From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 4 Mar 2013 22:50:26 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a9cc2cc5c9cda0ab49f26ccfb7a1aa30531e6ecf;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 2ca3b87..627e152 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -89,7 +89,10 @@ import org.forester.ws.seqdb.UniProtTaxonomy;
 public final class AptxUtil {
 
     final static String           UNIPROT_KB                     = "http://www.uniprot.org/uniprot/";
-    final static Pattern          UNIPROT_KB_PATTERN             = Pattern
+    final static Pattern          UNIPROT_KB_PATTERN_1             = Pattern
+            .compile( "\\bsp|tr.\\S([A-Z0-9]{5,6})\\b" );
+
+    final static Pattern          UNIPROT_KB_PATTERN_2             = Pattern
                                                                          .compile( "\\b[A-Z0-9]{5,6}_[A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA\\b" );
     private final static Pattern  seq_identifier_pattern_1       = Pattern
                                                                          .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index dcc130c..9e6fcc6 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -3242,21 +3242,31 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         .toLowerCase() ) ) {
             return true;
         }
-        if ( !ForesterUtil.isEmpty( node.getName() ) && AptxUtil.UNIPROT_KB_PATTERN.matcher( node.getName() ).find() ) {
+        if ( !ForesterUtil.isEmpty( node.getName() )
+                && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( node.getName() ).find()
+                        || AptxUtil.UNIPROT_KB_PATTERN_2.matcher( node.getName() ).find()
+                        ) ) {
             return true;
         }
         if ( node.getNodeData().isHasSequence() ) {
             Sequence seq = node.getNodeData().getSequence();
-            if ( !ForesterUtil.isEmpty( seq.getName() ) && AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getName() ).find() ) {
+            if ( !ForesterUtil.isEmpty( seq.getName() ) && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getName() ).find()
+                    ||  AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getName() ).find()
+                    
+                    ) ) {
                 return true;
             }
             if ( !ForesterUtil.isEmpty( seq.getSymbol() )
-                    && AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getSymbol() ).find() ) {
+                    && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getSymbol() ).find() 
+                          ||  AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getSymbol() ).find() ) ) {
                 return true;
             }
             if ( ( node.getNodeData().getSequence().getAccession() != null )
                     && !ForesterUtil.isEmpty( seq.getAccession().getValue() )
-                    && AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getAccession().getValue() ).find() ) {
+                    && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getAccession().getValue() ).find() 
+                            
+                            || AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getAccession().getValue() ).find() 
+                            ) ) {
                 return true;
             }
         }
@@ -3298,21 +3308,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             if ( node.getNodeData().isHasSequence() ) {
                 Sequence seq = node.getNodeData().getSequence();
                 if ( !ForesterUtil.isEmpty( seq.getSymbol() )
-                        && AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getSymbol() ).find() ) {
-                    upkb = AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getSymbol() ).group();
+                        && AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getSymbol() ).find() ) {
+                    upkb = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getSymbol() ).group();
                 }
                 else if ( !ForesterUtil.isEmpty( seq.getName() )
-                        && AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getName() ).find() ) {
-                    upkb = AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getName() ).group();
+                        && AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getName() ).find() ) {
+                    upkb = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getName() ).group();
                 }
                 else if ( ( node.getNodeData().getSequence().getAccession() != null )
                         && !ForesterUtil.isEmpty( seq.getAccession().getValue() )
-                        && AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getAccession().getValue() ).find() ) {
-                    upkb = AptxUtil.UNIPROT_KB_PATTERN.matcher( seq.getAccession().getValue() ).group();
+                        && AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getAccession().getValue() ).find() ) {
+                    upkb = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getAccession().getValue() ).group();
                 }
             }
             if ( ForesterUtil.isEmpty( upkb ) && !ForesterUtil.isEmpty( node.getName() ) ) {
-                final Matcher m = AptxUtil.UNIPROT_KB_PATTERN.matcher( node.getName() );
+                final Matcher m = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( node.getName() );
                 if ( m.find() ) {
                     upkb = m.group();
                 }