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 38519e4..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;
 
@@ -32,30 +32,33 @@ import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Vector;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 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.util.ForesterUtil;
+import org.forester.util.SequenceAccessionTools;
 import org.forester.ws.wabi.RestUtil;
 
-public class Blast {
+public final class Blast {
 
-    final static Pattern identifier_pattern_1 = Pattern.compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z\\.]{4,40})\\s*$" );
-    final static Pattern identifier_pattern_2 = Pattern
-                                                      .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z\\.]{4,40})[|,; ].*$" );
-
-    public Blast() {
-    }
-
-    public static void NcbiBlastWeb( final String query, final JApplet applet, final TreePanel p ) {
+    final public static void openNcbiBlastWeb( final String query,
+                                               final boolean is_nucleic_acids,
+                                               final JApplet applet,
+                                               final TreePanel p ) {
         //http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE=Proteins&DATABASE=swissprot&QUERY=gi|163848401
         final StringBuilder uri_str = new StringBuilder();
-        uri_str.append( "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&DATABASE=nr&PAGE=Proteins&QUERY=" );
+        uri_str.append( "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&DATABASE=nr&PAGE=" );
+        if ( is_nucleic_acids ) {
+            uri_str.append( "Nucleotide" );
+        }
+        else {
+            uri_str.append( "Proteins" );
+        }
+        uri_str.append( "&QUERY=" );
         uri_str.append( query );
         try {
             AptxUtil.launchWebBrowser( new URI( uri_str.toString() ), applet != null, applet, "_aptx_blast" );
@@ -70,45 +73,57 @@ public class Blast {
         }
     }
 
-    public static String obtainQueryForBlast( final PhylogenyNode node ) {
+    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();
             }
-            query += node.getNodeData().getSequence().getAccession().getValue();
-        }
-        else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
-            final String name = node.getNodeData().getSequence().getName();
-            final Matcher matcher1 = identifier_pattern_1.matcher( name );
-            final Matcher matcher2 = identifier_pattern_2.matcher( name );
-            String group1 = "";
-            String group2 = "";
-            if ( matcher1.matches() ) {
-                group1 = matcher1.group( 1 );
-                group2 = matcher1.group( 2 );
-                System.out.println( "1 1=" + group1 );
-                System.out.println( "1 2=" + group2 );
+            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 ( matcher2.matches() ) {
-                group1 = matcher2.group( 1 );
-                group2 = matcher2.group( 2 );
-                System.out.println( "2 1=" + group1 );
-                System.out.println( "2 2=" + group2 );
+            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( group1 ) && !ForesterUtil.isEmpty( group2 ) ) {
-                query = group1 + "%7C" + group2;
+            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();
+                }
+            }
+        }
+        if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getName() ) ) {
+            final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getName() );
+            if ( id != null ) {
+                query = id.getValue();
             }
         }
-        System.out.println( query );
         return query;
     }
 
-    public void ddbjBlast( final String geneName ) {
+    final public static boolean isContainsQueryForBlast( final PhylogenyNode node ) {
+        return !ForesterUtil.isEmpty( obtainQueryForBlast( node ) );
+    }
+
+    final public void ddbjBlast( final String geneName ) {
         // Retrieve accession number list which has specified gene name from searchByXMLPath of ARSA. Please click here for details of ARSA.
         /*target: Sequence length is between 300bp and 1000bp.
         Feature key is CDS.