X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FNodeEditPanel.java;h=85476b120489579ce3352222f9e02687dce25eea;hb=fea4064e24c6cb362b0e033cf7047afd20f5f53f;hp=2392620e6635e238f4febdd4443c99165d968ff7;hpb=ebabb46561f996b5fcd59bd202defd7b189ea5b6;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
index 2392620..85476b1 100644
--- a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.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/
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -71,6 +71,71 @@ import org.forester.util.ForesterUtil;
 
 class NodeEditPanel extends JPanel {
 
+    private enum PHYLOXML_TAG {
+        NODE_NAME,
+        NODE_BRANCH_LENGTH,
+        NODE_BRANCH_WIDTH,
+        TAXONOMY_CODE,
+        TAXONOMY_SCIENTIFIC_NAME,
+        TAXONOMY_AUTHORITY,
+        TAXONOMY_COMMON_NAME,
+        TAXONOMY_SYNONYM,
+        TAXONOMY_RANK,
+        TAXONOMY_URI,
+        SEQ_SYMBOL,
+        SEQ_NAME,
+        SEQ_GENE_NAME,
+        SEQ_LOCATION,
+        SEQ_TYPE,
+        SEQ_MOL_SEQ,
+        SEQ_URI,
+        DATE_DESCRIPTION,
+        DATE_VALUE,
+        DATE_MIN,
+        DATE_MAX,
+        DATE_UNIT,
+        TAXONOMY_ID_VALUE,
+        TAXONOMY_ID_PROVIDER,
+        SEQ_ACC_VALUE,
+        SEQ_ACC_SOURCE,
+        CONFIDENCE_VALUE,
+        CONFIDENCE_TYPE,
+        LIT_REFERENCE_DESC,
+        LIT_REFERENCE_DOI,
+        EVENTS_DUPLICATIONS,
+        EVENTS_SPECIATIONS,
+        EVENTS_GENE_LOSSES,
+        DIST_DESC,
+        DIST_GEODETIC,
+        DIST_LAT,
+        DIST_LONG,
+        DIST_ALT,
+        DIST_ALT_UNIT
+    }
+
+    private class TagNumber {
+
+        final private PHYLOXML_TAG _tag;
+        final private int          _number;
+
+        TagNumber( final PHYLOXML_TAG tag, final int number ) {
+            _tag = tag;
+            _number = number;
+        }
+
+        @Override
+        public String toString() {
+            return getTag() + "_" + getNumber();
+        }
+
+        int getNumber() {
+            return _number;
+        }
+
+        PHYLOXML_TAG getTag() {
+            return _tag;
+        }
+    }
     private static final long                            serialVersionUID = 5120159904388100771L;
     private final JTree                                  _tree;
     private final JEditorPane                            _pane;
@@ -100,10 +165,10 @@ class NodeEditPanel extends JPanel {
         final JSplitPane split_pane = new JSplitPane( JSplitPane.VERTICAL_SPLIT );
         split_pane.setTopComponent( tree_view );
         // split_pane.setBottomComponent( data_view );
-        data_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
-        tree_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
+        data_view.setMinimumSize( AptxConstants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
+        tree_view.setMinimumSize( AptxConstants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
         // split_pane.setDividerLocation( 400 );
-        split_pane.setPreferredSize( Constants.NODE_PANEL_SIZE );
+        split_pane.setPreferredSize( AptxConstants.NODE_PANEL_SIZE );
         add( split_pane );
         getJTree().getSelectionModel().setSelectionMode( TreeSelectionModel.SINGLE_TREE_SELECTION );
         getJTree().addKeyListener( new KeyListener() {
@@ -337,6 +402,7 @@ class NodeEditPanel extends JPanel {
         }
         addSubelementEditable( category, NodePanel.SEQ_NAME, seq.getName(), PHYLOXML_TAG.SEQ_NAME );
         addSubelementEditable( category, NodePanel.SEQ_SYMBOL, seq.getSymbol(), PHYLOXML_TAG.SEQ_SYMBOL );
+        addSubelementEditable( category, NodePanel.SEQ_GENE_NAME, seq.getGeneName(), PHYLOXML_TAG.SEQ_GENE_NAME );
         addSubelementEditable( category,
                                NodePanel.SEQ_ACCESSION,
                                acc.getValue(),
@@ -490,6 +556,25 @@ class NodeEditPanel extends JPanel {
                                uri_counter );
     }
 
+    private void addUri( final DefaultMutableTreeNode mtn, final Uri uri, final int number, final MultipleUris mu ) {
+        if ( uri != null ) {
+            if ( mu.getUris() == null ) {
+                mu.setUris( new ArrayList<Uri>() );
+            }
+        }
+        if ( ( uri != null ) && ( mu.getUris() == null ) ) {
+            mu.setUris( new ArrayList<Uri>() );
+        }
+        if ( ( uri != null ) && ( mu.getUris().size() == number ) ) {
+            mu.getUris().add( uri );
+        }
+        if ( ( mu.getUris() != null ) && ( mu.getUris().size() != number ) ) {
+            mu.getUris().set( number, uri );
+        }
+        final ImageLoader il = new ImageLoader( getTreePanel() );
+        new Thread( il ).start();
+    }
+
     private void collapsePath( final String name ) {
         final TreePath tp = getJTree().getNextMatch( name, 0, Position.Bias.Forward );
         if ( tp != null ) {
@@ -540,10 +625,6 @@ class NodeEditPanel extends JPanel {
         return getMap().get( mtn );
     }
 
-    PhylogenyNode getMyNode() {
-        return _my_node;
-    }
-
     private DefaultMutableTreeNode getSelectedTreeNode() {
         final TreePath selectionPath = getJTree().getSelectionPath();
         if ( selectionPath != null ) {
@@ -616,13 +697,6 @@ class NodeEditPanel extends JPanel {
         return i;
     }
 
-    void writeAll() {
-        for( int i = 0; i < getJTree().getRowCount(); i++ ) {
-            final TreePath p = getJTree().getPathForRow( i );
-            writeBack( ( DefaultMutableTreeNode ) p.getLastPathComponent() );
-        }
-    }
-
     private void writeBack( final DefaultMutableTreeNode mtn ) {
         if ( !getMap().containsKey( mtn ) ) {
             final DefaultMutableTreeNode parent = ( DefaultMutableTreeNode ) mtn.getParent();
@@ -841,6 +915,10 @@ class NodeEditPanel extends JPanel {
                     break;
                 }
                 break;
+            case SEQ_GENE_NAME:
+                ForesterUtil.ensurePresenceOfSequence( getMyNode() );
+                getMyNode().getNodeData().getSequence().setGeneName( value );
+                break;
             case SEQ_TYPE:
                 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
                 try {
@@ -1030,87 +1108,14 @@ class NodeEditPanel extends JPanel {
         getTreePanel().repaint();
     }
 
-    private void addUri( final DefaultMutableTreeNode mtn, final Uri uri, final int number, final MultipleUris mu ) {
-        if ( uri != null ) {
-            if ( mu.getUris() == null ) {
-                mu.setUris( new ArrayList<Uri>() );
-            }
-        }
-        if ( ( uri != null ) && ( mu.getUris() == null ) ) {
-            mu.setUris( new ArrayList<Uri>() );
-        }
-        if ( ( uri != null ) && ( mu.getUris().size() == number ) ) {
-            mu.getUris().add( uri );
-        }
-        if ( ( mu.getUris() != null ) && ( mu.getUris().size() != number ) ) {
-            mu.getUris().set( number, uri );
-        }
-        final ImageLoader il = new ImageLoader( getTreePanel() );
-        new Thread( il ).start();
-    }
-
-    private enum PHYLOXML_TAG {
-        NODE_NAME,
-        NODE_BRANCH_LENGTH,
-        NODE_BRANCH_WIDTH,
-        TAXONOMY_CODE,
-        TAXONOMY_SCIENTIFIC_NAME,
-        TAXONOMY_AUTHORITY,
-        TAXONOMY_COMMON_NAME,
-        TAXONOMY_SYNONYM,
-        TAXONOMY_RANK,
-        TAXONOMY_URI,
-        SEQ_SYMBOL,
-        SEQ_NAME,
-        SEQ_LOCATION,
-        SEQ_TYPE,
-        SEQ_MOL_SEQ,
-        SEQ_URI,
-        DATE_DESCRIPTION,
-        DATE_VALUE,
-        DATE_MIN,
-        DATE_MAX,
-        DATE_UNIT,
-        TAXONOMY_ID_VALUE,
-        TAXONOMY_ID_PROVIDER,
-        SEQ_ACC_VALUE,
-        SEQ_ACC_SOURCE,
-        CONFIDENCE_VALUE,
-        CONFIDENCE_TYPE,
-        LIT_REFERENCE_DESC,
-        LIT_REFERENCE_DOI,
-        EVENTS_DUPLICATIONS,
-        EVENTS_SPECIATIONS,
-        EVENTS_GENE_LOSSES,
-        DIST_DESC,
-        DIST_GEODETIC,
-        DIST_LAT,
-        DIST_LONG,
-        DIST_ALT,
-        DIST_ALT_UNIT
+    PhylogenyNode getMyNode() {
+        return _my_node;
     }
 
-    private class TagNumber {
-
-        final private PHYLOXML_TAG _tag;
-        final private int          _number;
-
-        TagNumber( final PHYLOXML_TAG tag, final int number ) {
-            _tag = tag;
-            _number = number;
-        }
-
-        int getNumber() {
-            return _number;
-        }
-
-        PHYLOXML_TAG getTag() {
-            return _tag;
-        }
-
-        @Override
-        public String toString() {
-            return getTag() + "_" + getNumber();
+    void writeAll() {
+        for( int i = 0; i < getJTree().getRowCount(); i++ ) {
+            final TreePath p = getJTree().getPathForRow( i );
+            writeBack( ( DefaultMutableTreeNode ) p.getLastPathComponent() );
         }
     }
 }