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[jalview.git] / forester / java / src / org / forester / ws / seqdb / SequenceDbWsTools.java
diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
index f370e3d..f5f83e4 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -162,10 +162,19 @@ public final class SequenceDbWsTools {
             String query = null;
             Identifier id = null;
             Db db = Db.NONE;
-            if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )
+            if ( node.getNodeData().isHasSequence()
+                    && ( node.getNodeData().getSequence().getAccession() != null )
                     && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
                     && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
-                    && node.getNodeData().getSequence().getAccession().getValue().toLowerCase().startsWith( "uniprot" ) ) {
+                    && ( node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
+                            .startsWith( "uniprot" )
+                            || node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
+                                    .startsWith( "swissprot" )
+                            || node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
+                                    .startsWith( "trembl" )
+                            || node.getNodeData().getSequence().getAccession().getValue().toLowerCase()
+                                    .startsWith( "sp" ) || node.getNodeData().getSequence().getAccession().getValue()
+                            .toLowerCase().startsWith( "uniprotkb" ) ) ) {
                 query = node.getNodeData().getSequence().getAccession().getValue();
                 db = Db.UNIPROT;
             }
@@ -178,21 +187,63 @@ public final class SequenceDbWsTools {
                 query = node.getNodeData().getSequence().getAccession().getValue();
                 db = Db.EMBL;
             }
-            else if ( !ForesterUtil.isEmpty( node.getName() ) ) {
+            else if ( node.getNodeData().isHasSequence()
+                    && ( node.getNodeData().getSequence().getAccession() != null )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
+                    && ( node.getNodeData().getSequence().getAccession().getValue().toLowerCase().startsWith( "ncbi" ) || node
+                            .getNodeData().getSequence().getAccession().getValue().toLowerCase().startsWith( "genbank" ) ) ) {
+                query = node.getNodeData().getSequence().getAccession().getValue();
+                // db = Db.NCBI;
+            }
+            else if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
+                    && node.getNodeData().getSequence().getAccession().getValue().toLowerCase().startsWith( "refseq" ) ) {
+                query = node.getNodeData().getSequence().getAccession().getValue();
+                db = Db.REFSEQ;
+            }
+            else {
                 if ( ( query = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node ) ) != null ) {
                     db = Db.UNIPROT;
                 }
-                else if ( ( id = SequenceIdParser.parse( node.getName() ) ) != null ) {
-                    if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
-                        db = Db.NCBI;
+                else if ( node.getNodeData().isHasSequence() ) {
+                    if ( ( id = SequenceIdParser.parse( node.getName() ) ) != null ) {
+                        if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                            //  db = Db.NCBI;
+                        }
+                        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                            db = Db.REFSEQ;
+                        }
                     }
-                    else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
-                        db = Db.REFSEQ;
+                    else if ( ( id = SequenceIdParser.parse( node.getNodeData().getSequence().getName() ) ) != null ) {
+                        if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                            // = Db.NCBI;
+                        }
+                        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                            db = Db.REFSEQ;
+                        }
+                    }
+                    else if ( ( id = SequenceIdParser.parse( node.getNodeData().getSequence().getGeneName() ) ) != null ) {
+                        if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                            // db = Db.NCBI;
+                        }
+                        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                            db = Db.REFSEQ;
+                        }
+                    }
+                    else if ( ( id = SequenceIdParser.parse( node.getNodeData().getSequence().getSymbol() ) ) != null ) {
+                        if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                            // db = Db.NCBI;
+                        }
+                        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                            db = Db.REFSEQ;
+                        }
                     }
                 }
             }
             if ( db == Db.NONE ) {
-                not_found.add( node.getName() );
+                not_found.add( node.toString() );
             }
             SequenceDatabaseEntry db_entry = null;
             if ( !ForesterUtil.isEmpty( query ) ) {
@@ -202,22 +253,31 @@ public final class SequenceDbWsTools {
                     }
                     db_entry = obtainUniProtEntry( query, lines_to_return );
                 }
-                if ( ( db == Db.EMBL ) || ( ( db == Db.UNIPROT ) && ( db_entry == null ) ) ) {
+                else if ( db == Db.EMBL ) {
                     if ( DEBUG ) {
                         System.out.println( "embl: " + query );
                     }
                     db_entry = obtainEmblEntry( new Identifier( query ), lines_to_return );
-                    if ( ( db == Db.UNIPROT ) && ( db_entry != null ) ) {
-                        db = Db.EMBL;
+                }
+                else if ( db == Db.REFSEQ ) {
+                    if ( DEBUG ) {
+                        System.out.println( "refseq: " + query );
                     }
+                    db_entry = obtainRefSeqEntryFromEmbl( new Identifier( query ), lines_to_return );
                 }
+                //   else if ( db == Db.NCBI ) {
+                //       if ( DEBUG ) {
+                //           System.out.println( "ncbi: " + query );
+                //       }
+                //       db_entry = obtainNcbiEntry( new Identifier( query ), lines_to_return );
+                //  }
             }
             else if ( ( db == Db.REFSEQ ) && ( id != null ) ) {
                 db_entry = obtainRefSeqEntryFromEmbl( id, lines_to_return );
             }
-            else if ( ( db == Db.NCBI ) && ( id != null ) ) {
-                db_entry = obtainEmblEntry( id, lines_to_return ); //TODO ?
-            }
+            //else if ( ( db == Db.NCBI ) && ( id != null ) ) {
+            //    db_entry = obtainNcbiEntry( id, lines_to_return );
+            //}
             if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
                 final Sequence seq = node.getNodeData().isHasSequence() ? node.getNodeData().getSequence()
                         : new Sequence();
@@ -229,9 +289,9 @@ public final class SequenceDbWsTools {
                     else if ( db == Db.UNIPROT ) {
                         type = "uniprot";
                     }
-                    else if ( db == Db.NCBI ) {
-                        type = "ncbi";
-                    }
+                    //   else if ( db == Db.NCBI ) {
+                    //       type = "ncbi";
+                    //   }
                     else if ( db == Db.REFSEQ ) {
                         type = "refseq";
                     }
@@ -241,23 +301,28 @@ public final class SequenceDbWsTools {
                     seq.setName( db_entry.getSequenceName() );
                 }
                 if ( !ForesterUtil.isEmpty( db_entry.getGeneName() ) ) {
-                    final String gn = db_entry.getGeneName().replace( ' ', '_' );
+                    seq.setGeneName( db_entry.getGeneName() );
+                }
+                if ( !ForesterUtil.isEmpty( db_entry.getSequenceSymbol() ) ) {
                     try {
-                        seq.setSymbol( gn );
+                        seq.setSymbol( db_entry.getSequenceSymbol() );
                     }
-                    catch ( PhyloXmlDataFormatException e ) {
+                    catch ( final PhyloXmlDataFormatException e ) {
                         // Eat this exception.
                     }
                 }
-                if ( !ForesterUtil.isEmpty( db_entry.getGeneName() ) ) {
-                  //  seq.addAnnotation( new Annotation( "GN", db_entry.getGeneName() ) );
-                }
-                if ( db_entry.getGoTerms() != null &&  !db_entry.getGoTerms().isEmpty() ) {
+                if ( ( db_entry.getGoTerms() != null ) && !db_entry.getGoTerms().isEmpty() ) {
                     for( final GoTerm go : db_entry.getGoTerms() ) {
-                        seq.addAnnotation( new Annotation( go.getGoId().getId(), go.getName() ) );
+                        final Annotation ann = new Annotation( go.getGoId().getId() );
+                        ann.setDesc( go.getName() );
+                        seq.addAnnotation( ann );
+                    }
+                }
+                if ( ( db_entry.getCrossReferences() != null ) && !db_entry.getCrossReferences().isEmpty() ) {
+                    for( final Accession x : db_entry.getCrossReferences() ) {
+                        seq.addCrossReference( x );
                     }
                 }
-                
                 final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy()
                         : new Taxonomy();
                 if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {