X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyMethods.java;h=c3fbc95cb6b32731f0ee22c3525775f5cf7a21a9;hb=5cad5dbd4f9e8cf09a123d4ee490cf314c05fd2f;hp=459138beb2900ed34234c3ef77356b99512ea51c;hpb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 459138b..c3fbc95 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -107,7 +107,7 @@ public class PhylogenyMethods {
         return could_extract;
     }
 
-    public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
+    public static DescriptiveStatistics calculateBranchLengthStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
@@ -118,7 +118,7 @@ public class PhylogenyMethods {
         return stats;
     }
 
-    public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
+    public static List<DescriptiveStatistics> calculateConfidenceStatistics( final Phylogeny phy ) {
         final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
@@ -133,7 +133,7 @@ public class PhylogenyMethods {
                             if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
                                 if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
                                     throw new IllegalArgumentException( "support values in node [" + n.toString()
-                                                                        + "] appear inconsistently ordered" );
+                                            + "] appear inconsistently ordered" );
                                 }
                             }
                             stats.get( i ).setDescription( c.getType() );
@@ -305,7 +305,7 @@ public class PhylogenyMethods {
         return x;
     }
 
-    public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
+    public static DescriptiveStatistics calculateNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
@@ -936,12 +936,46 @@ public class PhylogenyMethods {
         }
     }
 
+    private static enum NDF {
+        NodeName( "NN" ),
+        TaxonomyCode( "TC" ),
+        TaxonomyCommonName( "CN" ),
+        TaxonomyScientificName( "TS" ),
+        TaxonomyIdentifier( "TI" ),
+        TaxonomySynonym( "SY" ),
+        SequenceName( "SN" ),
+        GeneName( "GN" ),
+        SequenceSymbol( "SS" ),
+        SequenceAccession( "SA" ),
+        Domain( "DO" ),
+        Annotation( "AN" ),
+        CrossRef( "XR" ),
+        BinaryCharacter( "BC" ),
+        MolecularSequence( "MS" );
+
+        private final String _text;
+
+        NDF( final String text ) {
+            _text = text;
+        }
+
+        public static NDF fromString( final String text ) {
+            for( final NDF n : NDF.values() ) {
+                if ( text.startsWith( n._text ) ) {
+                    return n;
+                }
+            }
+            return null;
+        }
+    }
+
     public static List<PhylogenyNode> searchData( final String query,
                                                   final Phylogeny phy,
                                                   final boolean case_sensitive,
                                                   final boolean partial,
                                                   final boolean regex,
-                                                  final boolean search_domains ) {
+                                                  final boolean search_domains,
+                                                  final double domains_confidence_threshold ) {
         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         if ( phy.isEmpty() || ( query == null ) ) {
             return nodes;
@@ -949,125 +983,160 @@ public class PhylogenyMethods {
         if ( ForesterUtil.isEmpty( query ) ) {
             return nodes;
         }
+        String my_query = query;
+        NDF ndf = null;
+        if ( ( my_query.length() > 2 ) && ( my_query.indexOf( ":" ) == 2 ) ) {
+            ndf = NDF.fromString( my_query );
+            if ( ndf != null ) {
+                my_query = my_query.substring( 3 );
+            }
+        }
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             boolean match = false;
-            if ( match( node.getName(), query, case_sensitive, partial, regex ) ) {
+            if ( ( ( ndf == null ) || ( ndf == NDF.NodeName ) )
+                    && match( node.getName(), my_query, case_sensitive, partial, regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy()
-                    && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial, regex ) ) {
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCode ) )
+                    && node.getNodeData().isHasTaxonomy()
+                    && match( node.getNodeData().getTaxonomy().getTaxonomyCode(),
+                              my_query,
+                              case_sensitive,
+                              partial,
+                              regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy()
-                    && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial, regex ) ) {
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCommonName ) )
+                    && node.getNodeData().isHasTaxonomy()
+                    && match( node.getNodeData().getTaxonomy().getCommonName(),
+                              my_query,
+                              case_sensitive,
+                              partial,
+                              regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy()
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyScientificName ) )
+                    && node.getNodeData().isHasTaxonomy()
                     && match( node.getNodeData().getTaxonomy().getScientificName(),
-                              query,
+                              my_query,
                               case_sensitive,
                               partial,
                               regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy()
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyIdentifier ) )
+                    && node.getNodeData().isHasTaxonomy()
                     && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
                     && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
-                              query,
+                              my_query,
                               case_sensitive,
                               partial,
                               regex ) ) {
                 match = true;
             }
-            else if ( node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
+            else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomySynonym ) ) && node.getNodeData().isHasTaxonomy()
+                    && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
                 final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
                 I: for( final String syn : syns ) {
-                    if ( match( syn, query, case_sensitive, partial, regex ) ) {
+                    if ( match( syn, my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break I;
                     }
                 }
             }
-            if ( !match && node.getNodeData().isHasSequence()
-                    && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial, regex ) ) {
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceName ) ) && node.getNodeData().isHasSequence()
+                    && match( node.getNodeData().getSequence().getName(), my_query, case_sensitive, partial, regex ) ) {
                 match = true;
             }
-            if ( !match && node.getNodeData().isHasSequence()
-                    && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial, regex ) ) {
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.GeneName ) ) && node.getNodeData().isHasSequence()
+                    && match( node.getNodeData().getSequence().getGeneName(), my_query, case_sensitive, partial, regex ) ) {
                 match = true;
             }
-            if ( !match && node.getNodeData().isHasSequence()
-                    && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial, regex ) ) {
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceSymbol ) ) && node.getNodeData().isHasSequence()
+                    && match( node.getNodeData().getSequence().getSymbol(), my_query, case_sensitive, partial, regex ) ) {
                 match = true;
             }
             if ( !match
+                    && ( ( ndf == null ) || ( ndf == NDF.SequenceAccession ) )
                     && node.getNodeData().isHasSequence()
                     && ( node.getNodeData().getSequence().getAccession() != null )
                     && match( node.getNodeData().getSequence().getAccession().getValue(),
-                              query,
+                              my_query,
                               case_sensitive,
                               partial,
                               regex ) ) {
                 match = true;
             }
-            if ( search_domains && !match && node.getNodeData().isHasSequence()
+            if ( !match && ( ( ( ndf == null ) && search_domains ) || ( ndf == NDF.Domain ) )
+                    && node.getNodeData().isHasSequence()
                     && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
                 final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
                 I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
-                    if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial, regex ) ) {
+                    if ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold )
+                            && ( match( da.getDomain( i ).getName(), my_query, case_sensitive, partial, regex ) ) ) {
                         match = true;
                         break I;
                     }
                 }
             }
-            if ( !match && node.getNodeData().isHasSequence()
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.Annotation ) ) && node.getNodeData().isHasSequence()
                     && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
                 for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
-                    if ( match( ann.getDesc(), query, case_sensitive, partial, regex ) ) {
+                    if ( match( ann.getDesc(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break;
                     }
-                    if ( match( ann.getRef(), query, case_sensitive, partial, regex ) ) {
+                    if ( match( ann.getRef(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break;
                     }
                 }
             }
-            if ( !match && node.getNodeData().isHasSequence()
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.CrossRef ) ) && node.getNodeData().isHasSequence()
                     && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
                 for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
-                    if ( match( x.getComment(), query, case_sensitive, partial, regex ) ) {
+                    if ( match( x.getComment(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break;
                     }
-                    if ( match( x.getSource(), query, case_sensitive, partial, regex ) ) {
+                    if ( match( x.getSource(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break;
                     }
-                    if ( match( x.getValue(), query, case_sensitive, partial, regex ) ) {
+                    if ( match( x.getValue(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break;
                     }
                 }
             }
-            //
-            if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+            if ( !match && ( ( ndf == null ) || ( ndf == NDF.BinaryCharacter ) )
+                    && ( node.getNodeData().getBinaryCharacters() != null ) ) {
                 Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
                 I: while ( it.hasNext() ) {
-                    if ( match( it.next(), query, case_sensitive, partial, regex ) ) {
+                    if ( match( it.next(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break I;
                     }
                 }
                 it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
                 I: while ( it.hasNext() ) {
-                    if ( match( it.next(), query, case_sensitive, partial, regex ) ) {
+                    if ( match( it.next(), my_query, case_sensitive, partial, regex ) ) {
                         match = true;
                         break I;
                     }
                 }
             }
+            if ( !match
+                    && ( ndf == NDF.MolecularSequence )
+                    && node.getNodeData().isHasSequence()
+                    && match( node.getNodeData().getSequence().getMolecularSequence(),
+                              my_query,
+                              case_sensitive,
+                              true,
+                              regex ) ) {
+                match = true;
+            }
             if ( match ) {
                 nodes.add( node );
             }
@@ -1079,7 +1148,8 @@ public class PhylogenyMethods {
                                                             final Phylogeny phy,
                                                             final boolean case_sensitive,
                                                             final boolean partial,
-                                                            final boolean search_domains ) {
+                                                            final boolean search_domains,
+                                                            final double domains_confidence_threshold ) {
         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
         if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
             return nodes;
@@ -1087,15 +1157,28 @@ public class PhylogenyMethods {
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             boolean all_matched = true;
-            for( final String query : queries ) {
+            for( String query : queries ) {
+                if ( query == null ) {
+                    continue;
+                }
+                query = query.trim();
+                NDF ndf = null;
+                if ( ( query.length() > 2 ) && ( query.indexOf( ":" ) == 2 ) ) {
+                    ndf = NDF.fromString( query );
+                    if ( ndf != null ) {
+                        query = query.substring( 3 );
+                    }
+                }
                 boolean match = false;
                 if ( ForesterUtil.isEmpty( query ) ) {
                     continue;
                 }
-                if ( match( node.getName(), query, case_sensitive, partial, false ) ) {
+                if ( ( ( ndf == null ) || ( ndf == NDF.NodeName ) )
+                        && match( node.getName(), query, case_sensitive, partial, false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCode ) )
+                        && node.getNodeData().isHasTaxonomy()
                         && match( node.getNodeData().getTaxonomy().getTaxonomyCode(),
                                   query,
                                   case_sensitive,
@@ -1103,7 +1186,8 @@ public class PhylogenyMethods {
                                   false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCommonName ) )
+                        && node.getNodeData().isHasTaxonomy()
                         && match( node.getNodeData().getTaxonomy().getCommonName(),
                                   query,
                                   case_sensitive,
@@ -1111,7 +1195,8 @@ public class PhylogenyMethods {
                                   false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyScientificName ) )
+                        && node.getNodeData().isHasTaxonomy()
                         && match( node.getNodeData().getTaxonomy().getScientificName(),
                                   query,
                                   case_sensitive,
@@ -1119,7 +1204,8 @@ public class PhylogenyMethods {
                                   false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyIdentifier ) )
+                        && node.getNodeData().isHasTaxonomy()
                         && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
                         && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
                                   query,
@@ -1128,7 +1214,7 @@ public class PhylogenyMethods {
                                   false ) ) {
                     match = true;
                 }
-                else if ( node.getNodeData().isHasTaxonomy()
+                else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomySynonym ) ) && node.getNodeData().isHasTaxonomy()
                         && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
                     final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
                     I: for( final String syn : syns ) {
@@ -1138,20 +1224,23 @@ public class PhylogenyMethods {
                         }
                     }
                 }
-                if ( !match && node.getNodeData().isHasSequence()
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceName ) ) && node.getNodeData().isHasSequence()
                         && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial, false ) ) {
                     match = true;
                 }
                 if ( !match
+                        && ( ( ndf == null ) || ( ndf == NDF.GeneName ) )
                         && node.getNodeData().isHasSequence()
                         && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial, false ) ) {
                     match = true;
                 }
-                if ( !match && node.getNodeData().isHasSequence()
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceSymbol ) )
+                        && node.getNodeData().isHasSequence()
                         && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial, false ) ) {
                     match = true;
                 }
                 if ( !match
+                        && ( ( ndf == null ) || ( ndf == NDF.SequenceAccession ) )
                         && node.getNodeData().isHasSequence()
                         && ( node.getNodeData().getSequence().getAccession() != null )
                         && match( node.getNodeData().getSequence().getAccession().getValue(),
@@ -1161,18 +1250,19 @@ public class PhylogenyMethods {
                                   false ) ) {
                     match = true;
                 }
-                if ( search_domains && !match && node.getNodeData().isHasSequence()
+                if ( !match && ( ( ( ndf == null ) && search_domains ) || ( ndf == NDF.Domain ) )
+                        && node.getNodeData().isHasSequence()
                         && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
                     final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
                     I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
-                        if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial, false ) ) {
+                        if ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold )
+                                && match( da.getDomain( i ).getName(), query, case_sensitive, partial, false ) ) {
                             match = true;
                             break I;
                         }
                     }
                 }
-                //
-                if ( !match && node.getNodeData().isHasSequence()
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.Annotation ) ) && node.getNodeData().isHasSequence()
                         && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
                     for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
                         if ( match( ann.getDesc(), query, case_sensitive, partial, false ) ) {
@@ -1185,7 +1275,7 @@ public class PhylogenyMethods {
                         }
                     }
                 }
-                if ( !match && node.getNodeData().isHasSequence()
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.CrossRef ) ) && node.getNodeData().isHasSequence()
                         && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
                     for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
                         if ( match( x.getComment(), query, case_sensitive, partial, false ) ) {
@@ -1202,8 +1292,8 @@ public class PhylogenyMethods {
                         }
                     }
                 }
-                //
-                if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+                if ( !match && ( ( ndf == null ) || ( ndf == NDF.BinaryCharacter ) )
+                        && ( node.getNodeData().getBinaryCharacters() != null ) ) {
                     Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
                     I: while ( it.hasNext() ) {
                         if ( match( it.next(), query, case_sensitive, partial, false ) ) {
@@ -1219,6 +1309,16 @@ public class PhylogenyMethods {
                         }
                     }
                 }
+                if ( !match
+                        && ( ndf == NDF.MolecularSequence )
+                        && node.getNodeData().isHasSequence()
+                        && match( node.getNodeData().getSequence().getMolecularSequence(),
+                                  query,
+                                  case_sensitive,
+                                  true,
+                                  false ) ) {
+                    match = true;
+                }
                 if ( !match ) {
                     all_matched = false;
                     break;
@@ -1365,7 +1465,7 @@ public class PhylogenyMethods {
             else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )
                     && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )
                     && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n
-                                                                                                              .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {
+                            .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {
                 nodes_to_delete.add( n );
             }
         }
@@ -1502,7 +1602,7 @@ public class PhylogenyMethods {
                             n.setName( "" );
                         }
                         n.getNodeData().getTaxonomy()
-                        .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+                                .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
                         break;
                     }
                     case TAXONOMY_ID_UNIPROT_2: {
@@ -1518,7 +1618,7 @@ public class PhylogenyMethods {
                             n.setName( "" );
                         }
                         n.getNodeData().getTaxonomy()
-                        .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+                                .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
                         break;
                     }
                     case TAXONOMY_ID: {