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 ed6387e..606d35a 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -49,21 +49,23 @@ 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;
 
 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_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 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_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;
+    private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = false;
 
     public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
                                                                            final int max_taxonomies_return )
@@ -380,6 +382,21 @@ public final class SequenceDbWsTools {
                     // Eat this exception.
                 }
             }
+            if ( ( db_entry.getMolecularSequence() != null )
+                    && !ForesterUtil.isEmpty( db_entry.getMolecularSequence().getMolecularSequenceAsString() )
+                    && ( ALLOW_TO_OVERWRITE_MOL_SEQ || 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() );