in progress...

diff --git a/forester/java/src/org/forester/application/cladinator.java b/forester/java/src/org/forester/application/cladinator.java
index 993e295..6dc17e3 100644 (file)
--- a/forester/java/src/org/forester/application/cladinator.java
+++ b/forester/java/src/org/forester/application/cladinator.java
@@ -52,8 +52,8 @@ import org.forester.util.UserException;
 public final class cladinator {
 
     final static private String        PRG_NAME                             = "cladinator";
-    final static private String        PRG_VERSION                          = "1.03";
-    final static private String        PRG_DATE                             = "170913";
+    final static private String        PRG_VERSION                          = "1.04";
+    final static private String        PRG_DATE                             = "170915";
     final static private String        PRG_DESC                             = "clades within clades of annotated labels -- analysis of pplacer-type outputs";
     final static private String        E_MAIL                               = "phyloxml@gmail.com";
     final static private String        WWW                                  = "https://sites.google.com/site/cmzmasek/home/software/forester";
@@ -66,6 +66,7 @@ public final class cladinator {
     final static private String        EXTRA_PROCESSING_OPTION1             = "x";
     final static private String        EXTRA_PROCESSING1_SEP_OPTION         = "xs";
     final static private String        EXTRA_PROCESSING1_KEEP_EXTRA_OPTION  = "xk";
+    final static private String        QUIET_OPTION                         = "Q";
     final static private String        VERBOSE_OPTION                       = "v";
     final static private double        SPECIFICS_CUTOFF_DEFAULT             = 0.8;
     final static private String        SEP_DEFAULT                          = ".";
@@ -108,6 +109,7 @@ public final class cladinator {
             allowed_options.add( EXTRA_PROCESSING1_SEP_OPTION );
             allowed_options.add( EXTRA_PROCESSING1_KEEP_EXTRA_OPTION );
             allowed_options.add( VERBOSE_OPTION );
+            allowed_options.add( QUIET_OPTION );
             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
             if ( dissallowed_options.length() > 0 ) {
                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
@@ -235,6 +237,13 @@ public final class cladinator {
             else {
                 verbose = false;
             }
+            final boolean quit;
+            if ( cla.isOptionSet( QUIET_OPTION ) ) {
+                quit = true;
+            }
+            else {
+                quit = false;
+            }
             System.out.println( "Input tree                 : " + intreefile );
             System.out.println( "Specific-hit support cutoff: " + cutoff_specifics );
             if ( mapping_file != null ) {
@@ -265,10 +274,10 @@ public final class cladinator {
             }
             System.out.println( "Number of input trees      : " + phys.length );
             if ( phys.length == 1 ) {
-                System.out.println( "Ext. nodes in input tree 1 : " + phys[ 0 ].getNumberOfExternalNodes() );
+                System.out.println( "Ext. nodes in input tree   : " + phys[ 0 ].getNumberOfExternalNodes() );
             }
             else {
-                System.out.println( "Ext. nodes in input tree   : " + phys[ 0 ].getNumberOfExternalNodes() );
+                System.out.println( "Ext. nodes in input tree 1 : " + phys[ 0 ].getNumberOfExternalNodes() );
             }
             final EasyWriter outtable_writer;
             if ( outtablefile != null ) {
@@ -277,6 +286,7 @@ public final class cladinator {
             else {
                 outtable_writer = null;
             }
+            int counter = 0;
             for( final Phylogeny phy : phys ) {
                 if ( map != null ) {
                     AnalysisMulti.performMapping( pattern, map, phy, verbose );
@@ -290,11 +300,19 @@ public final class cladinator {
                                                            verbose );
                 }
                 final ResultMulti res = AnalysisMulti.execute( phy, pattern, separator, cutoff_specifics );
-                printResult( res );
+                if ( !quit ) {
+                    if ( phys.length == 1 ) {
+                        printResult( res, -1 );
+                    }
+                    else {
+                        printResult( res, counter );
+                    }
+                }
                 if ( outtable_writer != null ) {
                     writeResultToTable( res, outtable_writer );
                     outtable_writer.flush();
                 }
+                ++counter;
             }
             if ( outtable_writer != null ) {
                 outtable_writer.flush();
@@ -313,10 +331,14 @@ public final class cladinator {
         }
     }
 
-    private final static void printResult( final ResultMulti res ) {
-        System.out.println();
-        System.out.println( "Result for " + res.getQueryNamePrefix() );
+    private final static void printResult( final ResultMulti res, final int counter ) {
         System.out.println();
+        if ( counter == -1 ) {
+            System.out.println( "Result for " + res.getQueryNamePrefix() );
+        }
+        else {
+            System.out.println( "Result for " + res.getQueryNamePrefix() + " [tree " + counter + "]" );
+        }
         if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
             System.out.println( " No match to query pattern!" );
         }
@@ -356,6 +378,9 @@ public final class cladinator {
                     System.out.println( " " + prefix );
                 }
             }
+            System.out.println();
+            System.out.println( " Total Number of Matches: " + res.getNumberOfMatches() + "/"
+                    + res.getReferenceTreeNumberOfExternalNodes() );
         }
         System.out.println();
     }
@@ -375,6 +400,10 @@ public final class cladinator {
                 w.print( prefix.getPrefix() );
                 w.print( "\t" );
                 w.print( df.format( prefix.getConfidence() ) );
+                w.print( "\t" );
+                w.print( String.valueOf( res.getNumberOfMatches() ) );
+                w.print( "\t" );
+                w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
                 w.println();
             }
             if ( res.isHasSpecificMultiHitsPrefixes() ) {
@@ -386,6 +415,10 @@ public final class cladinator {
                     w.print( prefix.getPrefix() );
                     w.print( "\t" );
                     w.print( df.format( prefix.getConfidence() ) );
+                    w.print( "\t" );
+                    w.print( String.valueOf( res.getNumberOfMatches() ) );
+                    w.print( "\t" );
+                    w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
                     w.println();
                 }
             }
@@ -398,6 +431,10 @@ public final class cladinator {
                     w.print( prefix.getPrefix() );
                     w.print( "\t" );
                     w.print( df.format( prefix.getConfidence() ) );
+                    w.print( "\t" );
+                    w.print( String.valueOf( res.getNumberOfMatches() ) );
+                    w.print( "\t" );
+                    w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
                     w.println();
                 }
             }
@@ -410,6 +447,10 @@ public final class cladinator {
                     w.print( prefix.getPrefix() );
                     w.print( "\t" );
                     w.print( df.format( prefix.getConfidence() ) );
+                    w.print( "\t" );
+                    w.print( String.valueOf( res.getNumberOfMatches() ) );
+                    w.print( "\t" );
+                    w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
                     w.println();
                 }
             }

diff --git a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
index 8eccc03..8096777 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
+++ b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
@@ -31,7 +31,6 @@
 package org.forester.clade_analysis;
 
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 import java.util.SortedMap;
 import java.util.regex.Matcher;
@@ -39,7 +38,6 @@ import java.util.regex.Pattern;
 
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 import org.forester.util.UserException;
@@ -73,28 +71,15 @@ public final class AnalysisMulti {
                                        final String separator,
                                        final double cutoff_for_specifics )
             throws UserException {
+        if ( ForesterUtil.isEmpty( separator ) ) {
+            throw new IllegalArgumentException( "separator must not be null or empty" );
+        }
         cleanUpExternalNames( p, separator );
         final List<PhylogenyNode> qnodes = p.getNodes( query );
-        String query_name_prefix = null;
-        for( final PhylogenyNode n : qnodes ) {
-            final String name = n.getName();
-            final Matcher matcher = query.matcher( name );
-            if ( matcher.find() ) {
-                final String prefix = name.substring( 0, matcher.start() );
-                if ( ForesterUtil.isEmpty( prefix ) ) {
-                    throw new UserException( "query nodes with empty label prefix found: \"" + prefix + "\"" );
-                }
-                if ( query_name_prefix == null ) {
-                    query_name_prefix = prefix;
-                }
-                else if ( !query_name_prefix.equals( prefix ) ) {
-                    throw new UserException( "query nodes with different label prefixes found: \"" + query_name_prefix
-                            + "\" and \"" + prefix + "\"" );
-                }
-            }
-        }
         final ResultMulti res = new ResultMulti();
-        res.setQueryNamePrefix( query_name_prefix );
+        res.setQueryNamePrefix( obtainQueryPrefix( query, qnodes ) );
+        res.setTotalNumberOfMatches( qnodes.size() );
+        res.setReferenceTreeNumberOfExternalNodes( p.getNumberOfExternalNodes() - qnodes.size() );
         for( int i = 0; i < qnodes.size(); ++i ) {
             final PhylogenyNode qnode = qnodes.get( i );
             if ( qnode.isRoot() ) {
@@ -127,7 +112,7 @@ public final class AnalysisMulti {
                 conf_str = matcher.group( 1 );
             }
             else {
-                throw new IllegalStateException( "pattern did not match -- this should have never happened!" );
+                throw new IllegalStateException( "query pattern does not match [this should have never happened!]" );
             }
             final double conf = Double.parseDouble( conf_str );
             if ( !ForesterUtil.isEmpty( greatest_common_prefix ) ) {
@@ -155,6 +140,29 @@ public final class AnalysisMulti {
         return res;
     }
 
+    private final static String obtainQueryPrefix( final Pattern query, final List<PhylogenyNode> qnodes )
+            throws UserException {
+        String query_name_prefix = null;
+        for( final PhylogenyNode n : qnodes ) {
+            final String name = n.getName();
+            final Matcher matcher = query.matcher( name );
+            if ( matcher.find() ) {
+                final String prefix = name.substring( 0, matcher.start() );
+                if ( ForesterUtil.isEmpty( prefix ) ) {
+                    throw new UserException( "query nodes with empty label prefix found: \"" + prefix + "\"" );
+                }
+                if ( query_name_prefix == null ) {
+                    query_name_prefix = prefix;
+                }
+                else if ( !query_name_prefix.equals( prefix ) ) {
+                    throw new UserException( "query nodes with different label prefixes found: \"" + query_name_prefix
+                            + "\" and \"" + prefix + "\"" );
+                }
+            }
+        }
+        return query_name_prefix;
+    }
+
     private final static void cleanUpExternalNames( final Phylogeny p, final String separator ) throws UserException {
         final Pattern pattern1 = Pattern.compile( "\\Q" + separator + "\\E" + "\\s+" );
         final Pattern pattern2 = Pattern.compile( "\\s+" + "\\Q" + separator + "\\E" );
@@ -212,30 +220,6 @@ public final class AnalysisMulti {
         return greatest_common_prefix;
     }
 
-    private final static String obtainConfidence( final PhylogenyNode n ) {
-        if ( ( n.getBranchData().getConfidences() != null ) && ( n.getBranchData().getConfidences().size() > 0 ) ) {
-            final List<Confidence> confidences = n.getBranchData().getConfidences();
-            boolean not_first = false;
-            Collections.sort( confidences );
-            final StringBuilder sb = new StringBuilder();
-            for( final Confidence confidence : confidences ) {
-                final double value = confidence.getValue();
-                if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
-                    if ( not_first ) {
-                        sb.append( " / " );
-                    }
-                    else {
-                        not_first = true;
-                    }
-                    sb.append( ( ForesterUtil.isEmpty( confidence.getType() ) ? "confidence: "
-                            : confidence.getType() + ": " ) + value );
-                }
-            }
-            return sb.toString();
-        }
-        return null;
-    }
-
     public final static void performMapping( final Pattern pattern,
                                              final SortedMap<String, String> map,
                                              final Phylogeny p,

diff --git a/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java b/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
index 5c725b6..14863d4 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
+++ b/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
@@ -87,12 +87,10 @@ public final class AnalysisSingle {
         }
         res.setLeastEncompassingCladeSize( lec_ext_nodes );
         res.setTreeSize( p_ext_nodes );
-       
         final String conf = obtainConfidence( qnode_pp );
         if ( conf != null ) {
-            res.setGreatestCommonCladeSubtreeConfidence(conf);
+            res.setGreatestCommonCladeSubtreeConfidence( conf );
         }
-        
         final String greatest_common_prefix_up[] = analyzeSiblings( qnode_p, qnode_pp, separator );
         res.setGreatestCommonPrefixUp( greatest_common_prefix_up[ 0 ] );
         if ( greatest_common_prefix_up[ 1 ] != null ) {
@@ -106,8 +104,6 @@ public final class AnalysisSingle {
         return res;
     }
 
-   
-
     private final static String[] analyzeSiblings( final PhylogenyNode child,
                                                    final PhylogenyNode parent,
                                                    final String separator ) {
@@ -133,9 +129,9 @@ public final class AnalysisSingle {
         final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( ext_nodes_names, separator );
         return new String[] { greatest_common_prefix, conf };
     }
-    
+
     private final static String obtainConfidence( final PhylogenyNode n ) {
-        if ( n.getBranchData().getConfidences() != null && n.getBranchData().getConfidences().size() > 0 ) {
+        if ( ( n.getBranchData().getConfidences() != null ) && ( n.getBranchData().getConfidences().size() > 0 ) ) {
             final List<Confidence> confidences = n.getBranchData().getConfidences();
             boolean not_first = false;
             Collections.sort( confidences );

diff --git a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java
index 35c08b5..ac826e0 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java
+++ b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java
@@ -732,7 +732,7 @@ public class CladeAnalysisTest {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
-            ResultMulti res2 = AnalysisMulti.execute( p1 );
+            final ResultMulti res2 = AnalysisMulti.execute( p1 );
             res2.analyze( 0.3 );
             System.out.print( res2.toString() );
             System.out.println( "------------------------- " );
@@ -751,7 +751,7 @@ public class CladeAnalysisTest {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
-            ResultMulti res = AnalysisMulti.execute( p1 );
+            final ResultMulti res = AnalysisMulti.execute( p1 );
             res.analyze( 0.3 );
             System.out.print( res.toString() );
             System.out.println( "------------------------- " );
@@ -770,7 +770,7 @@ public class CladeAnalysisTest {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
-            ResultMulti res = AnalysisMulti.execute( p1, 0.45 );
+            final ResultMulti res = AnalysisMulti.execute( p1, 0.45 );
             System.out.print( res.toString() );
             System.out.println( "------------------------- " );
             System.out.println();

diff --git a/forester/java/src/org/forester/clade_analysis/Prefix.java b/forester/java/src/org/forester/clade_analysis/Prefix.java
index e4bf8fa..009c63f 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/Prefix.java
+++ b/forester/java/src/org/forester/clade_analysis/Prefix.java
@@ -36,11 +36,11 @@ public final class Prefix {
         }
     }
 
-    public  String getPrefix() {
+    public String getPrefix() {
         return _prefix;
     }
 
-    public  String getPrefixFirstElement() {
+    public String getPrefixFirstElement() {
         return _first;
     }
 

diff --git a/forester/java/src/org/forester/clade_analysis/ResultMulti.java b/forester/java/src/org/forester/clade_analysis/ResultMulti.java
index 566a646..285e533 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/ResultMulti.java
+++ b/forester/java/src/org/forester/clade_analysis/ResultMulti.java
@@ -40,25 +40,31 @@ import org.forester.util.UserException;
 
 public final class ResultMulti {
 
-    private final String       _separator;
-    private final List<Prefix> _greatest_common_prefixes      = new ArrayList<>();
-    private final List<Prefix> _greatest_common_prefixes_up   = new ArrayList<>();
-    private final List<Prefix> _greatest_common_prefixes_down = new ArrayList<>();
-    private List<Prefix>       _all                           = null;
-    private List<Prefix>       _collapsed                     = null;
-    private List<Prefix>       _cleaned_spec                  = null;
-    private boolean            _has_specifics                 = false;
-    private List<Prefix>       _all_up                        = null;
-    private List<Prefix>       _collapsed_up                  = null;
-    private List<Prefix>       _cleaned_spec_up               = null;
-    private boolean            _has_specifics_up              = false;
-    private List<Prefix>       _all_down                      = null;
-    private List<Prefix>       _collapsed_down                = null;
-    private List<Prefix>       _cleaned_spec_down             = null;
-    private boolean            _has_specifics_down            = false;
-    private String             _query_name_prefix             = "";
+    private final static double MIN_DIFF                       = 1E-5;
+    private final String        _separator;
+    private final List<Prefix>  _greatest_common_prefixes      = new ArrayList<>();
+    private final List<Prefix>  _greatest_common_prefixes_up   = new ArrayList<>();
+    private final List<Prefix>  _greatest_common_prefixes_down = new ArrayList<>();
+    private List<Prefix>        _all                           = null;
+    private List<Prefix>        _collapsed                     = null;
+    private List<Prefix>        _cleaned_spec                  = null;
+    private boolean             _has_specifics                 = false;
+    private List<Prefix>        _all_up                        = null;
+    private List<Prefix>        _collapsed_up                  = null;
+    private List<Prefix>        _cleaned_spec_up               = null;
+    private boolean             _has_specifics_up              = false;
+    private List<Prefix>        _all_down                      = null;
+    private List<Prefix>        _collapsed_down                = null;
+    private List<Prefix>        _cleaned_spec_down             = null;
+    private boolean             _has_specifics_down            = false;
+    private int                 _matches                       = 0;
+    private int                 _ref_tree_ext_nodes            = 0;
+    private String              _query_name_prefix             = "";
 
     ResultMulti( final String separator ) {
+        if ( ForesterUtil.isEmpty( separator ) ) {
+            throw new IllegalArgumentException( "separator must not be null or empty" );
+        }
         _separator = separator;
         reset();
     }
@@ -120,6 +126,14 @@ public final class ResultMulti {
         return _query_name_prefix;
     }
 
+    public int getNumberOfMatches() {
+        return _matches;
+    }
+
+    public int getReferenceTreeNumberOfExternalNodes() {
+        return _ref_tree_ext_nodes;
+    }
+
     @Override
     public final String toString() {
         final StringBuilder sb = new StringBuilder();
@@ -172,6 +186,9 @@ public final class ResultMulti {
                 sb.append( ForesterUtil.LINE_SEPARATOR );
             }
         }
+        sb.append( ForesterUtil.LINE_SEPARATOR );
+        sb.append( "Total Number of Matches: " + getNumberOfMatches() + "/" + getReferenceTreeNumberOfExternalNodes() );
+        sb.append( ForesterUtil.LINE_SEPARATOR );
         return sb.toString();
     }
 
@@ -194,6 +211,20 @@ public final class ResultMulti {
         _query_name_prefix = query_name_prefix;
     }
 
+    void setTotalNumberOfMatches( final int matches ) {
+        if ( _matches > 0 ) {
+            throw new IllegalStateException( "illegal attempt to change the number of matches" );
+        }
+        _matches = matches;
+    }
+
+    public void setReferenceTreeNumberOfExternalNodes( final int ext_nodes ) {
+        if ( _ref_tree_ext_nodes > 0 ) {
+            throw new IllegalStateException( "illegal attempt to change the number of external nodes" );
+        }
+        _ref_tree_ext_nodes = ext_nodes;
+    }
+
     final void analyze( final double cutoff_for_specifics ) throws UserException {
         reset();
         analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, cutoff_for_specifics );
@@ -223,11 +254,11 @@ public final class ResultMulti {
         final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes, separator );
         if ( !ForesterUtil.isEmpty( l ) ) {
             sortPrefixesAccordingToConfidence( l );
-            _all = removeLessSpecificPrefixes( l );
+            _all = removeLessSpecificPrefixes( l, separator );
             _collapsed = collapse( _all );
             _has_specifics = false;
             if ( cutoff >= 0 ) {
-                _cleaned_spec = obtainSpecifics( cutoff, _all, _collapsed );
+                _cleaned_spec = obtainSpecifics( cutoff, _all, _collapsed, separator );
                 if ( !ForesterUtil.isEmpty( _cleaned_spec ) ) {
                     _has_specifics = true;
                 }
@@ -242,11 +273,11 @@ public final class ResultMulti {
         final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes_up, separator );
         if ( !ForesterUtil.isEmpty( l ) ) {
             sortPrefixesAccordingToConfidence( l );
-            _all_up = removeLessSpecificPrefixes( l );
+            _all_up = removeLessSpecificPrefixes( l, separator );
             _collapsed_up = collapse( _all_up );
             _has_specifics_up = false;
             if ( cutoff >= 0 ) {
-                _cleaned_spec_up = obtainSpecifics( cutoff, _all_up, _collapsed_up );
+                _cleaned_spec_up = obtainSpecifics( cutoff, _all_up, _collapsed_up, separator );
                 if ( !ForesterUtil.isEmpty( _cleaned_spec_up ) ) {
                     _has_specifics_up = true;
                 }
@@ -261,11 +292,11 @@ public final class ResultMulti {
         final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes_down, separator );
         if ( !ForesterUtil.isEmpty( l ) ) {
             sortPrefixesAccordingToConfidence( l );
-            _all_down = removeLessSpecificPrefixes( l );
+            _all_down = removeLessSpecificPrefixes( l, separator );
             _collapsed_down = collapse( _all_down );
             _has_specifics_down = false;
             if ( cutoff >= 0 ) {
-                _cleaned_spec_down = obtainSpecifics( cutoff, _all_down, _collapsed_down );
+                _cleaned_spec_down = obtainSpecifics( cutoff, _all_down, _collapsed_down, separator );
                 if ( !ForesterUtil.isEmpty( _cleaned_spec_down ) ) {
                     _has_specifics_down = true;
                 }
@@ -275,7 +306,8 @@ public final class ResultMulti {
 
     final static List<Prefix> obtainSpecifics( final double cutoff,
                                                final List<Prefix> cleaned,
-                                               final List<Prefix> collapsed ) {
+                                               final List<Prefix> collapsed,
+                                               final String separator ) {
         final List<Prefix> cleaned_spec = new ArrayList<>();
         final Set<String> collapsed_set = new HashSet<>();
         for( final Prefix prefix : collapsed ) {
@@ -290,10 +322,15 @@ public final class ResultMulti {
         for( final Prefix o : spec ) {
             boolean ok = true;
             for( final Prefix i : spec ) {
-                if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) ) ) {
+                if ( ( !o.getPrefix().equals( i.getPrefix() ) )
+                        && ( ForesterUtil.isContainsPrefix( i.getPrefix(), o.getPrefix(), separator ) ) ) {
                     ok = false;
                     break;
                 }
+                /* if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) ) ) {
+                    ok = false;
+                    break;
+                }*/
             }
             if ( ok ) {
                 cleaned_spec.add( o );
@@ -314,7 +351,7 @@ public final class ResultMulti {
                 confidence_sum += prefix.getConfidence();
             }
         }
-        if ( !ForesterUtil.isEqual( confidence_sum, 1.0, 1E-5 ) ) {
+        if ( !ForesterUtil.isEqual( confidence_sum, 1.0, MIN_DIFF ) ) {
             throw new UserException( "confidences add up to " + confidence_sum + " instead of 1.0" );
         }
         return collapsed;
@@ -330,12 +367,19 @@ public final class ResultMulti {
      * I.e. it removes less specific prefixes.
      *
      */
-    private final static List<Prefix> removeLessSpecificPrefixes( final List<Prefix> l ) {
+    private final static List<Prefix> removeLessSpecificPrefixes( final List<Prefix> l, final String separator ) {
         final List<Prefix> cleaned = new ArrayList<>();
         for( final Prefix o : l ) {
             boolean ok = true;
             for( final Prefix i : l ) {
-                if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) )
+                /*if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) )
+                        && ForesterUtil.isEqual( i.getConfidence(),
+                                                 o.getConfidence() ) ) {
+                    ok = false;
+                    break;
+                }*/
+                if ( ( !o.getPrefix().equals( i.getPrefix() ) )
+                        && ( ForesterUtil.isContainsPrefix( i.getPrefix(), o.getPrefix(), separator ) )
                         && ForesterUtil.isEqual( i.getConfidence(),
                                                  o.getConfidence() ) ) {
                     ok = false;
@@ -374,7 +418,7 @@ public final class ResultMulti {
         }
         for( final String key : map.keySet() ) {
             for( final Prefix prefix : greatest_common_prefixes ) {
-                if ( prefix.getPrefix().startsWith( key ) ) {
+                if ( ForesterUtil.isContainsPrefix( prefix.getPrefix(), key, separator ) ) {
                     map.put( key, map.get( key ) + prefix.getConfidence() );
                 }
             }

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 9cda7b7..e3666a8 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -219,7 +219,6 @@ public final class Test {
             succeeded++;
         }
         System.out.println( "OK." );
-        
         System.out.print( "Common prefix: " );
         if ( !testCommonPrefix() ) {
             System.out.println( "failed." );
@@ -229,7 +228,6 @@ public final class Test {
             succeeded++;
         }
         System.out.println( "OK." );
-        
         System.out.print( "Common prefix sep: " );
         if ( !testCommonPrefixSep() ) {
             System.out.println( "failed." );
@@ -239,8 +237,15 @@ public final class Test {
             succeeded++;
         }
         System.out.println( "OK." );
-        
-       
+        System.out.print( "Contains prefix: " );
+        if ( !testContainsPrefix() ) {
+            System.out.println( "failed." );
+            failed++;
+        }
+        else {
+            succeeded++;
+        }
+        System.out.println( "OK." );
         System.out.print( "Sequence writer: " );
         if ( testSequenceWriter() ) {
             System.out.println( "OK." );
@@ -1122,7 +1127,6 @@ public final class Test {
         }
     }
 
-   
     private static boolean testEngulfingOverlapRemoval() {
         try {
             final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
@@ -1132,7 +1136,7 @@ public final class Test {
             final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
             final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
             final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
-            final List<Boolean> covered = new ArrayList<Boolean>();
+            final List<Boolean> covered = new ArrayList<>();
             covered.add( true ); // 0
             covered.add( false ); // 1
             covered.add( true ); // 2
@@ -1364,7 +1368,7 @@ public final class Test {
             final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
             final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
             final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
-            final List<Boolean> covered = new ArrayList<Boolean>();
+            final List<Boolean> covered = new ArrayList<>();
             covered.add( true ); // 0
             covered.add( false ); // 1
             covered.add( true ); // 2
@@ -1885,30 +1889,26 @@ public final class Test {
         return true;
     }
 
-    
     private static boolean testCommonPrefix() {
-        final List<String> l0 = new ArrayList<String>();
+        final List<String> l0 = new ArrayList<>();
         l0.add( "abc" );
         if ( !ForesterUtil.greatestCommonPrefix( l0 ).equals( "abc" ) ) {
             return false;
         }
-        
-        final List<String> l1 = new ArrayList<String>();
+        final List<String> l1 = new ArrayList<>();
         l1.add( "abc" );
         l1.add( "abX" );
         if ( !ForesterUtil.greatestCommonPrefix( l1 ).equals( "ab" ) ) {
             return false;
         }
-        
-        final List<String> l2 = new ArrayList<String>();
+        final List<String> l2 = new ArrayList<>();
         l2.add( "abc" );
         l2.add( "abX" );
         l2.add( "axy" );
         if ( !ForesterUtil.greatestCommonPrefix( l2 ).equals( "a" ) ) {
             return false;
         }
-        
-        final List<String> l3 = new ArrayList<String>();
+        final List<String> l3 = new ArrayList<>();
         l3.add( "abXsdfsdfsdfsdfsdfsd" );
         l3.add( "abXsdfsdfsdfsdfsdfsd" );
         l3.add( "abc" );
@@ -1919,8 +1919,7 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l3 ).equals( "ab" ) ) {
             return false;
         }
-        
-        final List<String> l4 = new ArrayList<String>();
+        final List<String> l4 = new ArrayList<>();
         l4.add( "abXsdfsdfsdfsdfsdfsd" );
         l4.add( "abXsdfsdfsdfsdfsdfsd" );
         l4.add( "abc" );
@@ -1930,14 +1929,12 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l4 ).equals( "" ) ) {
             return false;
         }
-        
-        final List<String> l5 = new ArrayList<String>();
+        final List<String> l5 = new ArrayList<>();
         l5.add( "" );
         if ( !ForesterUtil.greatestCommonPrefix( l5 ).equals( "" ) ) {
             return false;
         }
-        
-        final List<String> l6 = new ArrayList<String>();
+        final List<String> l6 = new ArrayList<>();
         l6.add( "abc" );
         l6.add( "abX" );
         l6.add( "" );
@@ -1946,30 +1943,27 @@ public final class Test {
         }
         return true;
     }
-    
+
     private static boolean testCommonPrefixSep() {
-        final List<String> l0 = new ArrayList<String>();
+        final List<String> l0 = new ArrayList<>();
         l0.add( "a.b.c" );
-        if ( !ForesterUtil.greatestCommonPrefix( l0, ".").equals( "a.b.c" ) ) {
+        if ( !ForesterUtil.greatestCommonPrefix( l0, "." ).equals( "a.b.c" ) ) {
             return false;
         }
-        
-        final List<String> l1 = new ArrayList<String>();
+        final List<String> l1 = new ArrayList<>();
         l1.add( "a.b.c" );
         l1.add( "a.b.X" );
-        if ( !ForesterUtil.greatestCommonPrefix( l1 , ".").equals( "a.b" ) ) {
+        if ( !ForesterUtil.greatestCommonPrefix( l1, "." ).equals( "a.b" ) ) {
             return false;
         }
-        
-        final List<String> l2 = new ArrayList<String>();
+        final List<String> l2 = new ArrayList<>();
         l2.add( "a.b.c." );
         l2.add( "a.b.X." );
         l2.add( "a.x.y." );
-        if ( !ForesterUtil.greatestCommonPrefix( l2, ".").equals( "a" ) ) {
+        if ( !ForesterUtil.greatestCommonPrefix( l2, "." ).equals( "a" ) ) {
             return false;
         }
-        
-        final List<String> l3 = new ArrayList<String>();
+        final List<String> l3 = new ArrayList<>();
         l3.add( "a/b/X/s/d/f/s/d/f/s/d/f/s/d/f/s/d/f/s/d/" );
         l3.add( "a/b/X/s/d/f/s/d/f/s/d/f/s/d/f/s/d/f/s/d" );
         l3.add( "a/b/c" );
@@ -1980,8 +1974,7 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l3, "/" ).equals( "a/b" ) ) {
             return false;
         }
-       
-        final List<String> l4 = new ArrayList<String>();
+        final List<String> l4 = new ArrayList<>();
         l4.add( "a.b.X.s.d.f.s.d.f.s.d.f.s.d.f.s.d.f.s.d" );
         l4.add( "a.b.X.s.d.f.s.d.f.s.d.f.s.d.f.s.d.f.s.d" );
         l4.add( "a.b.c" );
@@ -1991,21 +1984,18 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l4, "." ).equals( "" ) ) {
             return false;
         }
-      
-        final List<String> l5 = new ArrayList<String>();
+        final List<String> l5 = new ArrayList<>();
         l5.add( "" );
         if ( !ForesterUtil.greatestCommonPrefix( l5, "_" ).equals( "" ) ) {
             return false;
         }
-        
-        final List<String> l6 = new ArrayList<String>();
+        final List<String> l6 = new ArrayList<>();
         l6.add( "_" );
         l6.add( "__" );
         if ( !ForesterUtil.greatestCommonPrefix( l6, "_" ).equals( "" ) ) {
             return false;
         }
-        
-        final List<String> l7 = new ArrayList<String>();
+        final List<String> l7 = new ArrayList<>();
         l7.add( "a,b,c" );
         l7.add( "a,b,X" );
         l7.add( "" );
@@ -2013,26 +2003,75 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l7, "," ).equals( "" ) ) {
             return false;
         }
-        
-        final List<String> l8 = new ArrayList<String>();
+        final List<String> l8 = new ArrayList<>();
         l8.add( "123.304.403.04" );
         l8.add( "123.304.403.04.02" );
         l8.add( "123.304.403.03.03" );
         if ( !ForesterUtil.greatestCommonPrefix( l8, "." ).equals( "123.304.403" ) ) {
             return false;
         }
-        
-        final List<String> l9 = new ArrayList<String>();
+        final List<String> l9 = new ArrayList<>();
         l9.add( "123.304.403.04" );
         l9.add( "123.304.403.04.02" );
         l9.add( "123.304.402.03.03" );
         if ( !ForesterUtil.greatestCommonPrefix( l9, "." ).equals( "123.304" ) ) {
             return false;
         }
+        final List<String> l10 = new ArrayList<>();
+        l10.add( "abcde" );
+        l10.add( "adc" );
+        if ( !ForesterUtil.greatestCommonPrefix( l10, "." ).equals( "" ) ) {
+            return false;
+        }
+        return true;
+    }
+
+    private static boolean testContainsPrefix() {
+        if ( !ForesterUtil.isContainsPrefix( "a.b", "a", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( "a.b.c", "a", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( "a.b.c", "a.b", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( "a.b", "a.b", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( "a", "a", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( ".a.b", ".a", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( ".a.b.", ".a", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( ".a.b.", ".a.", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( "a..b.", "a", "." ) ) {
+            return false;
+        }
+        if ( !ForesterUtil.isContainsPrefix( "a..b.", "a..", "." ) ) {
+            return false;
+        }
+        if ( ForesterUtil.isContainsPrefix( "a", "a.b", "." ) ) {
+            return false;
+        }
+        if ( ForesterUtil.isContainsPrefix( "a_b", "a", "." ) ) {
+            return false;
+        }
+        if ( ForesterUtil.isContainsPrefix( ".a.", ".a.b.", "." ) ) {
+            return false;
+        }
+        if ( ForesterUtil.isContainsPrefix( "a.b.c", "a.x", "." ) ) {
+            return false;
+        }
         return true;
     }
 
-    
     private static boolean testUTF8ParsingFromFile() {
         try {
             final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
@@ -3167,7 +3206,7 @@ public final class Test {
             p.addProteinDomain( A20 );
             p.addProteinDomain( B25 );
             p.addProteinDomain( D80 );
-            List<String> domains_ids = new ArrayList<String>();
+            List<String> domains_ids = new ArrayList<>();
             domains_ids.add( "A" );
             domains_ids.add( "B" );
             domains_ids.add( "C" );
@@ -3184,7 +3223,7 @@ public final class Test {
             if ( p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<String>();
+            domains_ids = new ArrayList<>();
             domains_ids.add( "A" );
             domains_ids.add( "C" );
             domains_ids.add( "D" );
@@ -3194,7 +3233,7 @@ public final class Test {
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<String>();
+            domains_ids = new ArrayList<>();
             domains_ids.add( "A" );
             domains_ids.add( "D" );
             domains_ids.add( "C" );
@@ -3204,7 +3243,7 @@ public final class Test {
             if ( p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<String>();
+            domains_ids = new ArrayList<>();
             domains_ids.add( "A" );
             domains_ids.add( "A" );
             domains_ids.add( "B" );
@@ -3214,7 +3253,7 @@ public final class Test {
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<String>();
+            domains_ids = new ArrayList<>();
             domains_ids.add( "A" );
             domains_ids.add( "A" );
             domains_ids.add( "A" );
@@ -3226,7 +3265,7 @@ public final class Test {
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<String>();
+            domains_ids = new ArrayList<>();
             domains_ids.add( "A" );
             domains_ids.add( "A" );
             domains_ids.add( "B" );
@@ -3255,7 +3294,7 @@ public final class Test {
 
     private static boolean testBasicTable() {
         try {
-            final BasicTable<String> t0 = new BasicTable<String>();
+            final BasicTable<String> t0 = new BasicTable<>();
             if ( t0.getNumberOfColumns() != 0 ) {
                 return false;
             }
@@ -3954,7 +3993,7 @@ public final class Test {
             final ProteinDomain d2 = new ProteinDomain( "domain2", 50, 60 );
             final ProteinDomain d3 = new ProteinDomain( "domain3", 70, 80 );
             final ProteinDomain d4 = new ProteinDomain( "domain4", 90, 100 );
-            final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
+            final ArrayList<PhylogenyData> domains0 = new ArrayList<>();
             domains0.add( d2 );
             domains0.add( d0 );
             domains0.add( d3 );
@@ -3973,7 +4012,7 @@ public final class Test {
             if ( ds1.getNumberOfDomains() != 4 ) {
                 return false;
             }
-            final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
+            final ArrayList<PhylogenyData> domains1 = new ArrayList<>();
             domains1.add( d1 );
             domains1.add( d2 );
             domains1.add( d4 );
@@ -5710,7 +5749,7 @@ public final class Test {
 
     private static boolean testGeneralTable() {
         try {
-            final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
+            final GeneralTable<Integer, String> t0 = new GeneralTable<>();
             t0.setValue( 3, 2, "23" );
             t0.setValue( 10, 1, "error" );
             t0.setValue( 10, 1, "110" );
@@ -5746,7 +5785,7 @@ public final class Test {
             if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
                 return false;
             }
-            final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
+            final GeneralTable<String, String> t1 = new GeneralTable<>();
             t1.setValue( "3", "2", "23" );
             t1.setValue( "10", "1", "error" );
             t1.setValue( "10", "1", "110" );
@@ -6757,7 +6796,7 @@ public final class Test {
 
     private static boolean testMafft( final String path ) {
         try {
-            final List<String> opts = new ArrayList<String>();
+            final List<String> opts = new ArrayList<>();
             opts.add( "--maxiterate" );
             opts.add( "1000" );
             opts.add( "--localpair" );
@@ -6853,7 +6892,7 @@ public final class Test {
             final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
             final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
             final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
-            final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
+            final List<MolecularSequence> l = new ArrayList<>();
             l.add( s0 );
             l.add( s1 );
             l.add( s2 );
@@ -6894,7 +6933,7 @@ public final class Test {
             final MolecularSequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
             final MolecularSequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
             final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
-            final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
+            final List<MolecularSequence> l = new ArrayList<>();
             l.add( s0 );
             l.add( s1 );
             l.add( s2 );
@@ -6917,7 +6956,7 @@ public final class Test {
             //            System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
             //            System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
             //            System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
-            final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
+            final List<MolecularSequence> l2 = new ArrayList<>();
             l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
             l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
             l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
@@ -6961,7 +7000,7 @@ public final class Test {
             final MolecularSequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
             final MolecularSequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
             final MolecularSequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
-            final List<MolecularSequence> l0 = new ArrayList<MolecularSequence>();
+            final List<MolecularSequence> l0 = new ArrayList<>();
             l0.add( s0 );
             l0.add( s1 );
             l0.add( s2 );
@@ -7009,7 +7048,7 @@ public final class Test {
             final MolecularSequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
             final MolecularSequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
             final MolecularSequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
-            final List<MolecularSequence> l1 = new ArrayList<MolecularSequence>();
+            final List<MolecularSequence> l1 = new ArrayList<>();
             l1.add( s_0 );
             l1.add( s_1 );
             l1.add( s_2 );
@@ -7049,7 +7088,7 @@ public final class Test {
             final MolecularSequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
             final MolecularSequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
             final MolecularSequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
-            final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
+            final List<MolecularSequence> l2 = new ArrayList<>();
             l2.add( s__0 );
             l2.add( s__1 );
             l2.add( s__2 );
@@ -7115,7 +7154,7 @@ public final class Test {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             PhylogenyNode n;
-            List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
+            List<PhylogenyNode> ext = new ArrayList<>();
             final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
             final Phylogeny t0 = factory.create( sb0.toString(), new NHXParser() )[ 0 ];
             t0.getNode( "cd" ).setCollapse( true );
@@ -7150,7 +7189,7 @@ public final class Test {
             t1.getNode( "cd" ).setCollapse( true );
             t1.getNode( "cde" ).setCollapse( true );
             n = t1.getNode( "ab" );
-            ext = new ArrayList<PhylogenyNode>();
+            ext = new ArrayList<>();
             while ( n != null ) {
                 ext.add( n );
                 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
@@ -7181,7 +7220,7 @@ public final class Test {
             t2.getNode( "e" ).setCollapse( true );
             t2.getNode( "gh" ).setCollapse( true );
             n = t2.getNode( "ab" );
-            ext = new ArrayList<PhylogenyNode>();
+            ext = new ArrayList<>();
             while ( n != null ) {
                 ext.add( n );
                 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
@@ -7210,7 +7249,7 @@ public final class Test {
             t3.getNode( "gh" ).setCollapse( true );
             t3.getNode( "fgh" ).setCollapse( true );
             n = t3.getNode( "ab" );
-            ext = new ArrayList<PhylogenyNode>();
+            ext = new ArrayList<>();
             while ( n != null ) {
                 ext.add( n );
                 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
@@ -12526,7 +12565,7 @@ public final class Test {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
             //Archaeopteryx.createApplication( p0 );
-            final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
+            final Set<PhylogenyNode> ex = new HashSet<>();
             ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12539,13 +12578,13 @@ public final class Test {
             final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, false, ex );
             // System.out.println( s0.toString() );
             //
-            Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
+            Set<PhylogenyNode> query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12557,7 +12596,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12565,7 +12604,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
@@ -12574,7 +12613,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12583,20 +12622,20 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12605,14 +12644,14 @@ public final class Test {
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12620,13 +12659,13 @@ public final class Test {
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
@@ -12634,7 +12673,7 @@ public final class Test {
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12643,71 +12682,71 @@ public final class Test {
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12780,7 +12819,7 @@ public final class Test {
             //                return false;
             //            }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12789,7 +12828,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12799,7 +12838,7 @@ public final class Test {
             }
             ///////////////////////////
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12808,7 +12847,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12817,7 +12856,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12826,7 +12865,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12835,7 +12874,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12844,7 +12883,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
@@ -12852,7 +12891,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12862,7 +12901,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12872,7 +12911,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12882,7 +12921,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12904,7 +12943,7 @@ public final class Test {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final Phylogeny p0 = factory.create( "(((A,B,C),D),(E,(F,G)))R", new NHXParser() )[ 0 ];
-            final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
+            final Set<PhylogenyNode> ex = new HashSet<>();
             ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12913,13 +12952,13 @@ public final class Test {
             ex.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             final TreeSplitMatrix s0 = new TreeSplitMatrix( p0, true, ex );
-            Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
+            Set<PhylogenyNode> query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12931,7 +12970,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12939,7 +12978,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
@@ -12948,7 +12987,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12957,7 +12996,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
@@ -12965,14 +13004,14 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12982,7 +13021,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12990,7 +13029,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12999,14 +13038,14 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
@@ -13015,7 +13054,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -13025,7 +13064,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
@@ -13033,49 +13072,49 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
@@ -13083,7 +13122,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
@@ -13091,7 +13130,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -13099,7 +13138,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<PhylogenyNode>();
+            query_nodes = new HashSet<>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -13634,12 +13673,11 @@ public final class Test {
         }
         return true;
     }
-    
+
     private static boolean testPhylogenyMethods() {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)r", new NHXParser() )[ 0 ];
-          
             if ( PhylogenyMethods.calculateLevel( t0.getNode( "A" ) ) != 0 ) {
                 return false;
             }
@@ -13667,7 +13705,8 @@ public final class Test {
             if ( PhylogenyMethods.calculateLevel( t0.getNode( "r" ) ) != 4 ) {
                 return false;
             }
-            final Phylogeny t1 = factory.create( "((((A,B)ab,C)abc,D)abcd,E,((((((X)1)2)3)4)5)6)r", new NHXParser() )[ 0 ];
+            final Phylogeny t1 = factory.create( "((((A,B)ab,C)abc,D)abcd,E,((((((X)1)2)3)4)5)6)r",
+                                                 new NHXParser() )[ 0 ];
             if ( PhylogenyMethods.calculateLevel( t1.getNode( "r" ) ) != 7 ) {
                 return false;
             }
@@ -13695,7 +13734,6 @@ public final class Test {
             if ( PhylogenyMethods.calculateLevel( t1.getNode( "abcd" ) ) != 3 ) {
                 return false;
             }
-            
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 5d70578..6c14975 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -407,7 +407,7 @@ public final class ForesterUtil {
     }
 
     public static String[][] file22dArray( final File file ) throws IOException {
-        final List<String> list = new ArrayList<String>();
+        final List<String> list = new ArrayList<>();
         final BufferedReader in = new BufferedReader( new FileReader( file ) );
         String str;
         while ( ( str = in.readLine() ) != null ) {
@@ -445,7 +445,7 @@ public final class ForesterUtil {
     }
 
     final public static List<String> file2list( final File file ) throws IOException {
-        final List<String> list = new ArrayList<String>();
+        final List<String> list = new ArrayList<>();
         final BufferedReader in = new BufferedReader( new FileReader( file ) );
         String str;
         while ( ( str = in.readLine() ) != null ) {
@@ -461,7 +461,7 @@ public final class ForesterUtil {
     }
 
     final public static SortedSet<String> file2set( final File file ) throws IOException {
-        final SortedSet<String> set = new TreeSet<String>();
+        final SortedSet<String> set = new TreeSet<>();
         final BufferedReader in = new BufferedReader( new FileReader( file ) );
         String str;
         while ( ( str = in.readLine() ) != null ) {
@@ -543,8 +543,8 @@ public final class ForesterUtil {
 
     final public static MolecularSequence.TYPE guessMolecularSequenceType( final String mol_seq ) {
         final String s = mol_seq.toUpperCase();
-        if ( s.contains( "L" ) || s.contains( "I" ) || s.contains( "E" ) || s.contains( "H" )
-                || s.contains( "D" ) || s.contains( "Q" ) ) {
+        if ( s.contains( "L" ) || s.contains( "I" ) || s.contains( "E" ) || s.contains( "H" ) || s.contains( "D" )
+                || s.contains( "Q" ) ) {
             return TYPE.AA;
         }
         else {
@@ -723,7 +723,7 @@ public final class ForesterUtil {
         }
         return null;
     }
-    
+
     final public static String isWritableFile( final String s ) {
         return isWritableFile( new File( s ) );
     }
@@ -744,7 +744,7 @@ public final class ForesterUtil {
     }
 
     final public static SortedMap<Object, Integer> listToSortedCountsMap( final List<?> list ) {
-        final SortedMap<Object, Integer> map = new TreeMap<Object, Integer>();
+        final SortedMap<Object, Integer> map = new TreeMap<>();
         for( final Object key : list ) {
             if ( !map.containsKey( key ) ) {
                 map.put( key, 1 );
@@ -1176,7 +1176,7 @@ public final class ForesterUtil {
         //urlc.setRequestProperty( "User-Agent", "" );
         final BufferedReader in = new BufferedReader( new InputStreamReader( urlc.getInputStream() ) );
         String line;
-        final List<String> result = new ArrayList<String>();
+        final List<String> result = new ArrayList<>();
         while ( ( line = in.readLine() ) != null ) {
             result.add( line );
         }
@@ -1211,7 +1211,7 @@ public final class ForesterUtil {
                                                          protein.getSpecies().getSpeciesId(),
                                                          protein.getLength() );
         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
-        final List<Boolean> covered_positions = new ArrayList<Boolean>();
+        final List<Boolean> covered_positions = new ArrayList<>();
         for( final Domain domain : sorted ) {
             if ( ( ( max_allowed_overlap < 0 )
                     || ( ForesterUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
@@ -1518,7 +1518,7 @@ public final class ForesterUtil {
             is.close();
         }
         catch ( final Exception e ) {
-            // ignore  
+            // ignore
         }
         return trees;
     }
@@ -1550,7 +1550,7 @@ public final class ForesterUtil {
         File the_one = null;
         do {
             int matches = 0;
-            for( File file : files ) {
+            for( final File file : files ) {
                 if ( file.getName().startsWith( my_prefix ) ) {
                     matches++;
                     if ( matches > 1 ) {
@@ -1598,6 +1598,24 @@ public final class ForesterUtil {
         return a.substring( 0, min_length );
     }
 
+    public final static boolean isContainsPrefix( final String word, final String prefix, final String separator ) {
+        if ( ForesterUtil.isEmpty( separator ) ) {
+            throw new IllegalArgumentException( "separator must not be null or empty" );
+        }
+        final String[] word_ary = word.split( Pattern.quote( separator ) );
+        final String[] prefix_ary = prefix.split( Pattern.quote( separator ) );
+        if ( word_ary.length < prefix_ary.length ) {
+            return false;
+        }
+        final int prefix_ary_length = prefix_ary.length;
+        for( int i = 0; i < prefix_ary_length; ++i ) {
+            if ( !( word_ary[ i ].equals( prefix_ary[ i ] ) ) ) {
+                return false;
+            }
+        }
+        return true;
+    }
+
     public final static String greatestCommonPrefix( final String a, final String b, final String separator ) {
         if ( ForesterUtil.isEmpty( separator ) ) {
             throw new IllegalArgumentException( "separator must not be null or empty" );
@@ -1607,7 +1625,7 @@ public final class ForesterUtil {
         final int min_length = Math.min( as.length, bs.length );
         for( int i = 0; i < min_length; ++i ) {
             if ( !( as[ i ].equals( bs[ i ] ) ) ) {
-                StringBuilder sb = new StringBuilder();
+                final StringBuilder sb = new StringBuilder();
                 boolean first = true;
                 for( int j = 0; j < i; ++j ) {
                     if ( first ) {
@@ -1621,7 +1639,7 @@ public final class ForesterUtil {
                 return sb.toString();
             }
         }
-        StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
         boolean first = true;
         for( int j = 0; j < min_length; ++j ) {
             if ( first ) {
@@ -1666,12 +1684,9 @@ public final class ForesterUtil {
         return common;
     }
 
-    private ForesterUtil() {
-    }
-
     public static List<String> spliIntoPrefixes( final String prefix, final String separator ) {
         final String[] a = prefix.split( Pattern.quote( separator ) );
-        final List<String> l = new ArrayList<String>();
+        final List<String> l = new ArrayList<>();
         for( int i = 0; i < a.length; ++i ) {
             final StringBuilder sb = new StringBuilder();
             for( int j = 0; j <= i; ++j ) {
@@ -1680,15 +1695,16 @@ public final class ForesterUtil {
                     sb.append( separator );
                 }
             }
-            //  System.out.println( sb.toString() );
             l.add( sb.toString() );
         }
         return l;
     }
 
-    //
     public static boolean isLooksLikeFasta( final File file ) throws IOException {
         final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
         return ( ( !isEmptyTrimmed( first_line ) && first_line.trim().startsWith( ">" ) ) );
     }
+
+    private ForesterUtil() {
+    }
 }