null || jobName.isBlank())
    		sb.append("Job name cannot be empty!<br>");
    	
		if (sb.length() > 0)
    	{
    		sb.insert(0, "<html>");
    		sb.append("</html>");
    		
    		Dialogs.showMessageDialog(sb.toString(), "Invalid Parameter(s)", this.getPanel(), Dialogs.DialogIcon.ERROR);
    		return false;
    	}
		else
		{
			StringBuilder sbWarn = new StringBuilder();
			
			
			String runtime_Value = getValueAsString(OptionIndex.RUNTIME_);
			double runtime_Double = Double.parseDouble(runtime_Value);
			/*
			if (specify_runtype_Value  !=  null && specify_runtype_Value .equals(runType1))
				sbWarn.append(String.format("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x %s cpu hours<br>", runtime_Value));
			
			if (specify_runtype_Value  !=  null && specify_runtype_Value .equals(runType2) && 
				specify_numparts_Value != null && Integer.parseInt(specify_numparts_Value) > 12)
				sbWarn.append(String.format("The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x %s cpu hours<br>", runtime_Value));
			
			if (specify_runtype_Value  !=  null && specify_runtype_Value .equals(runType2) && 
				specify_numparts_Value != null && Integer.parseInt(specify_numparts_Value) == 1 &&
				specify_mem_Value != null && Integer.parseInt(specify_mem_Value) >= 60)
				sbWarn.append(String.format("The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x %s cpu hours<br>", runtime_Value));
			
			if (specify_runtype_Value  !=  null && specify_runtype_Value .equals(runType2) && 
				specify_numparts_Value != null && Integer.parseInt(specify_numparts_Value) < 13 &&
				(specify_mem_Value == null || specify_mem_Value.isBlank()))
				sbWarn.append(String.format("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x %s cpu hours", runtime_Value));
			
			if (specify_runtype_Value  !=  null && specify_runtype_Value .equals(runType2) && 
					specify_numparts_Value != null && Integer.parseInt(specify_numparts_Value) == 1 &&
					specify_mem_Value != null && Integer.parseInt(specify_mem_Value) < 60)
					sbWarn.append(String.format("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x %s cpu hours", runtime_Value));
			*/
			String sequence_type_Value_special = sequence_type_Value != null ? sequence_type_Value : (String)" ";
			String pfile = getValueAsString(OptionIndex.PARTITION_FILE_);
			boolean partition_file_Boolean = (pfile == null? false : (pfile.isBlank()? false : true));
			Boolean more_memory_Boolean =  getValueAsBoolean(OptionIndex.MORE_MEMORY_);
			Boolean more_memory2_Boolean =  getValueAsBoolean(OptionIndex.MORE_MEMORY2_);
			String specfy_numpatterns_Value = getValueAsString(OptionIndex.SPECIFY_NUMPATTERNS_);
			int specify_numpatterns_Int =  Integer.parseInt(specfy_numpatterns_Value);
			
			issueWarning(sbWarn, sequence_type_Value_special, partition_file_Boolean, more_memory_Boolean, specify_numpatterns_Int, runtime_Double, more_memory2_Boolean );
			
			String specify_numquartets_Value = getValueAsString(OptionIndex.SPECIFY_NUMQUARTETS_);
			if (specify_numquartets_Value != null)
	    	{
	    		if (Integer.parseInt(specify_numquartets_Value) < 100)
	    			sbWarn.append("The authors recommend at least 100 quartets for stable values<br>");
	    	}
			
			if (sbWarn.length() > 0)
			{
	    		sbWarn.insert(0, "<html>");
	    		sbWarn.append("</html>");
				return (Dialogs.showContinueCancelDialog(sbWarn.toString(), "Continue with job submission?", this.getPanel(), Dialogs.DialogIcon.QUESTION));
		
			}
		}
    	return true;
    }
   
    private void issueWarning(StringBuilder sbWarn, String sequence_type_Value, boolean partition_file_Value, Boolean more_memory_Value, int specify_numpatterns_Value, double runtime_Value, Boolean more_memory2_Value ) 
    {
    	if ( more_memory_Value && !sequence_type_Value.equals("AA") && partition_file_Value  )
    	{
    	sbWarn.append("The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x  " + runtime_Value  + " cpu hours");

    	}
    	else if ( more_memory2_Value && !sequence_type_Value.equals("AA") && partition_file_Value  )
    	{
    	sbWarn.append("As configured this job will require a full node. If it runs for the entire configured time, it will consume 128 x  " + runtime_Value  + " cpu hours");

    	}    	
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value  <3000)
    	{
    	sbWarn.append("The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x  " + runtime_Value  + " cpu hours");
    	}
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 2999 && specify_numpatterns_Value  <5000)
    	{
    	sbWarn.append("The job will run on 8 processors as configured. If it runs for the entire configured time, it will consume 8 x  " + runtime_Value  + " cpu hours");
    	}
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 4999 && specify_numpatterns_Value  <7000)
    	{
    	sbWarn.append("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x  " + runtime_Value  + " cpu hours");
    	}
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 6999 && specify_numpatterns_Value  <40000)
    	{
    	sbWarn.append("The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x  " + runtime_Value  + " cpu hours");
    	}
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 39999 && specify_numpatterns_Value  <300000)
    	{
    	sbWarn.append("The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x  " + runtime_Value  + " cpu hours");
    	} 
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 299999)
    	{
    	sbWarn.append("The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x  " + runtime_Value  + " cpu hours");
    } 
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 299999 && runtime_Value >= 24 && runtime_Value <= 48)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 3000 - 6000 cpu hours. Please consider if you want to do this.");
    	} 
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 299999 && runtime_Value > 48 && runtime_Value <= 72)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 6000 - 9000 cpu hours. Please consider if you want to do this.");
    	}  	   	
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 299999 && runtime_Value > 72 && runtime_Value <= 96)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 9000 - 12000 cpu hours. Please consider if you want to do this.");
    	}
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 299999 && runtime_Value > 96 && runtime_Value <= 120)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 12000 - 15000 cpu hours. Please consider if you want to do this.");
    	} 
    	else if ( !sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 299999 && runtime_Value > 144 && runtime_Value <= 168)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 18000 - 21000 cpu hours. Please consider if you want to do this.");
    	} 
 	   	
    	else if ( sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value  <1800)
    	{
    	sbWarn.append("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x  " + runtime_Value  + " cpu hours");
    	}
    	else if ( sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value  > 1799 &&  specify_numpatterns_Value  < 6000)
    	{
    	sbWarn.append("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 24 x  " + runtime_Value  + " cpu hours");
    	}  	
    	else if ( sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value  > 5999 &&  specify_numpatterns_Value  < 40000)
    	{
    	sbWarn.append("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 48 x  " + runtime_Value  + " cpu hours");
    	}
    	else if ( sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value  > 39999 )
    	{
    	sbWarn.append("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 128 x  " + runtime_Value  + " cpu hours");
    	}
    	else if ( sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 39999 && runtime_Value > 48 && runtime_Value <= 72)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 6000 - 9000 cpu hours. Please consider if you want to do this.");
    	} 
    	else if ( sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 39999 && runtime_Value > 72 && runtime_Value <= 96)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 9000 - 12000 cpu hours. Please consider if you want to do this.");
    	}
    	else if ( sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 39999 && runtime_Value > 96 && runtime_Value <= 128)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 12000 - 15000 cpu hours. Please consider if you want to do this.");
    	}     
    	else if ( sequence_type_Value.equals("AA") && (! more_memory_Value  &&  !more_memory2_Value ) &&  specify_numpatterns_Value > 39999 && runtime_Value >= 168)
    	{
    	sbWarn.append("If your job runs for the full configured time, it will consume 18000 - 21000 cpu hours. Please consider if you want to do this.");
    	}
    	
    	
    	
    }
    private void issueWarning_old(StringBuilder sbWarn, String sequence_type_Value, boolean partition_file_Value, Boolean more_memory_Value, int specify_numpatterns_Value, double runtime_Value ) 
    {
    	// runtime
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  < 2000)
    	{
    	sbWarn.append("The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x  " + runtime_Value  + " cpu hours");
    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 1999 &&  specify_numpatterns_Value  < 6000 )
    	{
    	sbWarn.append("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x  " + runtime_Value  + " cpu hours");
    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 5999 &&  specify_numpatterns_Value  < 40000 )
    	{
    	sbWarn.append("The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x  " + runtime_Value  + " cpu hours");

    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 39999 &&  specify_numpatterns_Value  < 300000 )
    	{
    	sbWarn.append("The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x  " + runtime_Value  + " cpu hours");

    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 299999 )
    	{
    	sbWarn.append("The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x  " + runtime_Value  + " cpu hours");

    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 299999 &&  runtime_Value  >= 24 &&  runtime_Value  <= 48)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 3,000 - 6,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 299999 &&  runtime_Value  > 48 &&  runtime_Value  <= 72)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 6,000 - 9,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 299999 &&  runtime_Value  > 72 &&  runtime_Value  <= 96)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 9,000 - 12,000 cpu hours. Please consider if you want to do this.");
 
    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 299999 &&  runtime_Value  > 96 &&  runtime_Value  <= 120)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 12,000 - 15,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 299999 &&  runtime_Value  > 120 &&  runtime_Value  <= 144)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 15,000 - 18,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( !sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 299999 &&  runtime_Value  > 144 &&  runtime_Value  <= 168)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 18,000 - 21,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( !sequence_type_Value.equals("AA") &&  partition_file_Value  && ! more_memory_Value  )
    	{
    	sbWarn.append("The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x  " + runtime_Value  + " cpu hours");

    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  < 1800 )
    	{
    	sbWarn.append("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x  " + runtime_Value  + " cpu hours");

    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 1799 &&  specify_numpatterns_Value  < 6000 )
    	{
    	sbWarn.append("The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x  " + runtime_Value  + " cpu hours");
 
    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 5999 &&  specify_numpatterns_Value  < 40000 )
    	{
    	sbWarn.append("The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x  " + runtime_Value  + " cpu hours");
 
    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 39999 )
    	{
    	sbWarn.append("The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x  " + runtime_Value  + " cpu hours");

    	}
    	if ( sequence_type_Value.equals("AA") &&  partition_file_Value  && ! more_memory_Value )
    	{
    	sbWarn.append("The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x  " + runtime_Value  + " cpu hours");

    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 39999 &&  runtime_Value  >= 24 &&  runtime_Value  <= 48)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 3,000 - 6,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 39999 &&  runtime_Value  > 48 &&  runtime_Value  <= 72)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 6,000 - 9,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 39999 &&  runtime_Value  > 72 &&  runtime_Value  <= 96)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 9,000 - 12,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 39999 &&  runtime_Value  > 96 &&  runtime_Value  <= 120)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 12,000 - 15,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 39999 &&  runtime_Value  > 120 &&  runtime_Value  <= 144)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 15,000 - 18,000 cpu hours. Please consider if you want to do this.");

    	}
    	if ( sequence_type_Value.equals("AA") && (!  partition_file_Value  ||  more_memory_Value ) &&  specify_numpatterns_Value  > 39999 &&  runtime_Value  > 144 &&  runtime_Value  <= 168)
    	{
    	sbWarn.append("WARNING: If your job runs for the full configured time, it will consume 18,000 - 21,000 cpu hours. Please consider if you want to do this.");

    	}
    	sbWarn.append("<br>");
    
    }
    
    private boolean checkValueIsInteger(StringBuilder sb, String specify_Value, String special_Value, OptionIndex index)
    {
    	boolean checkOK = true;
	  	//String specify_Value = getValueAsString(OptionIndex.SPECIFY_RESAMPLEINT_);
	  	if (specify_Value != null && !specify_Value.isBlank() && (special_Value != null ? !specify_Value.equals(special_Value) : true))
	  	{
	  		int resampleint = 0;
	  		try
	  		{
	  			resampleint = Integer.parseInt(specify_Value);
	  		}
	  		catch (Exception e)
	  		{
	  		
	  		}
	  		if (resampleint <= 0)
	  		{
	  			sb.append("This field (" + nameAndLabels[index.ordinal()].label + ") must be either '" + (special_Value == null? "" : special_Value) + "' or an integer that is bigger than zero<br>");
	  			checkOK = false;
	  		}
	  	}
	  	return checkOK;
    }
    private Options getOptionsFromIndex(OptionIndex index)
    {
    	if (index.ordinal() <= OptionIndex.SPECIFY_PREFIX_.ordinal())
    		return simpleOptions;
    	else if (index.ordinal() <= OptionIndex.THOROUGH_ESTIMATION_.ordinal())
    		return advancedOptions;
    	else if (index.ordinal() <= OptionIndex.SPECIFY_ANCESTRALTREE_FILE_.ordinal())
    		return advancedOptions2;
    	else if (index.ordinal() <= OptionIndex.SPECIFY_TREEFILENAME_.ordinal())
    		return advancedOptions3;
    	else
    		return advancedOptions4;
    }
    
    private String getValueAsString(OptionIndex index)
    {

    	return filterOutExceptions(index, getValueAsString(getOptionsFromIndex(index), nameAndLabels[index.ordinal()].name));
    }
    
    private Boolean getValueAsBoolean(OptionIndex index)
    {
    	return getValueAsBoolean(getOptionsFromIndex(index), nameAndLabels[index.ordinal()].name);
    }
    
    private String filterOutExceptions(OptionIndex index, String value)
    {
    	if (value == null || value.isBlank())
    		return value;
    	if (value.strip().isBlank())
    		return value.strip();
    	
    	if (index == OptionIndex.ITER_INTERVAL_ || index == OptionIndex.NUM_RELL_ || index == OptionIndex.SPECIFY_MINCAT_ ||
    		index == OptionIndex.SPECIFY_MAXCAT_  || 
    		index == OptionIndex.MAX_ITERS_  ||
    		index == OptionIndex.SPECIFY_NUMQUARTETS_ )
    	{
    		if (Integer.parseInt(value) == 0)
    			return null;
    	}
    	if (index == OptionIndex.CC_UFBOOT_  || index == OptionIndex.SPECIFY_TIEBREAKER_ )
    	{
    		if (Double.parseDouble(value) == 0.0)
    			return null;
    	}
    	return value;
    }
    
    private void setFileSelectorEnabled(OptionIndex index, boolean enabled)
    {
    	setFileSelectorEnabled(getOptionsFromIndex(index),
    			nameAndLabels[index.ordinal()].name, enabled);
    }
    
    
    private JSONObject jsonCommand = new JSONObject();
    private Map<String, String> inputParams = new HashMap<String, String>();
    
    @SuppressWarnings("unchecked")
	public void populateJsonCommand()
    {
    	for (OptionIndex opt : OptionIndex.values())
    	{
    		if (nameAndLabels[opt.ordinal()].isFile)
    			continue;
    		setParam(opt, ParamType.VParam);
    	}
    }
    
    public JSONObject getJsonCommand() {
		return jsonCommand;
	}
    
    public Map<String, Collection<String>> getVParams() {
    	return MrBayesUtilities.getVParams(jsonCommand);
    }
    
    public Map<String, String> getInputParams() {
    	List<File> files = new ArrayList<File>();
        final AnnotatedPluginDocument doc = selectedDocuments[0];

    	try {
        final SequenceAlignmentDocument alignmentDoc = (SequenceAlignmentDocument) doc.getDocument();
        
        File tempFolder;
		
		tempFolder = FileUtilities.createTempFile("Geneious", "IQTREEXSEDE_1_01_01", false);
		tempFolder.delete();
	    tempFolder.mkdirs();


	    StringBuilder inFileBldr = new StringBuilder();

	    List<SequenceDocument> seqDocList = alignmentDoc.getSequences();
	    
        for(SequenceDocument seqDocument: seqDocList){
        	
        	//MrBayes does not like space or dot(s) in taxa name
        	String seqName = seqDocument.getName().trim()
        					.replaceAll(SPACE, UNDERSCORE)
        					.replaceAll("\\"+ DOT, "")
        					.replaceAll("\\(","")
        					.replaceAll("\\)","");
        	
        	String seqString = seqDocument.getSequenceString().trim();
        	
        	//System.out.println(seqString);
        	//System.out.println(seqName + TAB + seqString);
        	
        	inFileBldr.append( ">" + seqName + NEWLINE + seqString + NEWLINE);
        	
        }

        File outputFile = new File(tempFolder, GENEIOUS_FORMAT);
        files.add(outputFile);
        SafePrintWriter out = new SafePrintWriter(new FileWriter(outputFile));
        out.println(inFileBldr.toString()); 
        out.close();
		} catch (IOException | DocumentOperationException e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
		}
    	//Map<String, String> inputParams = new HashMap<String, String>();
    	//inputParams.put("infile_", "C:\\Users\\mzhuang\\Cipres_input\\infile1");
    	inputParams.put("infile_", files.get(0).toString());
    	
    	for (OptionIndex opt : OptionIndex.values())
    	{
    		if (!nameAndLabels[opt.ordinal()].isFile)
    			continue;
    		setParam(opt, ParamType.InputParam);    	
    	}
 
    	return inputParams;
    }
    
    public HashMap<String, String> getMetadata(String jobName){
    	jobName = getJobName();
    	return MrBayesUtilities.getMetadata(jobName);    	
    }
    
    @SuppressWarnings("unchecked")
	private void setParam(OptionIndex index, ParamType type)
    {
    	Option opt = findOptionByName(getOptionsFromIndex(index), nameAndLabels[index.ordinal()].name);
    	if (opt == null || !opt.isEnabled())
    		return;
    	
    	String value = null;
    	if (opt instanceof BooleanOption)
    		value = getBooleanValueAsString(index);
    	else
    		value = getValueAsString(index);
    	
    	if (value != null && !value.isBlank())
    	{
    		if (type.equals(ParamType.VParam))
    			jsonCommand.put(nameAndLabels[index.ordinal()].parameter, value);
    		else if (type.equals(ParamType.InputParam))
    			inputParams.put(nameAndLabels[index.ordinal()].parameter, value);
    	}
    }
    
    private String getBooleanValueAsString(OptionIndex index)
    {
    	BooleanOption bo = (BooleanOption)findOptionByName(getOptionsFromIndex(index), nameAndLabels[index.ordinal()].name);
    
    	if (!bo.isEnabled())
    		return null;
    	
    	if (index == OptionIndex.PARAMETRICAL_TEST_ || index == OptionIndex.SPECIFY_SAFE_)
    	{
    		if (!bo.getValue())
    			return null;
    	}
    	if (bo.getValue())
    		return ONE;
    	else
    		return ZERO;
    }
}