in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 627e152..18e80e7 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -90,7 +90,7 @@ public final class AptxUtil {
 
     final static String           UNIPROT_KB                     = "http://www.uniprot.org/uniprot/";
     final static Pattern          UNIPROT_KB_PATTERN_1             = Pattern
-            .compile( "\\bsp|tr.\\S([A-Z0-9]{5,6})\\b" );
+            .compile( "\\b(sp|tr)\\W([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" );

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 988daf4..d9723d6 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,8 +42,8 @@ public final class Constants {
     public final static boolean __SYNTH_LF                                                    = false;                                                               // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9803";
-    final static String         PRG_DATE                                                      = "130225";
+    final static String         VERSION                                                       = "0.9804";
+    final static String         PRG_DATE                                                      = "130304";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Verdana", "Tahoma",
             "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 9e6fcc6..b94080f 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -3243,30 +3243,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return true;
         }
         if ( !ForesterUtil.isEmpty( node.getName() )
-                && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( node.getName() ).find()
-                        || AptxUtil.UNIPROT_KB_PATTERN_2.matcher( node.getName() ).find()
-                        ) ) {
+                && ( 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_1.matcher( seq.getName() ).find()
-                    ||  AptxUtil.UNIPROT_KB_PATTERN_2.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_1.matcher( seq.getSymbol() ).find() 
-                          ||  AptxUtil.UNIPROT_KB_PATTERN_2.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_1.matcher( seq.getAccession().getValue() ).find() 
-                            
-                            || AptxUtil.UNIPROT_KB_PATTERN_2.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;
             }
         }
@@ -3307,24 +3303,57 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             String upkb = null;
             if ( node.getNodeData().isHasSequence() ) {
                 Sequence seq = node.getNodeData().getSequence();
-                if ( !ForesterUtil.isEmpty( seq.getSymbol() )
-                        && AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getSymbol() ).find() ) {
-                    upkb = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getSymbol() ).group();
+                Matcher m;
+                if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
+                    m = AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getSymbol() );
+                    if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
+                        if ( m.find() ) {
+                            upkb = m.group( 2 );
+                        }
+                        else {
+                            m = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getSymbol() );
+                            if ( m.find() ) {
+                                upkb = m.group();
+                            }
+                        }
+                    }
                 }
-                else if ( !ForesterUtil.isEmpty( seq.getName() )
-                        && AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getName() ).find() ) {
-                    upkb = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getName() ).group();
+                if ( ForesterUtil.isEmpty( upkb ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
+                    m = AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getName() );
+                    if ( m.find() ) {
+                        upkb = m.group( 2 );
+                    }
+                    else {
+                        m = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getName() );
+                        if ( m.find() ) {
+                            upkb = m.group();
+                        }
+                    }
                 }
-                else if ( ( node.getNodeData().getSequence().getAccession() != null )
-                        && !ForesterUtil.isEmpty( seq.getAccession().getValue() )
-                        && 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 ) && ( node.getNodeData().getSequence().getAccession() != null )
+                        && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
+                    m = AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getAccession().getValue() );
+                    if ( m.find() ) {
+                        upkb = m.group( 2 );
+                    }
+                    else {
+                        m = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getAccession().getValue() );
+                        if ( m.find() ) {
+                            upkb = m.group();
+                        }
+                    }
                 }
             }
             if ( ForesterUtil.isEmpty( upkb ) && !ForesterUtil.isEmpty( node.getName() ) ) {
-                final Matcher m = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( node.getName() );
-                if ( m.find() ) {
-                    upkb = m.group();
+                final Matcher m1 = AptxUtil.UNIPROT_KB_PATTERN_1.matcher( node.getName() );
+                if ( m1.find() ) {
+                    upkb = m1.group( 2 );
+                }
+                else {
+                    final Matcher m2 = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( node.getName() );
+                    if ( m2.find() ) {
+                        upkb = m2.group();
+                    }
                 }
             }
             try {

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index b0c862d..9cbfb09 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,8 +27,8 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.022";
-    public final static String  FORESTER_DATE               = "130225";
+    public final static String  FORESTER_VERSION            = "1.023";
+    public final static String  FORESTER_DATE               = "130304";
     public final static String  PHYLO_XML_VERSION           = "1.10";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";
     public final static String  PHYLO_XML_XSD               = "phyloxml.xsd";