in progress

[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 29376bd..da16246 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -49,6 +49,7 @@ import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sequence.MolecularSequence.TYPE;
 import org.forester.util.ForesterUtil;
 import org.forester.util.SequenceAccessionTools;
 
@@ -56,13 +57,14 @@ public final class SequenceDbWsTools {
 
     public final static String   BASE_UNIPROT_URL        = "http://www.uniprot.org/";
     public final static int      DEFAULT_LINES_TO_RETURN = 4000;
-    //public final static String   EMBL_DBS_EMBL           = "embl";
     public final static String   EMBL_DBS_REFSEQ_N       = "refseqn";
     public final static String   EMBL_DBS_REFSEQ_P       = "refseqp";
     public final static String   EMBL_GENBANK            = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
     public final static String   EMBL_REFSEQ             = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=";
+    public final static String   EMBL_EMBL               = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id=";
     private final static boolean DEBUG                   = true;
     private final static String  URL_ENC                 = "UTF-8";
+    private final static int     SLEEP                   = 200;
 
     public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
                                                                            final int max_taxonomies_return )
@@ -249,7 +251,7 @@ public final class SequenceDbWsTools {
         in.close();
         try {
             // To prevent accessing online dbs in too quick succession. 
-            Thread.sleep( 20 );
+            Thread.sleep( SLEEP );
         }
         catch ( final InterruptedException e ) {
             e.printStackTrace();
@@ -257,28 +259,24 @@ public final class SequenceDbWsTools {
         return result;
     }
 
-    public static List<String> queryEmblDb( final Accession id, final int max_lines_to_return ) throws IOException {
+    public static List<String> queryEmblDb( final Accession acc, final int max_lines_to_return ) throws IOException {
         final StringBuilder url_sb = new StringBuilder();
         //  url_sb.append( BASE_EMBL_DB_URL );
-        if ( id.getSource().equals( Source.NCBI.toString() ) ) {
+        System.out.println( "source: " + acc.getSource() );
+        if ( acc.getSource().equals( Source.NCBI.toString() ) ) {
             url_sb.append( EMBL_GENBANK );
             //url_sb.append( '/' );
         }
-        else if ( id.getSource().equals( Source.REFSEQ.toString() ) ) {
+        else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
             url_sb.append( EMBL_REFSEQ );
-            //            if ( id.getValue().toUpperCase().indexOf( 'P' ) == 1 ) {
-            //                url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_P );
-            //                url_sb.append( '/' );
-            //            }
-            //            else {
-            //                url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_N );
-            //                url_sb.append( '/' );
-            //            }
+        }
+        else if ( acc.getSource().equals( Source.EMBL.toString() ) ) {
+            url_sb.append( EMBL_EMBL );
         }
         else {
-            throw new IllegalArgumentException( "unable to handle source: " + id.getSource() );
+            throw new IllegalArgumentException( "unable to handle source: " + acc.getSource() );
         }
-        return queryDb( id.getValue(), max_lines_to_return, url_sb.toString() );
+        return queryDb( acc.getValue(), max_lines_to_return, url_sb.toString() );
     }
 
     public static List<String> queryEmblDbForRefSeqEntry( final Accession id, final int max_lines_to_return )
@@ -330,20 +328,32 @@ public final class SequenceDbWsTools {
                 // Eat this, and move to next.
             }
         }
-        else if ( acc.getSource().equals( Source.EMBL.toString() ) ) {
+        else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
             if ( DEBUG ) {
-                System.out.println( "embl: " + query );
+                System.out.println( "refseq: " + query );
             }
             try {
-                db_entry = obtainEmblEntry( new Accession( query ), lines_to_return );
+                db_entry = obtainRefSeqEntryFromEmbl( new Accession( query ), lines_to_return );
             }
             catch ( final FileNotFoundException e ) {
                 // Eat this, and move to next.
             }
         }
-        else if ( acc.getSource().equals( Source.REFSEQ.toString() ) ) {
+        else if ( acc.getSource().equals( Source.EMBL.toString() ) || acc.getSource().equals( Source.NCBI.toString() )
+                || acc.getSource().equals( Source.EMBL.toString() ) ) {
             if ( DEBUG ) {
-                System.out.println( "refseq: " + query );
+                System.out.println( acc.toString() );
+            }
+            try {
+                db_entry = obtainEmblEntry( acc, lines_to_return );
+            }
+            catch ( final FileNotFoundException e ) {
+                // Eat this, and move to next.
+            }
+        }
+        else if ( acc.getSource().equals( Source.GI.toString() ) ) {
+            if ( DEBUG ) {
+                System.out.println( "gi: " + query );
             }
             try {
                 db_entry = obtainRefSeqEntryFromEmbl( new Accession( query ), lines_to_return );
@@ -371,6 +381,21 @@ public final class SequenceDbWsTools {
                     // Eat this exception.
                 }
             }
+            if ( ( db_entry.getMolecularSequence() != null )
+                    && !ForesterUtil.isEmpty( db_entry.getMolecularSequence().getMolecularSequenceAsString() )
+                    && seq.getMolecularSequence().isEmpty() ) {
+                seq.setMolecularSequence( db_entry.getMolecularSequence().getMolecularSequenceAsString() );
+                seq.setMolecularSequenceAligned( false );
+                if ( db_entry.getMolecularSequence().getType() == TYPE.AA ) {
+                    seq.setType( "protein" );
+                }
+                else if ( db_entry.getMolecularSequence().getType() == TYPE.DNA ) {
+                    seq.setType( "dna" );
+                }
+                else if ( db_entry.getMolecularSequence().getType() == TYPE.RNA ) {
+                    seq.setType( "rna" );
+                }
+            }
             if ( ( db_entry.getGoTerms() != null ) && !db_entry.getGoTerms().isEmpty() ) {
                 for( final GoTerm go : db_entry.getGoTerms() ) {
                     final Annotation ann = new Annotation( go.getGoId().getId() );
@@ -408,7 +433,7 @@ public final class SequenceDbWsTools {
             }
         }
         try {
-            Thread.sleep( 10 );// Sleep for 10 ms
+            Thread.sleep( SLEEP );
         }
         catch ( final InterruptedException ie ) {
         }