diff --git a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
index fdde6c8b6259b9419efcbf214d7162bc035a845e..aa5ac8292193ec968b1c8a09855e9b646a729f1d 100644
--- a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+++ b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
@@ -24,22 +24,32 @@
package uk.ac.sanger.artemis.components;
+import java.awt.BorderLayout;
import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
+import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
+import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
-import javax.swing.JTextArea;
+import javax.swing.JScrollPane;
+import javax.swing.SwingConstants;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
@@ -72,6 +82,7 @@ class TransferAnnotationTool extends JFrame
"isObsolete",
"timelastmodified",
"cytoplasm_location",
+ "membrane_structure",
"non_cytoplasm_location",
"orthologous_to",
"paralogous_to",
@@ -84,6 +95,8 @@ class TransferAnnotationTool extends JFrame
"transmembrane",
"previous_systematic_id"
};
+ private static org.apache.log4j.Logger logger4j =
+ org.apache.log4j.Logger.getLogger(TransferAnnotationTool.class);
public TransferAnnotationTool(final Feature feature,
final EntryGroup entryGroup,
@@ -92,27 +105,38 @@ class TransferAnnotationTool extends JFrame
super("Transfer Annotation Tool :: "
+ feature.getIDString());
- JPanel pane = (JPanel) getContentPane();
- pane.setLayout(new GridBagLayout());
+ FlowLayout flow = new FlowLayout(FlowLayout.LEFT);
+ JPanel panel = new JPanel(flow);
+ JPanel pane = new JPanel(new GridBagLayout());
+ JScrollPane jsp = new JScrollPane(panel);
+
+ panel.add(pane);
+
+ JPanel framePanel = (JPanel)getContentPane();
+ framePanel.add(jsp, BorderLayout.CENTER);
+ framePanel.setPreferredSize(new Dimension(600,600));
+
GridBagConstraints c = new GridBagConstraints();
int nrows = 0;
- c.gridx = 0;
+ c.anchor = GridBagConstraints.NORTHWEST;
+ c.gridx = 2;
c.gridy = 0;
+
JLabel geneLabel = new JLabel(feature.getIDString() + " Qualifiers");
geneLabel.setFont(geneLabel.getFont().deriveFont(Font.BOLD));
pane.add(geneLabel, c);
- c.gridx = 1;
+ c.gridx = 0;
JLabel label = new JLabel("Gene List");
label.setFont(label.getFont().deriveFont(Font.BOLD));
pane.add(label, c);
- c.gridx = 0;
+ c.gridy = ++nrows;
c.gridy = ++nrows;
c.anchor = GridBagConstraints.WEST;
- final Vector qualifierCheckBoxes = new Vector();
+ final Hashtable qualifierCheckBoxes = new Hashtable();
final QualifierVector qualifiers = feature.getQualifiers();
for(int i = 0; i < qualifiers.size(); i++)
{
@@ -121,66 +145,108 @@ class TransferAnnotationTool extends JFrame
if(isNonTransferable(qualifier.getName()))
continue;
- JCheckBox checkBox = new JCheckBox(qualifier.getName(), false);
- pane.add(checkBox, c);
- qualifierCheckBoxes.add(checkBox);
+ 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;
}
-
- c.gridx = 1;
- c.gridy = 1;
+ c.gridx = 0;
+ c.gridy = 2;
c.gridheight = nrows;
c.fill = GridBagConstraints.BOTH;
- final JTextArea geneNameTextArea = new JTextArea("gene1");
- geneNameTextArea.setEditable(true);
- pane.add(geneNameTextArea, c);
+
+ final Vector geneNameCheckBoxes = new Vector();
+ final Box geneNameBox = Box.createVerticalBox();
+ pane.add(geneNameBox, c);
+
if(geneNames != null)
{
- geneNameTextArea.setText("");
- for(int i=0;i<geneNames.size(); i++)
- {
- geneNameTextArea.append((String) geneNames.get(i)+"\n");
- }
+ for(int i = 0; i < geneNames.size(); i++)
+ {
+ JCheckBox cb = new JCheckBox((String) geneNames.get(i),true);
+ geneNameBox.add(cb);
+ geneNameCheckBoxes.add(cb);
+ }
}
- c.gridy = ++nrows;
+ c.gridy = 1;
c.gridheight = 1;
c.fill = GridBagConstraints.NONE;
- c.gridx = 0;
- final JButton toggle = new JButton("Toggle Selection");
+ c.gridx = 2;
+ final JButton toggle = new JButton("Toggle");
toggle.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- for(int i = 0; i < qualifierCheckBoxes.size(); i++)
+ Enumeration enumQualifiers = qualifierCheckBoxes.keys();
+ while(enumQualifiers.hasMoreElements())
{
- JCheckBox cb = (JCheckBox) qualifierCheckBoxes.get(i);
+ JCheckBox cb = (JCheckBox) enumQualifiers.nextElement();
cb.setSelected(!cb.isSelected());
}
}
});
pane.add(toggle, c);
+
+
+ final JButton toggleGeneList = new JButton("Toggle");
+ toggleGeneList.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ for(int i = 0; i < geneNameCheckBoxes.size(); i++)
+ {
+ JCheckBox cb = (JCheckBox) geneNameCheckBoxes.get(i);
+ cb.setSelected(!cb.isSelected());
+ }
+ }
+ });
+ c.gridx = 0;
+ pane.add(toggleGeneList, c);
+
final JCheckBox sameKeyCheckBox = new JCheckBox("Add to feature of same key", true);
-
+
+ Box buttonBox = Box.createHorizontalBox();
final JButton transfer = new JButton(">>TRANSFER");
transfer.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- transferAnnotation(qualifierCheckBoxes, geneNameTextArea, feature,
+ transferAnnotation(qualifierCheckBoxes, geneNameCheckBoxes, feature,
entryGroup, sameKeyCheckBox.isSelected());
}
});
- c.gridx = 1;
- pane.add(transfer, c);
+ Box yBox = Box.createVerticalBox();
+ yBox.add(transfer);
+ yBox.add(sameKeyCheckBox);
+ buttonBox.add(yBox);
- c.gridy = ++nrows;
- c.gridx = 1;
- pane.add(sameKeyCheckBox, c);
-
final JButton close = new JButton("CLOSE");
close.addActionListener(new ActionListener()
{
@@ -189,12 +255,61 @@ class TransferAnnotationTool extends JFrame
dispose();
}
});
- c.gridy = ++nrows;
- pane.add(close, c);
+ yBox = Box.createVerticalBox();
+ yBox.add(close);
+ yBox.add(Box.createVerticalGlue());
+ buttonBox.add(yBox);
+ buttonBox.add(Box.createHorizontalGlue());
+ framePanel.add(buttonBox, BorderLayout.SOUTH);
+
pack();
setVisible(true);
}
+ private Vector setExpanderButton(final JButton butt,
+ final Qualifier qualifier,
+ final Box qualifierValueBox,
+ final JCheckBox qualifierNameCheckBox,
+ final JPanel pane)
+ {
+ butt.setMargin(new Insets(0,0,0,0));
+ butt.setHorizontalAlignment(SwingConstants.RIGHT);
+ butt.setBorderPainted(false);
+ butt.setFont(new Font("SansSerif", Font.BOLD, 11));
+ butt.setPreferredSize(new Dimension(butt.getPreferredSize().width,11));
+
+ butt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if(butt.getText().equals("+"))
+ {
+ butt.setText("-");
+ qualifierValueBox.setVisible(true);
+ }
+ else
+ {
+ butt.setText("+");
+ qualifierValueBox.setVisible(false);
+ }
+ pane.revalidate();
+ }
+ });
+
+ // set-up qualifier values list
+ qualifierValueBox.setVisible(false);
+ Vector qualifierValuesCheckBox = new Vector();
+ StringVector values = qualifier.getValues();
+ for(int i=0; i<values.size(); i++)
+ {
+ JCheckBox cb = new JCheckBox((String)values.get(i),
+ qualifierNameCheckBox.isSelected());
+ qualifierValueBox.add(cb);
+ qualifierValuesCheckBox.add(cb);
+ }
+ return qualifierValuesCheckBox;
+ }
+
/**
* Returns true if this qualifier is non-transferable
* @param qualifierName
@@ -218,27 +333,73 @@ class TransferAnnotationTool extends JFrame
* @param feature - feature to copy from
* @param entryGroup
*/
- private void transferAnnotation(final Vector qualifierCheckBoxes,
- final JTextArea geneNameTextArea,
- final Feature orginatingFeature,
- final EntryGroup entryGroup,
- final boolean sameKey)
+ private void transferAnnotation(final Hashtable qualifierCheckBoxes,
+ final Vector geneNameCheckBoxes,
+ final Feature orginatingFeature,
+ final EntryGroup entryGroup,
+ final boolean sameKey)
{
setCursor(new Cursor(Cursor.WAIT_CURSOR));
// transfer selected annotation to genes
- final QualifierVector qualifiers = orginatingFeature.getQualifiers();
- final QualifierVector qualifiersToTransfer = new QualifierVector();
- for(int i = 0; i < qualifierCheckBoxes.size(); i++)
+ final QualifierVector qualifiers = orginatingFeature.getQualifiers();
+ final QualifierVector qualifiersToTransfer = new QualifierVector();
+
+ Enumeration enumQualifiers = qualifierCheckBoxes.keys();
+ while(enumQualifiers.hasMoreElements())
{
- JCheckBox cb = (JCheckBox) qualifierCheckBoxes.get(i);
- if(cb.isSelected())
- {
- qualifiersToTransfer.addElement(
- qualifiers.getQualifierByName(cb.getText()).copy());
- }
+ JCheckBox cb = (JCheckBox) enumQualifiers.nextElement();
+ if (cb.isSelected())
+ {
+ Vector qualifierValuesCheckBox = (Vector)qualifierCheckBoxes.get(cb);
+ StringVector values = qualifiers.getQualifierByName(cb.getText()).getValues();
+ StringVector valuesToTransfer = new StringVector(values);
+
+ logger4j.debug("TRANSFER "+cb.getText());
+ for(int i=0; i<qualifierValuesCheckBox.size(); i++)
+ {
+ JCheckBox valuesCb = (JCheckBox) qualifierValuesCheckBox.get(i);
+ if(!valuesCb.isSelected())
+ {
+ valuesToTransfer.remove(valuesCb.getText());
+ logger4j.debug("NOT TRANSFERING "+valuesCb.getText());
+ }
+ }
+
+ if(valuesToTransfer.size() < 1)
+ continue;
+ qualifiersToTransfer.addElement(new Qualifier(cb.getText(), valuesToTransfer));
+ }
}
+
+ int count = 0;
+ for(int i =0; i<geneNameCheckBoxes.size(); i++)
+ {
+ if( ((JCheckBox)geneNameCheckBoxes.get(i)).isSelected() )
+ count++;
+ }
+
+ if(count < 1)
+ {
+ setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ JOptionPane.showMessageDialog(this,
+ "No genes selected.",
+ "Warning", JOptionPane.WARNING_MESSAGE);
+ return;
+ }
- String geneNames[] = geneNameTextArea.getText().split("\\s");
+ String geneNames[] = new String[count];
+ count = 0;
+ for(int i =0; i<geneNameCheckBoxes.size(); i++)
+ {
+ JCheckBox cb = (JCheckBox)geneNameCheckBoxes.get(i);
+ if( cb.isSelected() )
+ {
+ geneNames[count] = cb.getText();
+ logger4j.debug("TRANSFER ANNOTATION TO "+geneNames[count]);
+ count++;
+ }
+ }
+ //geneNameTextArea.getText().split("\\s");
final String key = orginatingFeature.getKey().getKeyString();
final FeatureVector features = entryGroup.getAllFeatures();
@@ -257,20 +418,20 @@ class TransferAnnotationTool extends JFrame
DatabaseDocument doc = (DatabaseDocument) db_entry.getDocument();
Vector genesNotFound = null;
- for(int i=0; i<geneNames.length; i++)
- {
- DatabaseDocumentEntry newDbEntry =
- GeneEdit.makeGeneEntry(null, geneNames[i], doc, null);
-
- if(newDbEntry == null)
- {
- if(genesNotFound == null)
- genesNotFound = new Vector();
- genesNotFound.add(geneNames[i]);
- continue;
- }
-
- char[] c = new char[1];
+ for (int i = 0; i < geneNames.length; i++)
+ {
+ DatabaseDocumentEntry newDbEntry = GeneEdit.makeGeneEntry(null,
+ geneNames[i], doc, null);
+
+ if (newDbEntry == null)
+ {
+ if (genesNotFound == null)
+ genesNotFound = new Vector();
+ genesNotFound.add(geneNames[i]);
+ continue;
+ }
+
+ char[] c = new char[1];
PartialSequence ps = new PartialSequence(c, 100, 0, null, null);
newDbEntry.setPartialSequence(ps);
Entry entry = null;
@@ -278,26 +439,29 @@ class TransferAnnotationTool extends JFrame
{
entry = new Entry(newDbEntry);
}
- catch(Exception e) { e.printStackTrace(); }
-
+ 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);
-
- transfer(entry.getAllFeatures(), qualifiersToTransfer, key,
- sameKey, 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);
- }
+
+ transfer(entry.getAllFeatures(), qualifiersToTransfer, key, sameKey,
+ 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);
+ }
setCursor(new Cursor(Cursor.DEFAULT_CURSOR));