diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 8e00d327128cbc1ff1bdb3bc4b3b0cbfd74ac425..ea163b8b30a45b5507e6124f0a0d7968595328ce 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -1228,8 +1228,10 @@ public class ChadoTransactionManager
{
if(synonym_tags == null)
{
- synonym_tags = DatabaseDocument.getSynonymTypeNames(
+ 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.
diff --git a/uk/ac/sanger/artemis/components/FeatureEdit.java b/uk/ac/sanger/artemis/components/FeatureEdit.java
index 6b459dd7387a478e29adcea0e34ebcebf4fb40ff..1626ba3b8dde6429f4350ce7bb8caf75c3d61bfb 100644
--- a/uk/ac/sanger/artemis/components/FeatureEdit.java
+++ b/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");
@@ -1438,8 +1442,8 @@ 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)
cvForm.updateFromFeature(getFeature());
@@ -1541,9 +1545,7 @@ 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)
{
@@ -1679,7 +1682,7 @@ public class FeatureEdit extends JPanel
{
final String newName = ((String) (qualifiers.getQualifierByName("ID").getValues().get(0))).trim();
final String oldName = ((String) (gffFeature.getQualifierByName("ID").getValues().get(0))).trim();
-
+
if(!newName.equals(oldName))
{
int val = JOptionPane.showConfirmDialog(null,
@@ -1704,7 +1707,7 @@ public class FeatureEdit extends JPanel
}
}
}
- catch(Exception e){ }
+ catch(Exception e){ e.printStackTrace(); }
}
}
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneEditorPanel.java b/uk/ac/sanger/artemis/components/genebuilder/GeneEditorPanel.java
index 5cf4c1d64d0455f5417677ea1d1518c5e6ccb42a..2851efa8f18712ce755160ef4ed94f8806442a42 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneEditorPanel.java
+++ b/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
*/
@@ -92,22 +91,32 @@ public class GeneEditorPanel extends JPanel
coreButton = addOpenClosePanel("Core",qualifier_text_area, this, null);
add(qualifier_text_area);
- addDarkSeparator(this);
- refButton = addOpenClosePanel("References",refPanel, this, null);
- add(refPanel);
-
- addDarkSeparator(this);
- cvButton = addOpenClosePanel("Controlled Vocabulary", cvForm, this,
+ 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);
-
- addDarkSeparator(this);
- matchButton = addOpenClosePanel("Match", matchForm, this,
+ add(cvForm);
+ }
+
+ if(matchForm != null)
+ {
+ addDarkSeparator(this);
+ matchButton = addOpenClosePanel("Match", matchForm, this,
MatchPanel.getDescription());
- add(matchForm);
-
+ add(matchForm);
+ }
+
add(Box.createVerticalGlue());
}
+
/**
* Open/close the sections if they contain elements or
@@ -116,9 +125,12 @@ public class GeneEditorPanel extends JPanel
public void updatePanelState()
{
coreButton.setOpen(!qualifier_text_area.getText().equals(""));
- cvButton.setOpen(!cvForm.isEmpty());
- refButton.setOpen(!refPanel.isEmpty());
- matchButton.setOpen(!matchForm.isEmpty());
+ 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());
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
index a02fe756316efafb50093f3b6a467cc59b0eae3d..03a72b4a5378bdaa538e7bf8b15b68cd1e9c08bb 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
+++ b/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;
@@ -184,7 +183,9 @@ 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);