inprogress

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 616135a..97c04d3 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -180,7 +180,7 @@ public class surfacing {
     final static private String                               PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION                                       = "dc_regain_stats";
     final static private String                               DA_ANALYSIS_OPTION                                                            = "DA_analyis";
     final static private String                               USE_LAST_IN_FITCH_OPTION                                                      = "last";
-    public final static String                               PAIRWISE_DOMAIN_COMPARISONS_PREFIX                                            = "pwc_";
+    public final static String                                PAIRWISE_DOMAIN_COMPARISONS_PREFIX                                            = "pwc_";
     final static private String                               PAIRWISE_DOMAIN_COMPARISONS_OPTION                                            = "pwc";
     final static private String                               OUTPUT_FILE_OPTION                                                            = "o";
     final static private String                               PFAM_TO_GO_FILE_USE_OPTION                                                    = "p2g";
@@ -222,22 +222,22 @@ public class surfacing {
     final static private boolean                              IGNORE_DUFS_DEFAULT                                                           = true;
     final static private boolean                              IGNORE_COMBINATION_WITH_SAME_DEFAULLT                                         = false;
     final static private double                               MAX_E_VALUE_DEFAULT                                                           = -1;
-    public final static int                                  MAX_ALLOWED_OVERLAP_DEFAULT                                                   = -1;
+    public final static int                                   MAX_ALLOWED_OVERLAP_DEFAULT                                                   = -1;
     private static final String                               RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION                                        = "random_seed";
     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS                                      = "consider_bdc_direction";
     private static final String                               CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY                        = "consider_bdc_adj";
-    public static final String                               SEQ_EXTRACT_SUFFIX                                                            = ".prot";
-    public static final String                               PLUS_MINUS_ANALYSIS_OPTION                                                    = "plus_minus";
-    public static final String                               PLUS_MINUS_DOM_SUFFIX                                                         = "_plus_minus_dom.txt";
-    public static final String                               PLUS_MINUS_DOM_SUFFIX_HTML                                                    = "_plus_minus_dom.html";
-    public static final String                               PLUS_MINUS_DC_SUFFIX_HTML                                                     = "_plus_minus_dc.html";
-    public static final int                                  PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT                                          = 0;
-    public static final double                               PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT                                            = 1.0;
-    public static final String                               PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX                                              = "_plus_minus_go_ids_all.txt";
-    public static final String                               PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX                                          = "_plus_minus_go_ids_passing.txt";
+    public static final String                                SEQ_EXTRACT_SUFFIX                                                            = ".prot";
+    public static final String                                PLUS_MINUS_ANALYSIS_OPTION                                                    = "plus_minus";
+    public static final String                                PLUS_MINUS_DOM_SUFFIX                                                         = "_plus_minus_dom.txt";
+    public static final String                                PLUS_MINUS_DOM_SUFFIX_HTML                                                    = "_plus_minus_dom.html";
+    public static final String                                PLUS_MINUS_DC_SUFFIX_HTML                                                     = "_plus_minus_dc.html";
+    public static final int                                   PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT                                          = 0;
+    public static final double                                PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT                                            = 1.0;
+    public static final String                                PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX                                              = "_plus_minus_go_ids_all.txt";
+    public static final String                                PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX                                          = "_plus_minus_go_ids_passing.txt";
     private static final String                               OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS                                           = "all_prot";
     final static private String                               OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION                         = "all_prot_e";
-    public static final boolean                              VERBOSE                                                                       = false;
+    public static final boolean                               VERBOSE                                                                       = false;
     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX              = "_fitch_dc_gains_counts";
     private static final String                               OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX                = "_fitch_dc_losses_counts";
     private static final String                               DOMAIN_LENGTHS_ANALYSIS_SUFFIX                                                = "_domain_lengths_analysis";
@@ -407,17 +407,10 @@ public class surfacing {
         if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
             ignore_species_specific_domains = true;
         }
-        
-        
-        
         if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
             ForesterUtil.fatalError( surfacing.PRG_NAME, "no input species tree file given: "
                     + surfacing.INPUT_SPECIES_TREE_OPTION + "=<file>" );
         }
-        
-        
-        
-        
         File output_file = null;
         if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
             if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
@@ -530,10 +523,10 @@ public class surfacing {
         final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
         final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
         SurfacingUtil.processPlusMinusAnalysisOption( cla,
-                                        plus_minus_analysis_high_copy_base_species,
-                                        plus_minus_analysis_high_copy_target_species,
-                                        plus_minus_analysis_high_low_copy_species,
-                                        plus_minus_analysis_numbers );
+                                                      plus_minus_analysis_high_copy_base_species,
+                                                      plus_minus_analysis_high_copy_target_species,
+                                                      plus_minus_analysis_high_low_copy_species,
+                                                      plus_minus_analysis_numbers );
         File input_genomes_file = null;
         if ( cla.isOptionSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
             if ( !cla.isOptionValueSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
@@ -551,9 +544,6 @@ public class surfacing {
             ForesterUtil.fatalError( surfacing.PRG_NAME, "no input genomes file given: "
                     + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
         }
-      
-        
-        
         DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
         if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
             if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) {
@@ -779,9 +769,9 @@ public class surfacing {
                     + "=<suffix> to turn on pairwise analyses with less than three input files" );
         }
         SurfacingUtil.checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
-                                                 input_file_properties,
-                                                 automated_pairwise_comparison_suffix,
-                                                 out_dir );
+                                                               input_file_properties,
+                                                               automated_pairwise_comparison_suffix,
+                                                               out_dir );
         for( int i = 0; i < number_of_genomes; i++ ) {
             File dcc_outfile = new File( input_file_properties[ i ][ 1 ]
                     + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
@@ -916,9 +906,8 @@ public class surfacing {
                 intree_files[ 0 ] = new File( intrees_str );
             }
             intrees = SurfacingUtil.obtainAndPreProcessIntrees( intree_files, number_of_genomes, input_file_properties );
-            
         }
-        final Phylogeny intree_0_orig = SurfacingUtil.obtainFirstIntree( intree_files[ 0 ]);
+        final Phylogeny intree_0_orig = SurfacingUtil.obtainFirstIntree( intree_files[ 0 ] );
         long random_number_seed_for_fitch_parsimony = 0l;
         boolean radomize_fitch_parsimony = false;
         if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
@@ -1450,8 +1439,8 @@ public class surfacing {
             SurfacingUtil.log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
             System.out.println( "Processing                                     : " + input_file_properties[ i ][ 1 ]
                     + " [" + input_file_properties[ i ][ 0 ] + "]" );
-            SurfacingUtil.log( "Genome                                         : " + input_file_properties[ i ][ 1 ] + " ["
-                    + input_file_properties[ i ][ 0 ] + "]", log_writer );
+            SurfacingUtil.log( "Genome                                         : " + input_file_properties[ i ][ 1 ]
+                    + " [" + input_file_properties[ i ][ 0 ] + "]", log_writer );
             HmmscanPerDomainTableParser parser = null;
             INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
             if ( individual_score_cutoffs != null ) {
@@ -1522,57 +1511,70 @@ public class surfacing {
                                                                        distinct_domain_architecuture_counts );
             }
             System.out.println( "Number of proteins encountered                 : " + parser.getProteinsEncountered() );
-            SurfacingUtil.log( "Number of proteins encountered                 : " + parser.getProteinsEncountered(), log_writer );
+            SurfacingUtil.log( "Number of proteins encountered                 : " + parser.getProteinsEncountered(),
+                               log_writer );
             System.out.println( "Number of proteins stored                      : " + protein_list.size() );
             SurfacingUtil.log( "Number of proteins stored                      : " + protein_list.size(), log_writer );
             System.out.println( "Coverage                                       : "
                     + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" );
-            SurfacingUtil.log( "Coverage                                       : " + ForesterUtil.roundToInt( 100.0 * coverage )
-                    + "%", log_writer );
+            SurfacingUtil.log( "Coverage                                       : "
+                                       + ForesterUtil.roundToInt( 100.0 * coverage ) + "%",
+                               log_writer );
             System.out.println( "Domains encountered                            : " + parser.getDomainsEncountered() );
-            SurfacingUtil.log( "Domains encountered                            : " + parser.getDomainsEncountered(), log_writer );
+            SurfacingUtil.log( "Domains encountered                            : " + parser.getDomainsEncountered(),
+                               log_writer );
             System.out.println( "Domains stored                                 : " + parser.getDomainsStored() );
-            SurfacingUtil.log( "Domains stored                                 : " + parser.getDomainsStored(), log_writer );
+            SurfacingUtil.log( "Domains stored                                 : " + parser.getDomainsStored(),
+                               log_writer );
             System.out.println( "Distinct domains stored                        : "
                     + parser.getDomainsStoredSet().size() );
-            SurfacingUtil.log( "Distinct domains stored                        : " + parser.getDomainsStoredSet().size(), log_writer );
+            SurfacingUtil.log( "Distinct domains stored                        : "
+                    + parser.getDomainsStoredSet().size(), log_writer );
             System.out.println( "Domains ignored due to individual score cutoffs: "
                     + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
             SurfacingUtil.log( "Domains ignored due to individual score cutoffs: "
-                         + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
-                 log_writer );
+                                       + parser.getDomainsIgnoredDueToIndividualScoreCutoff(),
+                               log_writer );
             System.out.println( "Domains ignored due to E-value                 : "
                     + parser.getDomainsIgnoredDueToEval() );
-            SurfacingUtil.log( "Domains ignored due to E-value                 : " + parser.getDomainsIgnoredDueToEval(), log_writer );
+            SurfacingUtil.log( "Domains ignored due to E-value                 : "
+                                       + parser.getDomainsIgnoredDueToEval(),
+                               log_writer );
             System.out.println( "Domains ignored due to DUF designation         : "
                     + parser.getDomainsIgnoredDueToDuf() );
-            SurfacingUtil.log( "Domains ignored due to DUF designation         : " + parser.getDomainsIgnoredDueToDuf(), log_writer );
+            SurfacingUtil
+                    .log( "Domains ignored due to DUF designation         : " + parser.getDomainsIgnoredDueToDuf(),
+                          log_writer );
             if ( ignore_virus_like_ids ) {
                 System.out.println( "Domains ignored due virus like ids             : "
                         + parser.getDomainsIgnoredDueToVirusLikeIds() );
-                SurfacingUtil.log( "Domains ignored due virus like ids             : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
-                     log_writer );
+                SurfacingUtil.log( "Domains ignored due virus like ids             : "
+                                           + parser.getDomainsIgnoredDueToVirusLikeIds(),
+                                   log_writer );
             }
             System.out.println( "Domains ignored due negative domain filter     : "
                     + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
             SurfacingUtil.log( "Domains ignored due negative domain filter     : "
-                         + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
-                 log_writer );
+                                       + parser.getDomainsIgnoredDueToNegativeDomainFilter(),
+                               log_writer );
             System.out.println( "Domains ignored due to overlap                 : "
                     + parser.getDomainsIgnoredDueToOverlap() );
-            SurfacingUtil.log( "Domains ignored due to overlap                 : " + parser.getDomainsIgnoredDueToOverlap(),
-                 log_writer );
+            SurfacingUtil.log( "Domains ignored due to overlap                 : "
+                                       + parser.getDomainsIgnoredDueToOverlap(),
+                               log_writer );
             if ( negative_filter_file != null ) {
                 System.out.println( "Proteins ignored due to negative filter        : "
                         + parser.getProteinsIgnoredDueToFilter() );
-                SurfacingUtil.log( "Proteins ignored due to negative filter        : " + parser.getProteinsIgnoredDueToFilter(),
-                     log_writer );
+                SurfacingUtil.log( "Proteins ignored due to negative filter        : "
+                                           + parser.getProteinsIgnoredDueToFilter(),
+                                   log_writer );
             }
             if ( positive_filter_file != null ) {
                 System.out.println( "Proteins ignored due to positive filter        : "
                         + parser.getProteinsIgnoredDueToFilter() );
-                SurfacingUtil.log( "Proteins ignored due to positive filter        : " + parser.getProteinsIgnoredDueToFilter(),
-                     log_writer );
+                SurfacingUtil.log( "Proteins ignored due to positive filter        : "
+                                           + parser.getProteinsIgnoredDueToFilter(),
+                                   log_writer );
             }
             if ( da_analysis ) {
                 System.out.println( "Distinct domain architectures stored           : " + distinct_das );
@@ -1708,10 +1710,14 @@ public class surfacing {
             ForesterUtil.programMessage( PRG_NAME, "Range of proteins with a least one domain assigned: "
                     + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() )
                     + "%" );
-            SurfacingUtil.log( "Average of prot with a least one dom assigned  : " + ( 100 * protein_coverage_stats.arithmeticMean() )
-                    + "% (+/-" + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", log_writer );
-            SurfacingUtil.log( "Range of prot with a least one dom assigned    : " + ( 100 * protein_coverage_stats.getMin() ) + "%-"
-                    + ( 100 * protein_coverage_stats.getMax() ) + "%", log_writer );
+            SurfacingUtil.log( "Average of prot with a least one dom assigned  : "
+                                       + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-"
+                                       + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)",
+                               log_writer );
+            SurfacingUtil.log( "Range of prot with a least one dom assigned    : "
+                                       + ( 100 * protein_coverage_stats.getMin() ) + "%-"
+                                       + ( 100 * protein_coverage_stats.getMax() ) + "%",
+                               log_writer );
         }
         catch ( final IOException e2 ) {
             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
@@ -1903,11 +1909,11 @@ public class surfacing {
         }
         if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
             final StringBuilder parameters_sb = SurfacingUtil.createParametersAsString( ignore_dufs,
-                                                                          e_value_max,
-                                                                          max_allowed_overlap,
-                                                                          no_engulfing_overlaps,
-                                                                          cutoff_scores_file,
-                                                                          dc_type );
+                                                                                        e_value_max,
+                                                                                        max_allowed_overlap,
+                                                                                        no_engulfing_overlaps,
+                                                                                        cutoff_scores_file,
+                                                                                        dc_type );
             String s = "_";
             if ( radomize_fitch_parsimony ) {
                 s += random_number_seed_for_fitch_parsimony + "_";
@@ -1982,30 +1988,31 @@ public class surfacing {
         }
         if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
             SurfacingUtil.executePlusMinusAnalysis( output_file,
-                                      plus_minus_analysis_high_copy_base_species,
-                                      plus_minus_analysis_high_copy_target_species,
-                                      plus_minus_analysis_high_low_copy_species,
-                                      gwcd_list,
-                                      protein_lists_per_species,
-                                      domain_id_to_go_ids_map,
-                                      go_id_to_term_map,
-                                      plus_minus_analysis_numbers );
+                                                    plus_minus_analysis_high_copy_base_species,
+                                                    plus_minus_analysis_high_copy_target_species,
+                                                    plus_minus_analysis_high_low_copy_species,
+                                                    gwcd_list,
+                                                    protein_lists_per_species,
+                                                    domain_id_to_go_ids_map,
+                                                    go_id_to_term_map,
+                                                    plus_minus_analysis_numbers );
         }
         if ( output_protein_lists_for_all_domains ) {
             SurfacingUtil.writeProteinListsForAllSpecies( out_dir,
-                                            protein_lists_per_species,
-                                            gwcd_list,
-                                            output_list_of_all_proteins_per_domain_e_value_max );
+                                                          protein_lists_per_species,
+                                                          gwcd_list,
+                                                          output_list_of_all_proteins_per_domain_e_value_max );
         }
         gwcd_list = null;
         if ( all_bin_domain_combinations_gained_fitch != null ) {
             try {
-                SurfacingUtil.executeFitchGainsAnalysis( new File( output_file
-                                                   + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
-                                           all_bin_domain_combinations_gained_fitch,
-                                           all_domains_encountered.size(),
-                                           all_bin_domain_combinations_encountered,
-                                           true );
+                SurfacingUtil
+                        .executeFitchGainsAnalysis( new File( output_file
+                                                            + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+                                                    all_bin_domain_combinations_gained_fitch,
+                                                    all_domains_encountered.size(),
+                                                    all_bin_domain_combinations_encountered,
+                                                    true );
             }
             catch ( final IOException e ) {
                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
@@ -2013,12 +2020,13 @@ public class surfacing {
         }
         if ( all_bin_domain_combinations_lost_fitch != null ) {
             try {
-                SurfacingUtil.executeFitchGainsAnalysis( new File( output_file
-                                                   + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
-                                           all_bin_domain_combinations_lost_fitch,
-                                           all_domains_encountered.size(),
-                                           all_bin_domain_combinations_encountered,
-                                           false );
+                SurfacingUtil
+                        .executeFitchGainsAnalysis( new File( output_file
+                                                            + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+                                                    all_bin_domain_combinations_lost_fitch,
+                                                    all_domains_encountered.size(),
+                                                    all_bin_domain_combinations_encountered,
+                                                    false );
             }
             catch ( final IOException e ) {
                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index eda37d3..3eac2bd 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -309,14 +309,9 @@ public class Phylogeny {
 
     public final static Phylogeny createInstanceFromNhxString( final String nhx ) throws IOException {
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-        
         return factory.create( nhx, new NHXParser() )[ 0 ];
-        
-        
-        
     }
-    
-    
+
     /**
      * 
      * Warning. The order of the returned nodes is random

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index 4699869..07ece5b 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -100,7 +100,7 @@ public class PairwiseGenomeComparator {
                                             final boolean write_pairwise_comparisons,
                                             final Map<String, Integer> tax_code_to_id_map,
                                             final boolean calc_similarity_scores,
-                                            Phylogeny phy ) {
+                                            final Phylogeny phy ) {
         init();
         final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
         final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );

diff --git a/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java b/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
index 9abbe22..c8c30d6 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
@@ -189,7 +189,7 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
                                  final Map<String, Integer> tax_code_to_id_map,
                                  final Phylogeny phy ) {
         String hex = null;
-        if ( phy != null && !phy.isEmpty() ) {
+        if ( ( phy != null ) && !phy.isEmpty() ) {
             hex = obtainHexColorStringDependingOnTaxonomyGroup( tax_code, phy );
         }
         sb.append( "<b>" );
@@ -212,10 +212,10 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
     }
 
     private String obtainHexColorStringDependingOnTaxonomyGroup( final String tax_code, final Phylogeny phy ) {
-        if ( phy != null && !_TAXCODE_HEXCOLORSTRING_MAP.containsKey( tax_code ) ) {
-            List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
+        if ( ( phy != null ) && !_TAXCODE_HEXCOLORSTRING_MAP.containsKey( tax_code ) ) {
+            final List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
             Color c = null;
-            if ( nodes == null || nodes.isEmpty() ) {
+            if ( ( nodes == null ) || nodes.isEmpty() ) {
                 throw new RuntimeException( tax_code + " is not found" );
             }
             if ( nodes.size() != 1 ) {
@@ -228,7 +228,7 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
                     c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getNodeData().getTaxonomy()
                             .getScientificName() );
                 }
-                if ( c == null && !ForesterUtil.isEmpty( n.getName() ) ) {
+                if ( ( c == null ) && !ForesterUtil.isEmpty( n.getName() ) ) {
                     c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getName() );
                 }
                 if ( c != null ) {
@@ -419,7 +419,7 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
     @Override
     public StringBuffer toStringBuffer( final PrintableDomainSimilarity.PRINT_OPTION print_option,
                                         final Map<String, Integer> tax_code_to_id_map,
-                                        Phylogeny phy ) {
+                                        final Phylogeny phy ) {
         switch ( print_option ) {
             case SIMPLE_TAB_DELIMITED:
                 return toStringBufferSimpleTabDelimited();
@@ -430,7 +430,7 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
         }
     }
 
-    private StringBuffer toStringBufferDetailedHTML( final Map<String, Integer> tax_code_to_id_map, Phylogeny phy ) {
+    private StringBuffer toStringBufferDetailedHTML( final Map<String, Integer> tax_code_to_id_map, final Phylogeny phy ) {
         final StringBuffer sb = new StringBuffer();
         sb.append( "<tr>" );
         sb.append( "<td>" );

diff --git a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
index 55db1bd..92de951 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
+++ b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java
@@ -121,9 +121,7 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData {
         }
         if ( html ) {
             final Set<String> ids = getCombinableDomainIdToCountsMap().keySet();
-          
             for( final String domain_id : ids ) {
-                
                 sb.append( " " );
                 if ( html ) {
                     sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id + "\">" + domain_id

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 599fd73..1618c4f 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -2912,7 +2912,7 @@ public final class SurfacingUtil {
                                                       final DomainSimilarity.DomainSimilarityScoring scoring,
                                                       final boolean verbose,
                                                       final Map<String, Integer> tax_code_to_id_map,
-                                                      Phylogeny phy ) throws IOException {
+                                                      final Phylogeny phy ) throws IOException {
         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
             split_writers = new HashMap<Character, Writer>();
             split_writers.put( '_', single_writer );

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 68777de..66bff3d 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -759,9 +759,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        
-        
-        
         System.out.print( "Tree copy: " );
         if ( Test.testTreeCopy() ) {
             System.out.println( "OK." );
@@ -771,12 +768,6 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
-        
-        
-        
-        
-        
-        
         System.out.print( "Basic tree methods: " );
         if ( Test.testBasicTreeMethods() ) {
             System.out.println( "OK." );
@@ -2782,35 +2773,32 @@ public final class Test {
         }
         return true;
     }
-    
-    
+
     private static boolean testTreeCopy() {
         try {
             final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])";
             final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
             final Phylogeny t1 = t0.copy();
-            if ( !t1.toNewHampshireX().equals(  t0.toNewHampshireX() ) ) {
+            if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
                 return false;
             }
-            if ( !t1.toNewHampshireX().equals( str_0 )) {
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
                 return false;
             }
             t0.deleteSubtree( t0.getNode( "c" ), true );
             t0.deleteSubtree( t0.getNode( "a" ), true );
             t0.deleteSubtree( t0.getNode( "e" ), true );
-            if ( !t0.toNewHampshireX().equals( "(b,d)[&&NHX:S=lizards]" )) {
+            if ( !t0.toNewHampshireX().equals( "(b,d)[&&NHX:S=lizards]" ) ) {
                 return false;
             }
-            
-            if ( !t1.toNewHampshireX().equals( str_0 )) {
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
                 return false;
             }
             t0.deleteSubtree( t0.getNode( "b" ), true );
             t0.deleteSubtree( t0.getNode( "d" ), true );
-            if ( !t1.toNewHampshireX().equals( str_0 )) {
+            if ( !t1.toNewHampshireX().equals( str_0 ) ) {
                 return false;
             }
-            
         }
         catch ( final Exception e ) {
             e.printStackTrace();
@@ -2818,7 +2806,6 @@ public final class Test {
         }
         return true;
     }
-    
 
     private static boolean testCreateBalancedPhylogeny() {
         try {

diff --git a/forester/java/src/org/forester/ws/hmmer/Test.java b/forester/java/src/org/forester/ws/hmmer/Test.java
index f040d2b..7d53e61 100644 (file)
--- a/forester/java/src/org/forester/ws/hmmer/Test.java
+++ b/forester/java/src/org/forester/ws/hmmer/Test.java
@@ -8,7 +8,6 @@ import java.net.HttpURLConnection;
 import java.net.URL;
 import java.net.URLEncoder;
 
-
 public class Test {
 
     public static void main( final String[] args ) {