in progress

[jalview.git] / forester / java / src / org / forester / ws / seqdb / UniProtEntry.java

diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
index 77ebe4e..3f0df32 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
@@ -54,6 +54,8 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
     public final static Pattern  PharmGKB_PATTERN  = Pattern.compile( "PharmGKB;\\s+([0-9A-Z]+);" );
     public final static Pattern  Reactome_PATTERN  = Pattern.compile( "Reactome;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
     public final static Pattern  HGNC_PATTERN      = Pattern.compile( "HGNC;\\s+HGNC:(\\d+);" );
+    public final static Pattern  NCBI_TAXID_PATTERN= Pattern.compile( "NCBI_TaxID=(\\d+)" );
+    
     private String               _ac;
     private SortedSet<Accession> _cross_references;
     private String               _gene_name;
@@ -123,7 +125,7 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
                 && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() )
                 && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() )
                 && ForesterUtil.isEmpty( getSequenceSymbol() ) && ( ( getGoTerms() == null ) || getGoTerms().isEmpty() ) && ( ( getCrossReferences() == null ) || getCrossReferences()
-                .isEmpty() ) );
+                        .isEmpty() ) );
     }
 
     private void addCrossReference( final Accession accession ) {
@@ -190,20 +192,43 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
             }
             else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceName() ) ) {
                 if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
-                    e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
+                    if ( line.indexOf( "{" ) > 0  ) {
+                        e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", "{" ) );
+                    }
+                    else {
+                        e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
+                    }
                 }
                 else if ( ( line.indexOf( "SubName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
-                    e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
+                    if ( line.indexOf( "{" ) > 0  ) {
+                        e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", "{" ) );
+                    }
+                    else {
+                        e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
+                    }
+                    
                 }
             }
             else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceSymbol() ) ) {
+              
                 if ( line.indexOf( "Short=" ) > 0 ) {
-                    e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", ";" ) );
+                    if ( line.indexOf( "{" ) > 0  ) {
+                        e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", "{" ) );
+                    }
+                    else {
+                        e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", ";" ) );
+                    }
+                   
                 }
             }
             else if ( line.startsWith( "GN" ) && ForesterUtil.isEmpty( e.getGeneName() ) ) {
                 if ( line.indexOf( "Name=" ) > 0 ) {
-                    e.setGeneName( SequenceDbWsTools.extractFromTo( line, "Name=", ";" ) );
+                    if ( line.indexOf( "{" ) > 0  ) {
+                        e.setGeneName( SequenceDbWsTools.extractFromTo( line, "Name=", "{" ) );
+                    }
+                    else {
+                        e.setGeneName( SequenceDbWsTools.extractFromTo( line, "Name=", ";" ) );
+                    }
                 }
             }
             else if ( line.startsWith( "DR" ) ) {
@@ -300,7 +325,10 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
             }
             else if ( line.startsWith( "OX" ) ) {
                 if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
-                    e.setTaxId( SequenceDbWsTools.extractFromTo( line, "NCBI_TaxID=", ";" ) );
+                    final Matcher m = NCBI_TAXID_PATTERN.matcher( line );
+                    if ( m.find() ) {
+                        e.setTaxId( m.group( 1 ) );
+                    }
                 }
             }
             else if ( line.startsWith( "SQ" ) ) {