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 97120ad..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;
 
@@ -40,6 +40,7 @@ import org.forester.archaeopteryx.TreePanel;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Accession;
 import org.forester.util.ForesterUtil;
+import org.forester.util.SequenceAccessionTools;
 import org.forester.ws.wabi.RestUtil;
 
 public final class Blast {
@@ -74,20 +75,45 @@ 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 Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence()
+                                                                                     .getAccession().getValue() );
+                if ( id != null ) {
+                    query = id.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();
+                }
+            }
+            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();
+                }
+            }
+            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();
+                }
             }
-            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 Accession id = SequenceAccessionTools.parseAccessorFromString( node.getName() );
+            if ( id != null ) {
+                query = id.getValue();
             }
         }
         return query;