fixes

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5687 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java,v 1.20 2007-02-22 19:39:23 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java,v 1.21 2007-03-15 11:39:07 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components.genebuilder;
@@ -53,6 +53,7 @@ import uk.ac.sanger.artemis.GotoEventSource;
 import uk.ac.sanger.artemis.Selection;
 import uk.ac.sanger.artemis.components.FeatureEdit;
 import uk.ac.sanger.artemis.components.Utilities;
+import uk.ac.sanger.artemis.io.GFFEntryInformation;
 import uk.ac.sanger.artemis.io.GFFStreamFeature;
 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
 import uk.ac.sanger.artemis.io.InvalidRelationException;
@@ -152,14 +153,16 @@ public class GeneBuilderFrame extends JFrame
     all.setTopComponent(top);
     
     if(entry_group != null)
-    {
-      JTabbedPane tabpane = new JTabbedPane();
-    
       feature_editor = new FeatureEdit(feature, entry_group,
-                                       selection, goto_event_source, this);
-      tabpane.addTab("Annotation", feature_editor);
-      all.setBottomComponent(tabpane);
-    }
+                        selection, goto_event_source, this);
+    else
+      feature_editor = new FeatureEdit(feature, null,
+          null, null, this, new GFFEntryInformation());
+    
+    JTabbedPane tabpane = new JTabbedPane();
+    tabpane.addTab("Annotation", feature_editor);
+    all.setBottomComponent(tabpane);
+    
     getContentPane().add(all);
     
     addWindowListener(new WindowAdapter() 

uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java,v 1.15 2007-02-05 15:04:15 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java,v 1.16 2007-03-15 11:39:07 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components.genebuilder;
@@ -347,7 +347,8 @@ public class GeneComponentTree extends JTree
         feature = new uk.ac.sanger.artemis.Feature(embl_feature);    
       
       gene_builder.setActiveFeature(feature);
-      selection.set(feature);
+      if(selection != null)
+        selection.set(feature);
     }
   }
         

uk/ac/sanger/artemis/components/genebuilder/GeneEdit.java

@@ -47,7 +47,9 @@ import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
 import javax.swing.Box;
+import javax.swing.UIManager;
 
+import uk.ac.sanger.artemis.Options;
 import uk.ac.sanger.artemis.chado.*;
 import uk.ac.sanger.artemis.io.FeatureVector;
 import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
@@ -128,7 +130,7 @@ public class GeneEdit
 
     Box xbox = Box.createHorizontalBox();
     final JTextField gene_text = new JTextField(20);
-    gene_text.setText("SPAC212.04c"); //"SPAC212.04c");
+    gene_text.setText("BPSL3413"); //"SPAC212.04c");
     xbox.add(gene_text);
     xbox.add(schema_list);
     gene_text.selectAll();
@@ -165,9 +167,11 @@ public class GeneEdit
             break;
           }
         }
-          
-        new GeneBuilderFrame(new uk.ac.sanger.artemis.Feature(gff_gene_feature), 
-                             null, null, null);
+        
+        uk.ac.sanger.artemis.Feature feature =
+           new uk.ac.sanger.artemis.Feature(gff_gene_feature);
+
+        new GeneBuilderFrame(feature, null, null, null);
       }
     });
     xbox.add(findButt);
@@ -255,6 +259,17 @@ public class GeneEdit
 
   public static void main(String args[])
   {
+    final javax.swing.plaf.FontUIResource font_ui_resource =
+      Options.getOptions().getFontUIResource();
+
+    java.util.Enumeration keys = UIManager.getDefaults().keys();
+    while(keys.hasMoreElements()) 
+    {
+      Object key = keys.nextElement();
+      Object value = UIManager.get(key);
+      if(value instanceof javax.swing.plaf.FontUIResource) 
+        UIManager.put(key, font_ui_resource);
+    }
     new GeneEdit();
   }
 }

uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologPanel.java

+/* OrthologPanel.java
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2007  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologPanel.java,v 1.1 2007-03-15 11:39:07 tjc Exp $
+ */
+
+package uk.ac.sanger.artemis.components.genebuilder.ortholog;
+
+import java.awt.Component;
+import java.awt.FlowLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+
+import javax.swing.Box;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import uk.ac.sanger.artemis.FeatureChangeEvent;
+import uk.ac.sanger.artemis.FeatureChangeListener;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.io.Qualifier;
+import uk.ac.sanger.artemis.io.QualifierVector;
+
+public class OrthologPanel extends JPanel
+                      implements FeatureChangeListener
+{
+  private static final long serialVersionUID = 1L;
+  private QualifierVector orthologQualifiers;
+  
+  public OrthologPanel(final Feature feature)
+  {
+    super(new FlowLayout(FlowLayout.LEFT));
+    updateFromFeature(feature);
+  }
+  
+  /**
+   * Return true if this is a Ortholog qualifier
+   * @param qualifier
+   * @return
+   */
+  public boolean isOrthologTag(final Qualifier qualifier)
+  {
+    if(qualifier.getName().equals("ortholog"))
+      return true;
+    return false;
+  }
+  
+  private Component createOrthologQualifiersComponent()
+  {
+    int nrows = 0;
+    
+    Qualifier idQualifier = orthologQualifiers.getQualifierByName("ID");
+    
+    Box gffBox = Box.createVerticalBox();
+    gffBox.add(Box.createVerticalStrut(10));
+    
+    GridBagLayout grid = new GridBagLayout();
+    GridBagConstraints c = new GridBagConstraints();
+    c.ipady = 5;
+    JPanel gridPanel = new JPanel(grid);
+    
+
+    if(idQualifier != null)
+    {
+      final String uniquename = (String)idQualifier.getValues().get(0);
+      JLabel idField = new JLabel("ID");
+      
+      
+      c.gridx = 0;
+      c.gridy = 0;
+      c.ipadx = 5;
+      c.anchor = GridBagConstraints.EAST;
+      gridPanel.add(idField, c);
+      c.gridx = 1;
+      c.gridy = 0;
+      c.ipadx = 0;
+      c.anchor = GridBagConstraints.WEST;
+      //gridPanel.add(uniquenameTextField, c);
+      
+
+    }
+    
+    
+
+    gffBox.add(gridPanel);
+    return gffBox;
+  }
+  
+  public void updateFromFeature(final Feature feature)
+  {
+    removeAll();
+    if(orthologQualifiers != null)
+      feature.removeFeatureChangeListener(this);
+    orthologQualifiers = feature.getQualifiers().copy();
+    
+    orthologQualifiers = new QualifierVector();
+    final QualifierVector qualifiers = feature.getQualifiers();  
+    for(int i = 0 ; i < qualifiers.size(); ++i) 
+    {
+      Qualifier qualifier = (Qualifier)qualifiers.elementAt(i);
+      if(isOrthologTag(qualifier))
+        orthologQualifiers.addElement(qualifier.copy());
+    }
+   
+    feature.addFeatureChangeListener(this);  
+    add(createOrthologQualifiersComponent());
+    repaint();
+    revalidate();
+  }
+
+  /**
+   * Get the latest (edited) controlled vocab qualifiers
+   * @return
+   */
+  public QualifierVector getOrthologQualifiers()
+  {
+    // check editable components for changes
+    
+    // 
+    
+    return orthologQualifiers;
+  }
+  
+  public void featureChanged(FeatureChangeEvent event)
+  {
+    updateFromFeature(event.getFeature());
+  }
+}
\ No newline at end of file