X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FBlast.java;h=839a328fb61a0daf20b78c04a51906d924fb219e;hb=a9cc2cc5c9cda0ab49f26ccfb7a1aa30531e6ecf;hp=97120ad4969a7790881af51ef9bda92e04c87577;hpb=3be5f9e46469980f068a9f8170e1d20849b5eaf8;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java
index 97120ad..839a328 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx.tools;
 
@@ -38,8 +38,9 @@ import javax.swing.JApplet;
 import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.TreePanel;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Identifier;
 import org.forester.util.ForesterUtil;
+import org.forester.util.SequenceIdParser;
 import org.forester.ws.wabi.RestUtil;
 
 public final class Blast {
@@ -74,20 +75,35 @@ public final class Blast {
 
     final public static String obtainQueryForBlast( final PhylogenyNode node ) {
         String query = "";
-        if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
-            query = node.getNodeData().getSequence().getMolecularSequence();
-        }
-        else if ( ( node.getNodeData().getSequence().getAccession() != null )
-                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {
-            if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
-                query = node.getNodeData().getSequence().getAccession().getSource() + "%7C";
+        if ( node.getNodeData().isHasSequence() ) {
+            if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+                query = node.getNodeData().getSequence().getMolecularSequence();
+            }
+            if ( ForesterUtil.isEmpty( query ) && ( node.getNodeData().getSequence().getAccession() != null )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) {
+                final Identifier id = SequenceIdParser.parse( node.getNodeData().getSequence().getAccession()
+                        .getValue() );
+                if ( id != null ) {
+                    query = id.getValue();
+                }
+            }
+            if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
+                final Identifier id = SequenceIdParser.parse( node.getNodeData().getSequence().getName() );
+                if ( id != null ) {
+                    query = id.getValue();
+                }
+            }
+            if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
+                final Identifier id = SequenceIdParser.parse( node.getNodeData().getSequence().getSymbol() );
+                if ( id != null ) {
+                    query = id.getValue();
+                }
             }
-            query += node.getNodeData().getSequence().getAccession().getValue();
         }
-        else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
-            final Accession acc = AptxUtil.obtainSequenceAccessionFromName( node.getNodeData().getSequence().getName() );
-            if ( acc != null ) {
-                query = acc.getSource() + "%7C" + acc.getValue();
+        if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getName() ) ) {
+            final Identifier id = SequenceIdParser.parse( node.getName() );
+            if ( id != null ) {
+                query = id.getValue();
             }
         }
         return query;