changed for GFF properties panel

uk/ac/sanger/artemis/chado/ChadoTransactionManager.java

@@ -1228,8 +1228,10 @@ public class ChadoTransactionManager
   {
     if(synonym_tags == null)
     {
+      if(GeneUtils.isDatabaseEntry(feature))
         synonym_tags = DatabaseDocument.getSynonymTypeNames(
                               SYNONYM_TAG_CVNAME, feature);
+
       if(synonym_tags == null || synonym_tags.length < 1)
       {
         logger4j.debug("Using default synonym names");
@@ -1250,6 +1252,12 @@ public class ChadoTransactionManager
     return false;
   }
   
+  public static String[] getSynonymTags()
+  {
+    return synonym_tags;
+  }
+
+  
   /**
    * Compare the old and new keys and qualifiers and find the qualifiers 
    * that have changed or been added and UPDATE, INSERT or DELETE accordingly.

uk/ac/sanger/artemis/components/FeatureEdit.java

@@ -76,7 +76,6 @@ import java.util.Comparator;
 
 import javax.swing.*;
 
-
 /**
  *  FeatureEdit class
  *
@@ -860,7 +859,6 @@ public class FeatureEdit extends JPanel
         }
       });
 
-
       final JCheckBox oneView = new JCheckBox("Overview", false);
       oneView.addItemListener(new ItemListener()
       {
@@ -887,6 +885,12 @@ public class FeatureEdit extends JPanel
       fillerBox.add(Box.createHorizontalStrut( 
           tabbedView.getPreferredSize().width ));
     }
+    else if(getFeature().getEmblFeature() instanceof GFFStreamFeature)
+    {
+      propertiesPanel = new PropertiesPanel(getFeature());
+      addGffAnnotationView(lower_panel);
+
+    }
     else
       lower_panel.add(new JScrollPane(qualifier_text_area), "Center");
     
@@ -1438,7 +1442,7 @@ public class FeatureEdit extends JPanel
     
     qualifier_text_area.setText(getQualifierString());
     
-    if(GeneUtils.isDatabaseEntry(getFeature().getEmblFeature()))
+    if(getFeature().getEmblFeature() instanceof GFFStreamFeature)
     {
       // load synonym
       if(cvForm != null)
@@ -1542,8 +1546,6 @@ public class FeatureEdit extends JPanel
       qualifiers =
         qualifier_text_area.getParsedQualifiers(getEntryInformation ());
            
-      updateGffIds(qualifiers);
-      
       // if using controlled vocab form
       if(cvForm != null)
       {
@@ -1569,6 +1571,7 @@ public class FeatureEdit extends JPanel
         if(mapQualifiers != null && mapQualifiers.size() > 0)
           qualifiers.addAll(mapQualifiers);
       }
+      updateGffIds(qualifiers);
       
       if(matchForm != null)
       {
@@ -1704,7 +1707,7 @@ public class FeatureEdit extends JPanel
             }
           }
         }
-        catch(Exception e){ }
+        catch(Exception e){ e.printStackTrace(); }
       }
     }
   }

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

@@ -40,7 +40,6 @@ import uk.ac.sanger.artemis.components.genebuilder.cv.CVPanel;
 import uk.ac.sanger.artemis.components.genebuilder.gff.PropertiesPanel;
 import uk.ac.sanger.artemis.components.genebuilder.ortholog.MatchPanel;
 
-
 /**
  * Panel for display controlled vocabulary terms for Chado
  */
@@ -92,23 +91,33 @@ public class GeneEditorPanel extends JPanel
     coreButton = addOpenClosePanel("Core",qualifier_text_area, this, null);
     add(qualifier_text_area);
     
+    if(refPanel != null)
+    {
       addDarkSeparator(this);
       refButton = addOpenClosePanel("References",refPanel, this, null);
       add(refPanel);
+    }
 
+    if(cvForm != null)
+    {
       addDarkSeparator(this);
       cvButton = addOpenClosePanel("Controlled Vocabulary", cvForm, this,
         CVPanel.getDescription());
       add(cvForm);
+    }
 
+    if(matchForm != null)
+    {
       addDarkSeparator(this);
       matchButton = addOpenClosePanel("Match", matchForm, this,
         MatchPanel.getDescription());
       add(matchForm);
+    }
 
     add(Box.createVerticalGlue());
   }
   
+
   /**
    * Open/close the sections if they contain elements or
    * are empty.
@@ -116,8 +125,11 @@ public class GeneEditorPanel extends JPanel
   public void updatePanelState()
   {
     coreButton.setOpen(!qualifier_text_area.getText().equals(""));
+    if(cvForm != null)
       cvButton.setOpen(!cvForm.isEmpty());
+    if(refPanel != null)
       refButton.setOpen(!refPanel.isEmpty());
+    if(matchForm != null)
       matchButton.setOpen(!matchForm.isEmpty());
     propertiesButton.setOpen(!propertiesPanel.isEmpty());
   }

uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java

@@ -34,7 +34,6 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.Iterator;
 import java.util.Set;
-import java.util.Vector;
 
 import javax.swing.BorderFactory;
 import javax.swing.Box;
@@ -185,6 +184,8 @@ public class PropertiesPanel extends JPanel
     Qualifier idQualifier   = gffQualifiers.getQualifierByName("ID");
     Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name");
 
+    if(idQualifier == null)
+      return;
     final String uniquename = idQualifier.getValues().get(0);
     uniquenameTextField = new JTextField(uniquename);
     uniquenameTextField.setPreferredSize(calcPreferredMaxTextFieldWidth());
@@ -780,9 +781,13 @@ public class PropertiesPanel extends JPanel
   
   private void addSynonym()
   {
-    final Vector<CvTerm> synonyms = DatabaseDocument.getCvterms("", 
-        ChadoTransactionManager.SYNONYM_TAG_CVNAME, false);
-    final JExtendedComboBox list = new JExtendedComboBox(synonyms);
+    final JExtendedComboBox list;
+    if(GeneUtils.isDatabaseEntry(feature.getEmblFeature()))
+      list = new JExtendedComboBox(DatabaseDocument.getCvterms("", 
+          ChadoTransactionManager.SYNONYM_TAG_CVNAME, false));
+    else
+      list = new JExtendedComboBox(ChadoTransactionManager.getSynonymTags());
+
     final String options[] = { "CANCEL", "NEXT>"};   
     
     int select = JOptionPane.showOptionDialog(null, list,
@@ -790,12 +795,15 @@ public class PropertiesPanel extends JPanel
          JOptionPane.YES_NO_CANCEL_OPTION,
          JOptionPane.QUESTION_MESSAGE,
          null, options, options[1]);
-    
     if(select == 0)
       return;
 
     Box xBox = Box.createHorizontalBox();
-    final String synonymName = ((CvTerm)list.getSelectedItem()).getName();
+    final String synonymName;
+    if(list.getSelectedItem() instanceof CvTerm)
+      synonymName = ((CvTerm)list.getSelectedItem()).getName();
+    else
+      synonymName = (String) list.getSelectedItem();
     final JLabel name = new JLabel( synonymName );
     xBox.add(name);