removed diamond operator

diff --git a/forester/java/src/org/forester/application/cladinator.java b/forester/java/src/org/forester/application/cladinator.java
index a4b273f..6b66230 100644 (file)
--- a/forester/java/src/org/forester/application/cladinator.java
+++ b/forester/java/src/org/forester/application/cladinator.java
@@ -101,7 +101,7 @@ public final class cladinator {
                 print_help();
                 System.exit( -1 );
             }
-            final List<String> allowed_options = new ArrayList<>();
+            final List<String> allowed_options = new ArrayList<String>();
             allowed_options.add( SEP_OPTION );
             allowed_options.add( QUERY_PATTERN_OPTION );
             allowed_options.add( SPECIFICS_CUTOFF_OPTION );

diff --git a/forester/java/src/org/forester/application/fasta_split.java b/forester/java/src/org/forester/application/fasta_split.java
index 94a53a6..5dc963c 100644 (file)
--- a/forester/java/src/org/forester/application/fasta_split.java
+++ b/forester/java/src/org/forester/application/fasta_split.java
@@ -94,7 +94,7 @@ public final class fasta_split {
             ForesterUtil.fatalError( PRG_NAME, infile + " appears empty" );
         }
         System.out.println( "Read " + seqs.size() + " sequences" );
-        final Map<String, List<MolecularSequence>> output = new HashMap<>();
+        final Map<String, List<MolecularSequence>> output = new HashMap<String, List<MolecularSequence>>();
         for( final MolecularSequence seq : seqs ) {
             final Matcher m = pa.matcher( seq.getIdentifier() );
             if ( m.find() ) {

diff --git a/forester/java/src/org/forester/application/pplacer_summary.java b/forester/java/src/org/forester/application/pplacer_summary.java
index 91a488a..d914af8 100644 (file)
--- a/forester/java/src/org/forester/application/pplacer_summary.java
+++ b/forester/java/src/org/forester/application/pplacer_summary.java
@@ -19,7 +19,7 @@ public class pplacer_summary {
     public static void main( final String args[] ) {
         final File indir = new File( "." );
         final File[] list_of_files = indir.listFiles();
-        final List<File> infiles = new ArrayList<>();
+        final List<File> infiles = new ArrayList<File>();
         for( final File file : list_of_files ) {
             if ( file.isFile() && file.canRead() && file.toString().endsWith( ".sing.tre" ) ) {
                 infiles.add( file );

diff --git a/forester/java/src/org/forester/application/rid.java b/forester/java/src/org/forester/application/rid.java
index 9d25d8d..2b28777 100644 (file)
--- a/forester/java/src/org/forester/application/rid.java
+++ b/forester/java/src/org/forester/application/rid.java
@@ -108,7 +108,7 @@ public class rid {
                 print_help();
                 System.exit( -1 );
             }
-            final List<String> allowed_options = new ArrayList<>();
+            final List<String> allowed_options = new ArrayList<String>();
             allowed_options.add( OUTPUT_FORMAT_OPTION );
             allowed_options.add( ID_NORM_OPTION );
             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
@@ -265,7 +265,7 @@ public class rid {
             else {
                 System.out.println( "Alignment length      : " + ( int ) stats.getMax() );
             }
-            final List<MolecularSequence> output_seqs = new ArrayList<>();
+            final List<MolecularSequence> output_seqs = new ArrayList<MolecularSequence>();
             int counter = 0;
             final BufferedWriter output_map_writer;
             if ( normalize_identifiers ) {

diff --git a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
index 44f46cd..3970e5d 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
+++ b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
@@ -97,7 +97,7 @@ public final class AnalysisMulti {
             while ( qnode_pp.getNumberOfDescendants() == 1 ) {
                 qnode_pp = qnode_pp.getParent();
             }
-            final List<String> qnode_ext_nodes_names = new ArrayList<>();
+            final List<String> qnode_ext_nodes_names = new ArrayList<String>();
             for( final PhylogenyNode qnode_ext_node : qnode_pp.getAllExternalDescendants() ) {
                 final String name = qnode_ext_node.getName();
                 final Matcher m = query.matcher( name );
@@ -202,7 +202,7 @@ public final class AnalysisMulti {
                                                  final String separator,
                                                  final Pattern query ) {
         final int child_index = child.getChildNodeIndex();
-        final List<String> ext_nodes_names = new ArrayList<>();
+        final List<String> ext_nodes_names = new ArrayList<String>();
         final List<PhylogenyNode> descs = parent.getDescendants();
         for( int i = 0; i < descs.size(); ++i ) {
             if ( i != child_index ) {

diff --git a/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java b/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
index 14863d4..64f9d59 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
+++ b/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
@@ -62,7 +62,7 @@ public final class AnalysisSingle {
         final List<PhylogenyNode> qnode_ext_nodes = qnode_pp.getAllExternalDescendants();
         final int lec_ext_nodes = qnode_ext_nodes.size() - 1;
         final int p_ext_nodes = p.getNumberOfExternalNodes() - 1;
-        final List<String> qnode_ext_nodes_names = new ArrayList<>();
+        final List<String> qnode_ext_nodes_names = new ArrayList<String>();
         for( final PhylogenyNode qnode_ext_node : qnode_ext_nodes ) {
             String name = qnode_ext_node.getName();
             if ( ForesterUtil.isEmptyTrimmed( name ) ) {
@@ -108,7 +108,7 @@ public final class AnalysisSingle {
                                                    final PhylogenyNode parent,
                                                    final String separator ) {
         final int child_index = child.getChildNodeIndex();
-        final List<String> ext_nodes_names = new ArrayList<>();
+        final List<String> ext_nodes_names = new ArrayList<String>();
         final List<PhylogenyNode> descs = parent.getDescendants();
         String conf = null;
         for( int i = 0; i < descs.size(); ++i ) {

diff --git a/forester/java/src/org/forester/clade_analysis/ResultMulti.java b/forester/java/src/org/forester/clade_analysis/ResultMulti.java
index 285e533..3f55364 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/ResultMulti.java
+++ b/forester/java/src/org/forester/clade_analysis/ResultMulti.java
@@ -42,9 +42,9 @@ public final class ResultMulti {
 
     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 final List<Prefix>  _greatest_common_prefixes      = new ArrayList<Prefix>();
+    private final List<Prefix>  _greatest_common_prefixes_up   = new ArrayList<Prefix>();
+    private final List<Prefix>  _greatest_common_prefixes_down = new ArrayList<Prefix>();
     private List<Prefix>        _all                           = null;
     private List<Prefix>        _collapsed                     = null;
     private List<Prefix>        _cleaned_spec                  = null;
@@ -233,17 +233,17 @@ public final class ResultMulti {
     }
 
     private final void reset() {
-        _all = new ArrayList<>();
-        _collapsed = new ArrayList<>();
-        _cleaned_spec = new ArrayList<>();
+        _all = new ArrayList<Prefix>();
+        _collapsed = new ArrayList<Prefix>();
+        _cleaned_spec = new ArrayList<Prefix>();
         _has_specifics = false;
-        _all_up = new ArrayList<>();
-        _collapsed_up = new ArrayList<>();
-        _cleaned_spec_up = new ArrayList<>();
+        _all_up = new ArrayList<Prefix>();
+        _collapsed_up = new ArrayList<Prefix>();
+        _cleaned_spec_up = new ArrayList<Prefix>();
         _has_specifics_up = false;
-        _all_down = new ArrayList<>();
-        _collapsed_down = new ArrayList<>();
-        _cleaned_spec_down = new ArrayList<>();
+        _all_down = new ArrayList<Prefix>();
+        _collapsed_down = new ArrayList<Prefix>();
+        _cleaned_spec_down = new ArrayList<Prefix>();
         _has_specifics_down = false;
     }
 
@@ -308,12 +308,12 @@ public final class ResultMulti {
                                                final List<Prefix> cleaned,
                                                final List<Prefix> collapsed,
                                                final String separator ) {
-        final List<Prefix> cleaned_spec = new ArrayList<>();
-        final Set<String> collapsed_set = new HashSet<>();
+        final List<Prefix> cleaned_spec = new ArrayList<Prefix>();
+        final Set<String> collapsed_set = new HashSet<String>();
         for( final Prefix prefix : collapsed ) {
             collapsed_set.add( prefix.getPrefix() );
         }
-        final List<Prefix> spec = new ArrayList<>();
+        final List<Prefix> spec = new ArrayList<Prefix>();
         for( final Prefix prefix : cleaned ) {
             if ( ( prefix.getConfidence() >= cutoff ) && !collapsed_set.contains( prefix.getPrefix() ) ) {
                 spec.add( prefix );
@@ -340,8 +340,8 @@ public final class ResultMulti {
     }
 
     private final static List<Prefix> collapse( final List<Prefix> cleaned ) throws UserException {
-        final List<Prefix> collapsed = new ArrayList<>();
-        final Set<String> firsts = new HashSet<>();
+        final List<Prefix> collapsed = new ArrayList<Prefix>();
+        final Set<String> firsts = new HashSet<String>();
         double confidence_sum = 0;
         for( final Prefix prefix : cleaned ) {
             final String f = prefix.getPrefixFirstElement();
@@ -368,7 +368,7 @@ public final class ResultMulti {
      *
      */
     private final static List<Prefix> removeLessSpecificPrefixes( final List<Prefix> l, final String separator ) {
-        final List<Prefix> cleaned = new ArrayList<>();
+        final List<Prefix> cleaned = new ArrayList<Prefix>();
         for( final Prefix o : l ) {
             boolean ok = true;
             for( final Prefix i : l ) {
@@ -409,7 +409,7 @@ public final class ResultMulti {
 
     private final static List<Prefix> obtainAllPrefixes( final List<Prefix> greatest_common_prefixes,
                                                          final String separator ) {
-        final SortedMap<String, Double> map = new TreeMap<>();
+        final SortedMap<String, Double> map = new TreeMap<String, Double>();
         for( final Prefix prefix : greatest_common_prefixes ) {
             final List<String> prefixes = ForesterUtil.spliIntoPrefixes( prefix.getPrefix(), separator );
             for( final String p : prefixes ) {
@@ -423,7 +423,7 @@ public final class ResultMulti {
                 }
             }
         }
-        final List<Prefix> l = new ArrayList<>();
+        final List<Prefix> l = new ArrayList<Prefix>();
         for( final Entry<String, Double> entry : map.entrySet() ) {
             l.add( new Prefix( entry.getKey(), entry.getValue(), separator ) );
         }

diff --git a/forester/java/src/org/forester/clade_analysis/ResultSingle.java b/forester/java/src/org/forester/clade_analysis/ResultSingle.java
index a122d7e..5a7b2dd 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/ResultSingle.java
+++ b/forester/java/src/org/forester/clade_analysis/ResultSingle.java
@@ -35,7 +35,7 @@ public final class ResultSingle {
     private String             _greatest_common_prefix                        = "";
     private String             _greatest_common_prefix_up                     = "";
     private String             _greatest_common_prefix_down                   = "";
-    private final List<String> _warnings                                      = new ArrayList<>();
+    private final List<String> _warnings                                      = new ArrayList<String>();
     private int                _lec_ext_nodes                                 = 0;
     private int                _p_ext_nodes                                   = 0;
     private String             _greatest_common_clade_subtree_confidence      = "";

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index 0416f41..86aae06 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -327,7 +327,7 @@ public class Phylogeny {
      */
     public List<PhylogenyNode> getExternalNodes() {
         if ( _external_nodes_set == null ) {
-            _external_nodes_set = new ArrayList<>();
+            _external_nodes_set = new ArrayList<PhylogenyNode>();
             for( final PhylogenyNodeIterator it = iteratorPostorder(); it.hasNext(); ) {
                 final PhylogenyNode n = it.next();
                 if ( n.isExternal() ) {
@@ -441,7 +441,7 @@ public class Phylogeny {
         if ( isEmpty() ) {
             return null;
         }
-        final List<PhylogenyNode> nodes = new ArrayList<>();
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( n.getName().equals( name ) ) {
@@ -455,7 +455,7 @@ public class Phylogeny {
         if ( isEmpty() ) {
             return null;
         }
-        final List<PhylogenyNode> nodes = new ArrayList<>();
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( n.getName() != null ) {
@@ -472,7 +472,7 @@ public class Phylogeny {
         if ( isEmpty() ) {
             return null;
         }
-        final List<PhylogenyNode> nodes = new ArrayList<>();
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
@@ -486,7 +486,7 @@ public class Phylogeny {
         if ( isEmpty() ) {
             return null;
         }
-        final List<PhylogenyNode> nodes = new ArrayList<>();
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getSymbol().equals( seq_name ) ) {
@@ -500,7 +500,7 @@ public class Phylogeny {
         if ( isEmpty() ) {
             return null;
         }
-        final List<PhylogenyNode> nodes = new ArrayList<>();
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getGeneName().equals( seq_name ) ) {
@@ -514,7 +514,7 @@ public class Phylogeny {
         if ( isEmpty() ) {
             return null;
         }
-        final List<PhylogenyNode> nodes = new ArrayList<>();
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( n.getNodeData().isHasTaxonomy()
@@ -539,7 +539,7 @@ public class Phylogeny {
         if ( isEmpty() ) {
             return null;
         }
-        final List<PhylogenyNode> nodes = new ArrayList<>();
+        final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( PhylogenyMethods.getSpecies( n ).equals( specname ) ) {
@@ -638,8 +638,8 @@ public class Phylogeny {
     public List<PhylogenyNode> getParalogousNodes( final PhylogenyNode n, final String[] taxonomyCodeRange ) {
         PhylogenyNode node = n;
         PhylogenyNode prev = null;
-        final List<PhylogenyNode> v = new ArrayList<>();
-        final Map<PhylogenyNode, List<String>> map = new HashMap<>();
+        final List<PhylogenyNode> v = new ArrayList<PhylogenyNode>();
+        final Map<PhylogenyNode, List<String>> map = new HashMap<PhylogenyNode, List<String>>();
         getTaxonomyMap( getRoot(), map );
         if ( !node.isExternal() || isEmpty() ) {
             return null;
@@ -670,7 +670,7 @@ public class Phylogeny {
 
     public Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> getRelevantSequenceRelationTypes() {
         if ( _relevant_sequence_relation_types == null ) {
-            _relevant_sequence_relation_types = new Vector<>();
+            _relevant_sequence_relation_types = new Vector<SequenceRelation.SEQUENCE_RELATION_TYPE>();
         }
         return _relevant_sequence_relation_types;
     }
@@ -1208,7 +1208,7 @@ public class Phylogeny {
      * @return List node with the same taxonomy identifier
      */
     private List<PhylogenyNode> getNodeByTaxonomyID( final String taxonomyID, final List<PhylogenyNode> nodes ) {
-        final List<PhylogenyNode> retour = new ArrayList<>();
+        final List<PhylogenyNode> retour = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNode node : nodes ) {
             if ( taxonomyID.equals( PhylogenyMethods.getTaxonomyIdentifier( node ) ) ) {
                 retour.add( node );
@@ -1226,7 +1226,7 @@ public class Phylogeny {
      * @return species contains in all leaf under the param node
      */
     private List<String> getSubNodeTaxonomy( final PhylogenyNode node ) {
-        final List<String> taxonomyList = new ArrayList<>();
+        final List<String> taxonomyList = new ArrayList<String>();
         final List<PhylogenyNode> childs = node.getAllExternalDescendants();
         String speciesId = null;
         for( final PhylogenyNode phylogenyNode : childs ) {

diff --git a/forester/java/src/org/forester/rio/RIOUtil.java b/forester/java/src/org/forester/rio/RIOUtil.java
index 89b753c..638a757 100644 (file)
--- a/forester/java/src/org/forester/rio/RIOUtil.java
+++ b/forester/java/src/org/forester/rio/RIOUtil.java
@@ -6,7 +6,10 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.math.RoundingMode;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
 import java.util.SortedMap;
 import java.util.SortedSet;
 import java.util.TreeSet;
@@ -425,6 +428,14 @@ public final class RIOUtil {
         }
         if ( !replace_ids && id_map != null && id_map.size() > 0 ) {
             w.println();
+            
+            final Iterator<?> it = id_map.entrySet().iterator();
+            while (it.hasNext()) {
+                Map.Entry<String, String> pair = ( Entry<String, String> ) it.next();
+                w.println( pair.getKey()  + "\t" + pair.getValue() );
+            } //TODO
+            
+            /*
             id_map.forEach( ( k, v ) -> {
                 try {
                     w.println( k + "\t" + v );
@@ -432,7 +443,7 @@ public final class RIOUtil {
                 catch ( final IOException e ) {
                     //ignore
                 }
-            } );
+            } );*/
         }
         w.close();
         if ( verbose ) {

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index e3666a8..bbe2591 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -1136,7 +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<>();
+            final List<Boolean> covered = new ArrayList<Boolean>();
             covered.add( true ); // 0
             covered.add( false ); // 1
             covered.add( true ); // 2
@@ -1368,7 +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<>();
+            final List<Boolean> covered = new ArrayList<Boolean>();
             covered.add( true ); // 0
             covered.add( false ); // 1
             covered.add( true ); // 2
@@ -1890,25 +1890,25 @@ public final class Test {
     }
 
     private static boolean testCommonPrefix() {
-        final List<String> l0 = new ArrayList<>();
+        final List<String> l0 = new ArrayList<String>();
         l0.add( "abc" );
         if ( !ForesterUtil.greatestCommonPrefix( l0 ).equals( "abc" ) ) {
             return false;
         }
-        final List<String> l1 = new ArrayList<>();
+        final List<String> l1 = new ArrayList<String>();
         l1.add( "abc" );
         l1.add( "abX" );
         if ( !ForesterUtil.greatestCommonPrefix( l1 ).equals( "ab" ) ) {
             return false;
         }
-        final List<String> l2 = new ArrayList<>();
+        final List<String> l2 = new ArrayList<String>();
         l2.add( "abc" );
         l2.add( "abX" );
         l2.add( "axy" );
         if ( !ForesterUtil.greatestCommonPrefix( l2 ).equals( "a" ) ) {
             return false;
         }
-        final List<String> l3 = new ArrayList<>();
+        final List<String> l3 = new ArrayList<String>();
         l3.add( "abXsdfsdfsdfsdfsdfsd" );
         l3.add( "abXsdfsdfsdfsdfsdfsd" );
         l3.add( "abc" );
@@ -1919,7 +1919,7 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l3 ).equals( "ab" ) ) {
             return false;
         }
-        final List<String> l4 = new ArrayList<>();
+        final List<String> l4 = new ArrayList<String>();
         l4.add( "abXsdfsdfsdfsdfsdfsd" );
         l4.add( "abXsdfsdfsdfsdfsdfsd" );
         l4.add( "abc" );
@@ -1929,12 +1929,12 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l4 ).equals( "" ) ) {
             return false;
         }
-        final List<String> l5 = new ArrayList<>();
+        final List<String> l5 = new ArrayList<String>();
         l5.add( "" );
         if ( !ForesterUtil.greatestCommonPrefix( l5 ).equals( "" ) ) {
             return false;
         }
-        final List<String> l6 = new ArrayList<>();
+        final List<String> l6 = new ArrayList<String>();
         l6.add( "abc" );
         l6.add( "abX" );
         l6.add( "" );
@@ -1945,25 +1945,25 @@ public final class Test {
     }
 
     private static boolean testCommonPrefixSep() {
-        final List<String> l0 = new ArrayList<>();
+        final List<String> l0 = new ArrayList<String>();
         l0.add( "a.b.c" );
         if ( !ForesterUtil.greatestCommonPrefix( l0, "." ).equals( "a.b.c" ) ) {
             return false;
         }
-        final List<String> l1 = new ArrayList<>();
+        final List<String> l1 = new ArrayList<String>();
         l1.add( "a.b.c" );
         l1.add( "a.b.X" );
         if ( !ForesterUtil.greatestCommonPrefix( l1, "." ).equals( "a.b" ) ) {
             return false;
         }
-        final List<String> l2 = new ArrayList<>();
+        final List<String> l2 = new ArrayList<String>();
         l2.add( "a.b.c." );
         l2.add( "a.b.X." );
         l2.add( "a.x.y." );
         if ( !ForesterUtil.greatestCommonPrefix( l2, "." ).equals( "a" ) ) {
             return false;
         }
-        final List<String> l3 = new ArrayList<>();
+        final List<String> l3 = new ArrayList<String>();
         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" );
@@ -1974,7 +1974,7 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l3, "/" ).equals( "a/b" ) ) {
             return false;
         }
-        final List<String> l4 = new ArrayList<>();
+        final List<String> l4 = new ArrayList<String>();
         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" );
@@ -1984,18 +1984,18 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l4, "." ).equals( "" ) ) {
             return false;
         }
-        final List<String> l5 = new ArrayList<>();
+        final List<String> l5 = new ArrayList<String>();
         l5.add( "" );
         if ( !ForesterUtil.greatestCommonPrefix( l5, "_" ).equals( "" ) ) {
             return false;
         }
-        final List<String> l6 = new ArrayList<>();
+        final List<String> l6 = new ArrayList<String>();
         l6.add( "_" );
         l6.add( "__" );
         if ( !ForesterUtil.greatestCommonPrefix( l6, "_" ).equals( "" ) ) {
             return false;
         }
-        final List<String> l7 = new ArrayList<>();
+        final List<String> l7 = new ArrayList<String>();
         l7.add( "a,b,c" );
         l7.add( "a,b,X" );
         l7.add( "" );
@@ -2003,21 +2003,21 @@ public final class Test {
         if ( !ForesterUtil.greatestCommonPrefix( l7, "," ).equals( "" ) ) {
             return false;
         }
-        final List<String> l8 = new ArrayList<>();
+        final List<String> l8 = new ArrayList<String>();
         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<>();
+        final List<String> l9 = new ArrayList<String>();
         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<>();
+        final List<String> l10 = new ArrayList<String>();
         l10.add( "abcde" );
         l10.add( "adc" );
         if ( !ForesterUtil.greatestCommonPrefix( l10, "." ).equals( "" ) ) {
@@ -3206,7 +3206,7 @@ public final class Test {
             p.addProteinDomain( A20 );
             p.addProteinDomain( B25 );
             p.addProteinDomain( D80 );
-            List<String> domains_ids = new ArrayList<>();
+            List<String> domains_ids = new ArrayList<String>();
             domains_ids.add( "A" );
             domains_ids.add( "B" );
             domains_ids.add( "C" );
@@ -3223,7 +3223,7 @@ public final class Test {
             if ( p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<>();
+            domains_ids = new ArrayList<String>();
             domains_ids.add( "A" );
             domains_ids.add( "C" );
             domains_ids.add( "D" );
@@ -3233,7 +3233,7 @@ public final class Test {
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<>();
+            domains_ids = new ArrayList<String>();
             domains_ids.add( "A" );
             domains_ids.add( "D" );
             domains_ids.add( "C" );
@@ -3243,7 +3243,7 @@ public final class Test {
             if ( p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<>();
+            domains_ids = new ArrayList<String>();
             domains_ids.add( "A" );
             domains_ids.add( "A" );
             domains_ids.add( "B" );
@@ -3253,7 +3253,7 @@ public final class Test {
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<>();
+            domains_ids = new ArrayList<String>();
             domains_ids.add( "A" );
             domains_ids.add( "A" );
             domains_ids.add( "A" );
@@ -3265,7 +3265,7 @@ public final class Test {
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<>();
+            domains_ids = new ArrayList<String>();
             domains_ids.add( "A" );
             domains_ids.add( "A" );
             domains_ids.add( "B" );
@@ -3294,7 +3294,7 @@ public final class Test {
 
     private static boolean testBasicTable() {
         try {
-            final BasicTable<String> t0 = new BasicTable<>();
+            final BasicTable<String> t0 = new BasicTable<String>();
             if ( t0.getNumberOfColumns() != 0 ) {
                 return false;
             }
@@ -3993,7 +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<>();
+            final ArrayList<PhylogenyData> domains0 = new ArrayList<PhylogenyData>();
             domains0.add( d2 );
             domains0.add( d0 );
             domains0.add( d3 );
@@ -4012,7 +4012,7 @@ public final class Test {
             if ( ds1.getNumberOfDomains() != 4 ) {
                 return false;
             }
-            final ArrayList<PhylogenyData> domains1 = new ArrayList<>();
+            final ArrayList<PhylogenyData> domains1 = new ArrayList<PhylogenyData>();
             domains1.add( d1 );
             domains1.add( d2 );
             domains1.add( d4 );
@@ -5749,7 +5749,7 @@ public final class Test {
 
     private static boolean testGeneralTable() {
         try {
-            final GeneralTable<Integer, String> t0 = new GeneralTable<>();
+            final GeneralTable<Integer, String> t0 = new GeneralTable<Integer, String>();
             t0.setValue( 3, 2, "23" );
             t0.setValue( 10, 1, "error" );
             t0.setValue( 10, 1, "110" );
@@ -5785,7 +5785,7 @@ public final class Test {
             if ( !t0.getValueAsString( 22349, 3434344 ).equals( "" ) ) {
                 return false;
             }
-            final GeneralTable<String, String> t1 = new GeneralTable<>();
+            final GeneralTable<String, String> t1 = new GeneralTable<String, String>();
             t1.setValue( "3", "2", "23" );
             t1.setValue( "10", "1", "error" );
             t1.setValue( "10", "1", "110" );
@@ -6796,7 +6796,7 @@ public final class Test {
 
     private static boolean testMafft( final String path ) {
         try {
-            final List<String> opts = new ArrayList<>();
+            final List<String> opts = new ArrayList<String>();
             opts.add( "--maxiterate" );
             opts.add( "1000" );
             opts.add( "--localpair" );
@@ -6892,7 +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<>();
+            final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
             l.add( s0 );
             l.add( s1 );
             l.add( s2 );
@@ -6933,7 +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<>();
+            final List<MolecularSequence> l = new ArrayList<MolecularSequence>();
             l.add( s0 );
             l.add( s1 );
             l.add( s2 );
@@ -6956,7 +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<>();
+            final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
             l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
             l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
             l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
@@ -7000,7 +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<>();
+            final List<MolecularSequence> l0 = new ArrayList<MolecularSequence>();
             l0.add( s0 );
             l0.add( s1 );
             l0.add( s2 );
@@ -7048,7 +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<>();
+            final List<MolecularSequence> l1 = new ArrayList<MolecularSequence>();
             l1.add( s_0 );
             l1.add( s_1 );
             l1.add( s_2 );
@@ -7088,7 +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<>();
+            final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
             l2.add( s__0 );
             l2.add( s__1 );
             l2.add( s__2 );
@@ -7154,7 +7154,7 @@ public final class Test {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             PhylogenyNode n;
-            List<PhylogenyNode> ext = new ArrayList<>();
+            List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
             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 );
@@ -7189,7 +7189,7 @@ public final class Test {
             t1.getNode( "cd" ).setCollapse( true );
             t1.getNode( "cde" ).setCollapse( true );
             n = t1.getNode( "ab" );
-            ext = new ArrayList<>();
+            ext = new ArrayList<PhylogenyNode>();
             while ( n != null ) {
                 ext.add( n );
                 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
@@ -7220,7 +7220,7 @@ public final class Test {
             t2.getNode( "e" ).setCollapse( true );
             t2.getNode( "gh" ).setCollapse( true );
             n = t2.getNode( "ab" );
-            ext = new ArrayList<>();
+            ext = new ArrayList<PhylogenyNode>();
             while ( n != null ) {
                 ext.add( n );
                 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
@@ -7249,7 +7249,7 @@ public final class Test {
             t3.getNode( "gh" ).setCollapse( true );
             t3.getNode( "fgh" ).setCollapse( true );
             n = t3.getNode( "ab" );
-            ext = new ArrayList<>();
+            ext = new ArrayList<PhylogenyNode>();
             while ( n != null ) {
                 ext.add( n );
                 n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
@@ -12565,7 +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<>();
+            final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
             ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12578,13 +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<>();
+            Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12596,7 +12596,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12604,7 +12604,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
@@ -12613,7 +12613,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12622,20 +12622,20 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             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<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12644,14 +12644,14 @@ public final class Test {
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             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<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12659,13 +12659,13 @@ public final class Test {
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
@@ -12673,7 +12673,7 @@ public final class Test {
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12682,71 +12682,71 @@ public final class Test {
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             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<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             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<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             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<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             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<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12754,72 +12754,8 @@ public final class Test {
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            /////////
-            //            query_nodes = new HashSet<PhylogenyNode>();
-            //            query_nodes.add( new PhylogenyNode( "X" ) );
-            //            query_nodes.add( new PhylogenyNode( "Y" ) );
-            //            query_nodes.add( new PhylogenyNode( "A" ) );
-            //            query_nodes.add( new PhylogenyNode( "B" ) );
-            //            query_nodes.add( new PhylogenyNode( "C" ) );
-            //            query_nodes.add( new PhylogenyNode( "D" ) );
-            //            query_nodes.add( new PhylogenyNode( "E" ) );
-            //            query_nodes.add( new PhylogenyNode( "F" ) );
-            //            query_nodes.add( new PhylogenyNode( "G" ) );
-            //            if ( !s0.match( query_nodes ) ) {
-            //                return false;
-            //            }
-            //            query_nodes = new HashSet<PhylogenyNode>();
-            //            query_nodes.add( new PhylogenyNode( "X" ) );
-            //            query_nodes.add( new PhylogenyNode( "Y" ) );
-            //            query_nodes.add( new PhylogenyNode( "A" ) );
-            //            query_nodes.add( new PhylogenyNode( "B" ) );
-            //            query_nodes.add( new PhylogenyNode( "C" ) );
-            //            if ( !s0.match( query_nodes ) ) {
-            //                return false;
-            //            }
-            //            //
-            //            query_nodes = new HashSet<PhylogenyNode>();
-            //            query_nodes.add( new PhylogenyNode( "X" ) );
-            //            query_nodes.add( new PhylogenyNode( "Y" ) );
-            //            query_nodes.add( new PhylogenyNode( "D" ) );
-            //            query_nodes.add( new PhylogenyNode( "E" ) );
-            //            query_nodes.add( new PhylogenyNode( "F" ) );
-            //            query_nodes.add( new PhylogenyNode( "G" ) );
-            //            if ( !s0.match( query_nodes ) ) {
-            //                return false;
-            //            }
-            //            //
-            //            query_nodes = new HashSet<PhylogenyNode>();
-            //            query_nodes.add( new PhylogenyNode( "X" ) );
-            //            query_nodes.add( new PhylogenyNode( "Y" ) );
-            //            query_nodes.add( new PhylogenyNode( "A" ) );
-            //            query_nodes.add( new PhylogenyNode( "B" ) );
-            //            query_nodes.add( new PhylogenyNode( "C" ) );
-            //            query_nodes.add( new PhylogenyNode( "D" ) );
-            //            if ( !s0.match( query_nodes ) ) {
-            //                return false;
-            //            }
-            //            //
-            //            query_nodes = new HashSet<PhylogenyNode>();
-            //            query_nodes.add( new PhylogenyNode( "X" ) );
-            //            query_nodes.add( new PhylogenyNode( "Y" ) );
-            //            query_nodes.add( new PhylogenyNode( "E" ) );
-            //            query_nodes.add( new PhylogenyNode( "F" ) );
-            //            query_nodes.add( new PhylogenyNode( "G" ) );
-            //            if ( !s0.match( query_nodes ) ) {
-            //                return false;
-            //            }
-            //            //
-            //            query_nodes = new HashSet<PhylogenyNode>();
-            //            query_nodes.add( new PhylogenyNode( "X" ) );
-            //            query_nodes.add( new PhylogenyNode( "Y" ) );
-            //            query_nodes.add( new PhylogenyNode( "F" ) );
-            //            query_nodes.add( new PhylogenyNode( "G" ) );
-            //            if ( !s0.match( query_nodes ) ) {
-            //                return false;
-            //            }
-            //
-            query_nodes = new HashSet<>();
+           
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12828,7 +12764,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12836,9 +12772,8 @@ public final class Test {
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            ///////////////////////////
-            //
-            query_nodes = new HashSet<>();
+      
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12847,7 +12782,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12856,7 +12791,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12865,7 +12800,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12874,7 +12809,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12883,7 +12818,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
@@ -12891,7 +12826,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12901,7 +12836,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -12911,7 +12846,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12921,7 +12856,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -12943,7 +12878,7 @@ 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<>();
+            final Set<PhylogenyNode> ex = new HashSet<PhylogenyNode>();
             ex.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             ex.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12952,13 +12887,13 @@ 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<>();
+            Set<PhylogenyNode> query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12970,7 +12905,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12978,7 +12913,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
@@ -12987,7 +12922,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -12996,7 +12931,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
@@ -13004,14 +12939,14 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
@@ -13020,16 +12955,14 @@ public final class Test {
             if ( !s0.match( query_nodes ) ) {
                 return false;
             }
-            //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             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<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -13038,14 +12971,14 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
@@ -13054,7 +12987,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
@@ -13064,7 +12997,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
@@ -13072,49 +13005,49 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "C" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
             if ( s0.match( query_nodes ) ) {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
@@ -13122,7 +13055,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "B" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
@@ -13130,7 +13063,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );
@@ -13138,7 +13071,7 @@ public final class Test {
                 return false;
             }
             //
-            query_nodes = new HashSet<>();
+            query_nodes = new HashSet<PhylogenyNode>();
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "E" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "D" ) );
             query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "A" ) );

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 6c14975..f144a81 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<>();
+        final List<String> list = new ArrayList<String>();
         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<>();
+        final List<String> list = new ArrayList<String>();
         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<>();
+        final SortedSet<String> set = new TreeSet<String>();
         final BufferedReader in = new BufferedReader( new FileReader( file ) );
         String str;
         while ( ( str = in.readLine() ) != null ) {
@@ -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<>();
+        final SortedMap<Object, Integer> map = new TreeMap<Object, Integer>();
         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<>();
+        final List<String> result = new ArrayList<String>();
         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<>();
+        final List<Boolean> covered_positions = new ArrayList<Boolean>();
         for( final Domain domain : sorted ) {
             if ( ( ( max_allowed_overlap < 0 )
                     || ( ForesterUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
@@ -1686,7 +1686,7 @@ public final class 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<>();
+        final List<String> l = new ArrayList<String>();
         for( int i = 0; i < a.length; ++i ) {
             final StringBuilder sb = new StringBuilder();
             for( int j = 0; j <= i; ++j ) {