in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / tools / SequenceDataRetriver.java

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
index d389aec..3f4ddda 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
@@ -43,15 +43,16 @@ import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 import org.forester.util.SequenceIdParser;
-import org.forester.ws.uniprot.SequenceDatabaseEntry;
-import org.forester.ws.uniprot.SequenceDbWsTools;
+import org.forester.ws.seqdb.SequenceDatabaseEntry;
+import org.forester.ws.seqdb.SequenceDbWsTools;
 
 public final class SequenceDataRetriver extends RunnableProcess {
 
+    public final static int            DEFAULT_LINES_TO_RETURN = 50;
     private final Phylogeny            _phy;
     private final MainFrameApplication _mf;
     private final TreePanel            _treepanel;
-    private final static boolean       DEBUG = true;
+    private final static boolean       DEBUG                   = false;
 
     private enum Db {
         UNIPROT, EMBL, NCBI, NONE, REFSEQ;
@@ -67,7 +68,7 @@ public final class SequenceDataRetriver extends RunnableProcess {
         start( _mf, "sequence data" );
         SortedSet<String> not_found = null;
         try {
-            not_found = obtainSeqInformation( _phy );
+            not_found = obtainSeqInformation( _phy, false, true );
         }
         catch ( final UnknownHostException e ) {
             final String what = "_"; //TODO FIXME 
@@ -141,14 +142,18 @@ public final class SequenceDataRetriver extends RunnableProcess {
         }
     }
 
-    public static SortedSet<String> obtainSeqInformation( final Phylogeny phy ) throws IOException {
+    public static SortedSet<String> obtainSeqInformation( final Phylogeny phy,
+                                                          final boolean ext_nodes_only,
+                                                          final boolean allow_to_set_taxonomic_data )
+            throws IOException {
         final SortedSet<String> not_found = new TreeSet<String>();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
-            final Sequence seq = node.getNodeData().isHasSequence() ?  node.getNodeData().getSequence() : new Sequence() ;
-            final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy() : new Taxonomy() ;
-            
-           
+            if ( ext_nodes_only && node.isInternal() ) {
+                continue;
+            }
+            final Sequence seq = node.getNodeData().isHasSequence() ? node.getNodeData().getSequence() : new Sequence();
+            final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy() : new Taxonomy();
             String query = null;
             Identifier id = null;
             Db db = Db.NONE;
@@ -173,39 +178,40 @@ public final class SequenceDataRetriver extends RunnableProcess {
                     db = Db.UNIPROT;
                 }
                 else 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;
                     }
-                   
                 }
             }
+            if ( db == Db.NONE ) {
+                not_found.add( node.getName() );
+            }
             SequenceDatabaseEntry db_entry = null;
             if ( !ForesterUtil.isEmpty( query ) ) {
                 if ( db == Db.UNIPROT ) {
                     if ( DEBUG ) {
                         System.out.println( "uniprot: " + query );
                     }
-                    db_entry = SequenceDbWsTools.obtainUniProtEntry( query, 200 );
+                    db_entry = SequenceDbWsTools.obtainUniProtEntry( query, DEFAULT_LINES_TO_RETURN );
                 }
                 if ( ( db == Db.EMBL ) || ( ( db == Db.UNIPROT ) && ( db_entry == null ) ) ) {
                     if ( DEBUG ) {
                         System.out.println( "embl: " + query );
                     }
-                    db_entry = SequenceDbWsTools.obtainEmblEntry(  new Identifier( query ), 200 );
+                    db_entry = SequenceDbWsTools.obtainEmblEntry( new Identifier( query ), DEFAULT_LINES_TO_RETURN );
                     if ( ( db == Db.UNIPROT ) && ( db_entry != null ) ) {
                         db = Db.EMBL;
                     }
                 }
             }
             else if ( ( db == Db.REFSEQ ) && ( id != null ) ) {
-                db_entry = SequenceDbWsTools.obtainRefSeqEntryFromEmbl( id, 200 );
+                db_entry = SequenceDbWsTools.obtainRefSeqEntryFromEmbl( id, DEFAULT_LINES_TO_RETURN );
             }
             else if ( ( db == Db.NCBI ) && ( id != null ) ) {
-                db_entry = SequenceDbWsTools.obtainEmblEntry( id, 200 );
+                db_entry = SequenceDbWsTools.obtainEmblEntry( id, DEFAULT_LINES_TO_RETURN );
             }
             if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
                 if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) {
@@ -233,7 +239,7 @@ public final class SequenceDataRetriver extends RunnableProcess {
                 if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
                     tax.setScientificName( db_entry.getTaxonomyScientificName() );
                 }
-                if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyIdentifier() ) ) {
+                if ( allow_to_set_taxonomic_data && !ForesterUtil.isEmpty( db_entry.getTaxonomyIdentifier() ) ) {
                     tax.setIdentifier( new Identifier( db_entry.getTaxonomyIdentifier(), "uniprot" ) );
                 }
                 node.getNodeData().setTaxonomy( tax );
@@ -242,6 +248,11 @@ public final class SequenceDataRetriver extends RunnableProcess {
             else if ( db != Db.NONE ) {
                 not_found.add( node.getName() );
             }
+            try {
+                Thread.sleep( 10 );// Sleep for 10 ms
+            }
+            catch ( final InterruptedException ie ) {
+            }
         }
         return not_found;
     }