typed search is being added

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

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java
index 4d94450..cf34f4e 100644 (file)
--- 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;
 
@@ -39,9 +39,8 @@ 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.util.SequenceAccessionTools;
 import org.forester.ws.wabi.RestUtil;
 
 public final class Blast {
@@ -80,33 +79,43 @@ public final class Blast {
             if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
                 query = node.getNodeData().getSequence().getMolecularSequence();
             }
-            else if ( ( node.getNodeData().getSequence().getAccession() != null )
+            if ( ForesterUtil.isEmpty( query ) && ( 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";
+                final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+                                                                                     .getAccession().getValue() );
+                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.getNodeData().getSequence().getName() ) ) {
+                final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+                                                                                     .getName() );
+                if ( id != null ) {
+                    query = id.getValue();
                 }
             }
-        }
-        else if ( !ForesterUtil.isEmpty( node.getName() ) ) {
-            final Accession acc = AptxUtil.obtainSequenceAccessionFromName( node.getName() );
-            if ( acc != null ) {
-                query = acc.getSource() + "%7C" + acc.getValue();
+            if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
+                final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+                                                                                     .getSymbol() );
+                if ( id != null ) {
+                    query = id.getValue();
+                }
             }
-            else {
-                final Identifier id = SequenceIdParser.parse( node.getName() );
+            if ( ForesterUtil.isEmpty( query )
+                    && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
+                final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+                                                                                     .getGeneName() );
                 if ( id != null ) {
                     query = id.getValue();
                 }
             }
         }
+        if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getName() ) ) {
+            final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getName() );
+            if ( id != null ) {
+                query = id.getValue();
+            }
+        }
         return query;
     }