diff --git a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
index 83923de1cebdb99a9eaf29c48645f4563f2437b4..e7bd8cfda2ae24bef62e55e0f542d9ff13b5fa94 100644
--- a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+++ b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
@@ -89,6 +89,7 @@ class TransferAnnotationTool extends JFrame
"non_cytoplasm_location",
"orthologous_to",
"paralogous_to",
+ "pepstats_file",
"PlasmoAP_score",
"polypeptide_domain",
"fasta_file",
@@ -180,38 +181,8 @@ class TransferAnnotationTool extends JFrame
final QualifierVector qualifiers = feature.getQualifiers();
for(int i = 0; i < qualifiers.size(); i++)
{
- Qualifier qualifier = ((Qualifier) qualifiers.get(i));
-
- if(isNonTransferable(qualifier.getName()))
- continue;
-
- final JCheckBox qualifierNameCheckBox = new JCheckBox(qualifier.getName(), false);
- c.gridx = 1;
- Box qualifierValueBox = Box.createVerticalBox();
-
- JButton detailsShowHide = new JButton("+");
- final Vector qualifierValuesCheckBox = setExpanderButton(detailsShowHide,
- qualifier, qualifierValueBox, qualifierNameCheckBox, pane);
-
- qualifierNameCheckBox.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- for(int i=0; i<qualifierValuesCheckBox.size(); i++)
- {
- JCheckBox cb = (JCheckBox) qualifierValuesCheckBox.get(i);
- cb.setSelected(qualifierNameCheckBox.isSelected());
- }
- }
- });
- pane.add(detailsShowHide, c);
- c.gridx = 2;
-
- pane.add(qualifierNameCheckBox, c);
- qualifierCheckBoxes.put(qualifierNameCheckBox, qualifierValuesCheckBox);
- c.gridy = ++nrows;
- pane.add(qualifierValueBox, c);
- c.gridy = ++nrows;
+ nrows = addQualifierComponents(pane, (Qualifier) qualifiers.get(i),
+ qualifierCheckBoxes, c, nrows);
}
c.gridx = 0;
@@ -352,6 +323,55 @@ class TransferAnnotationTool extends JFrame
framePanel.add(buttonBox, BorderLayout.SOUTH);
}
+
+ /**
+ * Add a qualifier to the list of transferable annotation
+ * @param pane
+ * @param qualifier
+ * @param qualifierCheckBoxes
+ * @param c
+ * @param nrows
+ * @return
+ */
+ private int addQualifierComponents(final JPanel pane,
+ final Qualifier qualifier,
+ final Hashtable qualifierCheckBoxes,
+ final GridBagConstraints c,
+ int nrows)
+ {
+ if(isNonTransferable(qualifier.getName()))
+ return nrows;
+
+ final JCheckBox qualifierNameCheckBox = new JCheckBox(qualifier.getName(), false);
+ c.gridx = 1;
+ Box qualifierValueBox = Box.createVerticalBox();
+
+ JButton detailsShowHide = new JButton("+");
+ final Vector qualifierValuesCheckBox = setExpanderButton(detailsShowHide,
+ qualifier, qualifierValueBox, qualifierNameCheckBox, pane);
+
+ qualifierNameCheckBox.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ for(int i=0; i<qualifierValuesCheckBox.size(); i++)
+ {
+ JCheckBox cb = (JCheckBox) qualifierValuesCheckBox.get(i);
+ cb.setSelected(qualifierNameCheckBox.isSelected());
+ }
+ }
+ });
+ pane.add(detailsShowHide, c);
+ c.gridx = 2;
+
+ pane.add(qualifierNameCheckBox, c);
+ qualifierCheckBoxes.put(qualifierNameCheckBox, qualifierValuesCheckBox);
+ c.gridy = ++nrows;
+ pane.add(qualifierValueBox, c);
+ c.gridy = ++nrows;
+ return nrows;
+ }
+
/**
* Set up the expander button to display qualifier values.
* @param butt - expander button
@@ -435,7 +455,6 @@ class TransferAnnotationTool extends JFrame
final boolean sameKey,
final boolean overwrite)
{
- setCursor(new Cursor(Cursor.WAIT_CURSOR));
// transfer selected annotation to genes
final QualifierVector qualifiers = orginatingFeature.getQualifiers();
final QualifierVector qualifiersToTransfer = new QualifierVector();
@@ -482,6 +501,16 @@ class TransferAnnotationTool extends JFrame
"Warning", JOptionPane.WARNING_MESSAGE);
return;
}
+ else if(overwrite)
+ {
+ int res = JOptionPane.showConfirmDialog(this,
+ "Overwrite selected annotation for "+count+" feature(s)?",
+ "Overwrite", JOptionPane.OK_CANCEL_OPTION);
+ if(res == JOptionPane.CANCEL_OPTION)
+ return;
+ }
+
+ setCursor(new Cursor(Cursor.WAIT_CURSOR));
String geneNames[] = new String[count];
count = 0;
@@ -495,7 +524,6 @@ class TransferAnnotationTool extends JFrame
count++;
}
}
- //geneNameTextArea.getText().split("\\s");
final String key = orginatingFeature.getKey().getKeyString();
final FeatureVector features = entryGroup.getAllFeatures();
@@ -510,56 +538,58 @@ class TransferAnnotationTool extends JFrame
//
// Commit changes to genes not in Artemis but in the database
//
- DatabaseDocumentEntry db_entry =
- (DatabaseDocumentEntry) orginatingFeature.getEntry().getEMBLEntry();
- DatabaseDocument doc = (DatabaseDocument) db_entry.getDocument();
Vector genesNotFound = null;
-
- for (int i = 0; i < geneNames.length; i++)
+ if (orginatingFeature.getEntry().getEMBLEntry() instanceof DatabaseDocumentEntry)
{
- DatabaseDocumentEntry newDbEntry = GeneEdit.makeGeneEntry(null,
- geneNames[i], doc, null);
+ DatabaseDocumentEntry db_entry =
+ (DatabaseDocumentEntry) orginatingFeature.getEntry().getEMBLEntry();
+ DatabaseDocument doc = (DatabaseDocument) db_entry.getDocument();
- if (newDbEntry == null)
+ for (int i = 0; i < geneNames.length; i++)
{
- if (genesNotFound == null)
- genesNotFound = new Vector();
- genesNotFound.add(geneNames[i]);
- continue;
- }
+ DatabaseDocumentEntry newDbEntry = GeneEdit.makeGeneEntry(null,
+ geneNames[i], doc, null);
- char[] c = new char[1];
- PartialSequence ps = new PartialSequence(c, 100, 0, null, null);
- newDbEntry.setPartialSequence(ps);
- Entry entry = null;
- try
- {
- entry = new Entry(newDbEntry);
- }
- catch (Exception e)
- {
- e.printStackTrace();
- }
+ if (newDbEntry == null)
+ {
+ if (genesNotFound == null)
+ genesNotFound = new Vector();
+ genesNotFound.add(geneNames[i]);
+ continue;
+ }
- SimpleEntryGroup entry_group = new SimpleEntryGroup();
- entry_group.addElement(entry);
+ char[] c = new char[1];
+ PartialSequence ps = new PartialSequence(c, 100, 0, null, null);
+ newDbEntry.setPartialSequence(ps);
+ Entry entry = null;
+ try
+ {
+ entry = new Entry(newDbEntry);
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ SimpleEntryGroup entry_group = new SimpleEntryGroup();
+ entry_group.addElement(entry);
- ChadoTransactionManager ctm = new ChadoTransactionManager();
- entry_group.addFeatureChangeListener(ctm);
- entry_group.addEntryChangeListener(ctm);
- ctm.setEntryGroup(entry_group);
+ ChadoTransactionManager ctm = new ChadoTransactionManager();
+ entry_group.addFeatureChangeListener(ctm);
+ entry_group.addEntryChangeListener(ctm);
+ ctm.setEntryGroup(entry_group);
- transfer(entry.getAllFeatures(), qualifiersToTransfer, key, sameKey,
- overwrite, true, geneNames);
- ChadoTransactionManager.commit((DatabaseDocument) newDbEntry
- .getDocument(), false, ctm);
+ transfer(entry.getAllFeatures(), qualifiersToTransfer, key, sameKey,
+ overwrite, true, geneNames);
+ ChadoTransactionManager.commit((DatabaseDocument) newDbEntry
+ .getDocument(), false, ctm);
- entry_group.removeFeatureChangeListener(ctm);
- entry_group.removeEntryChangeListener(ctm);
- // if(newDbEntry != null)
- // GeneEdit.showGeneEditor(null, geneNames[i], newDbEntry);
+ entry_group.removeFeatureChangeListener(ctm);
+ entry_group.removeEntryChangeListener(ctm);
+ // if(newDbEntry != null)
+ // GeneEdit.showGeneEditor(null, geneNames[i], newDbEntry);
+ }
}
-
setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
if(genesNotFound != null)
@@ -721,7 +751,7 @@ class TransferAnnotationTool extends JFrame
public boolean testPredicate(Feature targetFeature)
{
String targetKey = targetFeature.getKey().getKeyString();
- if (!sameKey || !targetKey.equals(key))
+ if (sameKey && !targetKey.equals(key))
return false;
Vector chadoNames = null;
@@ -745,7 +775,6 @@ class TransferAnnotationTool extends JFrame
}
String thisFeatureSystematicName = targetFeature.getSystematicName();
-
for (int i = 0; i < geneNames.length; i++)
{
if(geneNames[i].equals(thisFeatureSystematicName) ||