in progress

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

diff --git a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
index f3ae59c..340fc3b 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
+++ b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
@@ -71,9 +71,10 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
         final Pattern mim_PATTERN = Pattern.compile( "\\s+/db_xref=\"MIM:(\\d+)\"" );
         final Pattern taxon_PATTERN = Pattern.compile( "\\s+/db_xref=\"taxon:(\\d+)\"" );
         final Pattern interpro_PATTERN = Pattern.compile( "\\s+/db_xref=\"InterPro:([A-Z0-9]+)\"" );
-        final Pattern uniprot_PATTERN = Pattern.compile( "\\s+/db_xref=\"UniProtKB/TrEMBL:(\\w+)\"" );
-        final Pattern hgnc_PATTERN = Pattern.compile( "\\s+/db_xref=\"HGNC:(\\d+)\"" );
+        final Pattern uniprot_PATTERN = Pattern.compile( "\\s+/db_xref=\"UniProtKB/[A-Za-z-]*:(\\w+)\"" );
+        final Pattern hgnc_PATTERN = Pattern.compile( "\\s+/db_xref=\"[A-Z:]*HGNC:(\\d+)\"" );
         final Pattern geneid_PATTERN = Pattern.compile( "\\s+/db_xref=\"GeneID:(\\d+)\"" );
+        final Pattern pdb_PATTERN = Pattern.compile( "\\s+/db_xref=\"PDB:([A-Z0-9]+)\"" );
         final Pattern ec_PATTERN = Pattern.compile( "\\s+/EC_number=\"([\\.\\-\\d]+)\"" );
         final Pattern product_PATTERN = Pattern.compile( "\\s+/product=\"(\\w{1,10})\"" );
         final EbiDbEntry e = new EbiDbEntry();
@@ -207,9 +208,17 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
                 in_protein = false;
             }
             if ( in_source ) {
-                final Matcher m = taxon_PATTERN.matcher( line );
-                if ( m.find() ) {
-                    e.setTaxId( m.group( 1 ) );
+                final Matcher ti = taxon_PATTERN.matcher( line );
+                if ( ti.find() ) {
+                    e.setTaxId( ti.group( 1 ) );
+                }
+                final Matcher chr = chromosome_PATTERN.matcher( line );
+                if ( chr.find() ) {
+                    e.setChromosome( chr.group( 1 ) );
+                }
+                final Matcher map = map_PATTERN.matcher( line );
+                if ( map.find() ) {
+                    e.setMap( map.group( 1 ) );
                 }
             }
             if ( in_cds || in_gene ) {
@@ -247,6 +256,10 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
                 if ( product.find() ) {
                     e.setSequenceSymbol( product.group( 1 ) );
                 }
+                final Matcher pdb = pdb_PATTERN.matcher( line );
+                if ( pdb.find() ) {
+                    e.addCrossReference( new Accession( pdb.group( 1 ), "pdb" ) );
+                }
             }
         }
         if ( def.length() > 0 ) {
@@ -254,7 +267,31 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
         }
         return e;
     }
+    private String _map;
+    private String _chromosome;
+
+    private void setMap( String map ) {
+        _map = map;
+        
+    }
+
+    private void setChromosome( String chromosome ) {
+        _chromosome = chromosome;
+        
+    }
 
+    @Override
+    public String getMap( ) {
+        return _map;
+        
+    }
+    @Override
+    public String  getChromosome() {
+        return _chromosome;
+        
+    }
+    
+    
     private static void x( final StringBuilder sb, final String s ) {
         if ( sb.length() > 0 ) {
             sb.append( " " );
@@ -575,7 +612,7 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
         return _symbol;
     }
 
-    private void setSequenceSymbol( String symbol ) {
+    private void setSequenceSymbol( final String symbol ) {
         _symbol = symbol;
     }