From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 18 Apr 2011 23:46:16 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4cf51c29478305a4e79c8bc7adf206c91b49136c;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index c91616a..1609344 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -859,6 +859,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                                     null,
                                                     options,
                                                     options[ 2 ] );
+        _nodes_in_preorder = null;
         boolean node_only = true;
         if ( r == 1 ) {
             node_only = false;
@@ -1701,6 +1702,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                            JOptionPane.WARNING_MESSAGE );
             return;
         }
+        _nodes_in_preorder = null;
         setWaitCursor();
         PhylogenyMethods.midpointRoot( _phylogeny );
         resetNodeIdToDistToLeafMap();
@@ -4649,6 +4651,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     final void swap( final PhylogenyNode node ) {
         if ( !node.isExternal() ) {
             _phylogeny.swapChildren( node );
+            _nodes_in_preorder = null;
         }
         repaint();
     }
diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomyEntry.java b/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomyEntry.java
new file mode 100644
index 0000000..1a0cbfa
--- /dev/null
+++ b/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomyEntry.java
@@ -0,0 +1,131 @@
+// $Id:
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// Copyright (C) 2010 Christian M Zmasek
+// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.ws.uniprot;
+
+import java.util.List;
+
+public final class UniProtTaxonomyEntry {
+
+    private String _id;
+    private String _ac;
+    private String _rec_name;
+    private String _os_scientific_name;
+    private String _os_common_name;
+    private String _tax_id;
+
+    private UniProtTaxonomyEntry() {
+    }
+
+    public static UniProtTaxonomyEntry createInstanceFromPlainText( final List<String> lines ) {
+        final UniProtTaxonomyEntry e = new UniProtTaxonomyEntry();
+        for( final String line : lines ) {
+            if ( line.startsWith( "ID" ) ) {
+                e.setId( line.split( "\\s+" )[ 1 ] );
+            }
+            else if ( line.startsWith( "AC" ) ) {
+                e.setAc( extract( line, "AC", ";" ) );
+            }
+            else if ( line.startsWith( "DE" ) ) {
+                if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
+                    e.setRecName( extract( line, "Full=", ";" ) );
+                }
+                if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
+                    e.setRecName( extract( line, "Full=", ";" ) );
+                }
+            }
+            else if ( line.startsWith( "OS" ) ) {
+                if ( line.indexOf( "(" ) > 0 ) {
+                    e.setOsScientificName( extract( line, "OS", "(" ) );
+                }
+                else {
+                    e.setOsScientificName( extract( line, "OS", "." ) );
+                }
+            }
+            else if ( line.startsWith( "OX" ) ) {
+                e.setTaxId( extract( line, "OX", ";" ) );
+            }
+        }
+        return e;
+    }
+
+    private static String extract( final String target, final String a, final String b ) {
+        final int i_a = target.indexOf( a );
+        final int i_b = target.indexOf( b );
+        if ( ( i_a < 0 ) || ( i_b < i_a ) ) {
+            throw new IllegalArgumentException( "attempt to extract from [" + target + "] between [" + a + "] and ["
+                    + b + "]" );
+        }
+        return target.substring( i_a + a.length() + 1, i_b - 1 ).trim();
+    }
+
+    public String getId() {
+        return _id;
+    }
+
+    private void setId( final String id ) {
+        _id = id;
+    }
+
+    public String getAc() {
+        return _ac;
+    }
+
+    private void setAc( final String ac ) {
+        _ac = ac;
+    }
+
+    public String getRecName() {
+        return _rec_name;
+    }
+
+    private void setRecName( final String rec_name ) {
+        _rec_name = rec_name;
+    }
+
+    public String getOsScientificName() {
+        return _os_scientific_name;
+    }
+
+    private void setOsScientificName( final String os_scientific_name ) {
+        _os_scientific_name = os_scientific_name;
+    }
+
+    public String getOsCommonName() {
+        return _os_common_name;
+    }
+
+    private void setOsCommonName( final String os_common_name ) {
+        _os_common_name = os_common_name;
+    }
+
+    public String getTaxId() {
+        return _tax_id;
+    }
+
+    private void setTaxId( final String tax_id ) {
+        _tax_id = tax_id;
+    }
+}