diff --git a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
index aa5ac8292193ec968b1c8a09855e9b646a729f1d..bd01b611a6f869c34522bf11c77c8ec66bcd2d3e 100644
--- a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+++ b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
@@ -1,10 +1,10 @@
/* TransferAnnotationTool.java
*
- * created: 2008
+ * created: 2009
*
* This file is part of Artemis
*
- * Copyright (C) 2008 Genome Research Limited
+ * Copyright (C) 2009 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
@@ -25,6 +25,7 @@
package uk.ac.sanger.artemis.components;
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.FlowLayout;
@@ -44,11 +45,13 @@ import java.util.Vector;
import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JCheckBox;
+import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
import javax.swing.SwingConstants;
import uk.ac.sanger.artemis.Entry;
@@ -95,12 +98,21 @@ class TransferAnnotationTool extends JFrame
"transmembrane",
"previous_systematic_id"
};
+
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(TransferAnnotationTool.class);
+ private Color STEEL_BLUE = new Color(25, 25, 112);
+
+ /**
+ * Tool for transferring annotation from one feature to other feature(s)
+ * @param feature
+ * @param entryGroup
+ * @param geneNames
+ */
public TransferAnnotationTool(final Feature feature,
- final EntryGroup entryGroup,
- final List geneNames)
+ final EntryGroup entryGroup,
+ final List geneNames)
{
super("Transfer Annotation Tool :: "
+ feature.getIDString());
@@ -109,20 +121,49 @@ class TransferAnnotationTool extends JFrame
JPanel panel = new JPanel(flow);
JPanel pane = new JPanel(new GridBagLayout());
JScrollPane jsp = new JScrollPane(panel);
-
+ panel.setBackground(Color.white);
+ pane.setBackground(Color.white);
panel.add(pane);
JPanel framePanel = (JPanel)getContentPane();
framePanel.add(jsp, BorderLayout.CENTER);
framePanel.setPreferredSize(new Dimension(600,600));
+ final Vector geneNameCheckBoxes = new Vector();
+ final Hashtable qualifierCheckBoxes = new Hashtable();
+
+ addMainPanel(feature, pane, qualifierCheckBoxes,
+ geneNameCheckBoxes, geneNames);
+ addBottomButtons(qualifierCheckBoxes, geneNameCheckBoxes,
+ framePanel, feature, entryGroup);
+
+ pack();
+ setVisible(true);
+ }
+
+ /**
+ * Construct the panel for setting up the gene list and the
+ * list of qualifiers to transfer.
+ * @param feature
+ * @param pane
+ * @param qualifierCheckBoxes
+ * @param geneNameCheckBoxes
+ * @param geneNames
+ */
+ private void addMainPanel(final Feature feature,
+ final JPanel pane,
+ final Hashtable qualifierCheckBoxes,
+ final Vector geneNameCheckBoxes,
+ final List geneNames)
+ {
GridBagConstraints c = new GridBagConstraints();
int nrows = 0;
c.anchor = GridBagConstraints.NORTHWEST;
c.gridx = 2;
c.gridy = 0;
-
+ c.ipadx = 0;
+
JLabel geneLabel = new JLabel(feature.getIDString() + " Qualifiers");
geneLabel.setFont(geneLabel.getFont().deriveFont(Font.BOLD));
pane.add(geneLabel, c);
@@ -135,8 +176,7 @@ class TransferAnnotationTool extends JFrame
c.gridy = ++nrows;
c.gridy = ++nrows;
c.anchor = GridBagConstraints.WEST;
-
- final Hashtable qualifierCheckBoxes = new Hashtable();
+
final QualifierVector qualifiers = feature.getQualifiers();
for(int i = 0; i < qualifiers.size(); i++)
{
@@ -179,7 +219,6 @@ class TransferAnnotationTool extends JFrame
c.gridheight = nrows;
c.fill = GridBagConstraints.BOTH;
- final Vector geneNameCheckBoxes = new Vector();
final Box geneNameBox = Box.createVerticalBox();
pane.add(geneNameBox, c);
@@ -213,7 +252,7 @@ class TransferAnnotationTool extends JFrame
});
pane.add(toggle, c);
-
+ Box xBox = Box.createHorizontalBox();
final JButton toggleGeneList = new JButton("Toggle");
toggleGeneList.addActionListener(new ActionListener()
{
@@ -226,25 +265,76 @@ class TransferAnnotationTool extends JFrame
}
}
});
- c.gridx = 0;
- pane.add(toggleGeneList, c);
+ xBox.add(toggleGeneList);
+ final JButton addGenes = new JButton("Add");
+ addGenes.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ JTextArea geneNameTextArea = new JTextArea();
+ geneNameTextArea.setEditable(true);
+ JScrollPane jsp = new JScrollPane(geneNameTextArea);
+
+ int res = JOptionPane.showConfirmDialog(TransferAnnotationTool.this,
+ jsp, "Paste Features to Add",
+ JOptionPane.OK_CANCEL_OPTION);
+ if(res == JOptionPane.CANCEL_OPTION)
+ return;
+
+ String geneNames[] = geneNameTextArea.getText().split("\\s");
+ for(int i=0;i<geneNames.length; i++)
+ {
+ if(geneNames[i] == null || geneNames[i].equals(""))
+ continue;
+ JCheckBox cb = new JCheckBox(geneNames[i],true);
+ geneNameBox.add(cb);
+ geneNameCheckBoxes.add(cb);
+ }
+ pane.revalidate();
+ }
+ });
+ xBox.add(addGenes);
+ c.gridx = 0;
+ pane.add(xBox, c);
+ }
+
+ /**
+ * Add panel for the transfer and close button.
+ * @param qualifierCheckBoxes
+ * @param geneNameCheckBoxes
+ * @param framePanel
+ * @param feature
+ * @param entryGroup
+ */
+ private void addBottomButtons(final Hashtable qualifierCheckBoxes,
+ final Vector geneNameCheckBoxes,
+ final JPanel framePanel,
+ final Feature feature,
+ final EntryGroup entryGroup)
+ {
final JCheckBox sameKeyCheckBox = new JCheckBox("Add to feature of same key", true);
+ final JCheckBox overwriteCheckBox = new JCheckBox("Overwrite", false);
+ overwriteCheckBox.setToolTipText("overwrite rather than append values");
+
Box buttonBox = Box.createHorizontalBox();
final JButton transfer = new JButton(">>TRANSFER");
+ transfer.setToolTipText("transfer annotation");
transfer.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
transferAnnotation(qualifierCheckBoxes, geneNameCheckBoxes, feature,
- entryGroup, sameKeyCheckBox.isSelected());
+ entryGroup, sameKeyCheckBox.isSelected(),
+ overwriteCheckBox.isSelected());
}
});
Box yBox = Box.createVerticalBox();
yBox.add(transfer);
yBox.add(sameKeyCheckBox);
+ yBox.add(overwriteCheckBox);
buttonBox.add(yBox);
final JButton close = new JButton("CLOSE");
@@ -261,49 +351,53 @@ class TransferAnnotationTool extends JFrame
buttonBox.add(yBox);
buttonBox.add(Box.createHorizontalGlue());
framePanel.add(buttonBox, BorderLayout.SOUTH);
-
- pack();
- setVisible(true);
}
-
+
+ /**
+ * Set up the expander button to display qualifier values.
+ * @param butt - expander button
+ * @param qualifier - the qualifer that is being displayed
+ * @param qualifierValueBox - Box containing the values
+ * @param qualifierNameCheckBox - JCheckBox for the given qualifier
+ * @param pane
+ * @return
+ */
private Vector setExpanderButton(final JButton butt,
final Qualifier qualifier,
final Box qualifierValueBox,
- final JCheckBox qualifierNameCheckBox,
+ final JCheckBox qualifierNameCheckBox,
final JPanel pane)
{
- butt.setMargin(new Insets(0,0,0,0));
+ butt.setMargin(new Insets(0, 0, 0, 0));
butt.setHorizontalAlignment(SwingConstants.RIGHT);
+ butt.setHorizontalTextPosition(SwingConstants.RIGHT);
butt.setBorderPainted(false);
- butt.setFont(new Font("SansSerif", Font.BOLD, 11));
- butt.setPreferredSize(new Dimension(butt.getPreferredSize().width,11));
+ butt.setFont(butt.getFont().deriveFont(Font.BOLD));
+ butt.setForeground(STEEL_BLUE);
butt.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- if(butt.getText().equals("+"))
- {
+ if (butt.getText().equals("+"))
butt.setText("-");
- qualifierValueBox.setVisible(true);
- }
else
- {
butt.setText("+");
- qualifierValueBox.setVisible(false);
- }
+
+ qualifierValueBox.setVisible(butt.getText().equals("-"));
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++)
+ for (int i = 0; i < values.size(); i++)
{
- JCheckBox cb = new JCheckBox((String)values.get(i),
- qualifierNameCheckBox.isSelected());
+ JCheckBox cb = new JCheckBox((String) values.get(i),
+ qualifierNameCheckBox.isSelected());
+ cb.setFont(cb.getFont().deriveFont(Font.ITALIC));
qualifierValueBox.add(cb);
qualifierValuesCheckBox.add(cb);
}
@@ -327,17 +421,20 @@ class TransferAnnotationTool extends JFrame
/**
* Transfer selected qualifiers to the list of features defined
- * by the names in the JTextArea
+ * by the selected names.
* @param qualifierCheckBoxes - list of qualifier check boxes
* @param geneNameTextArea - text with a list of feature names to transfer to
* @param feature - feature to copy from
* @param entryGroup
+ * @param sameKey
+ * @param overwrite
*/
private void transferAnnotation(final Hashtable qualifierCheckBoxes,
final Vector geneNameCheckBoxes,
final Feature orginatingFeature,
final EntryGroup entryGroup,
- final boolean sameKey)
+ final boolean sameKey,
+ final boolean overwrite)
{
setCursor(new Cursor(Cursor.WAIT_CURSOR));
// transfer selected annotation to genes
@@ -407,7 +504,8 @@ class TransferAnnotationTool extends JFrame
// transfer selected annotation
entryGroup.getActionController().startAction();
geneNames = transfer(features, qualifiersToTransfer, key,
- sameKey, GeneUtils.isDatabaseEntry(entryGroup), geneNames);
+ sameKey, overwrite,
+ GeneUtils.isDatabaseEntry(entryGroup), geneNames);
entryGroup.getActionController().endAction();
//
@@ -453,7 +551,7 @@ class TransferAnnotationTool extends JFrame
ctm.setEntryGroup(entry_group);
transfer(entry.getAllFeatures(), qualifiersToTransfer, key, sameKey,
- true, geneNames);
+ overwrite, true, geneNames);
ChadoTransactionManager.commit((DatabaseDocument) newDbEntry
.getDocument(), false, ctm);
@@ -484,7 +582,8 @@ class TransferAnnotationTool extends JFrame
private String[] transfer(final FeatureVector features,
final QualifierVector qualifiersToTransfer,
final String key,
- final boolean sameKey,
+ final boolean sameKey,
+ final boolean overwrite,
final boolean isDatabaseEntry,
String[] geneNames)
{
@@ -502,18 +601,23 @@ class TransferAnnotationTool extends JFrame
try
{
- final StringVector oldValues;
- if(thisFeature.getQualifierByName(newQualifier.getName()) == null)
- oldValues = null;
- else
- oldValues =
- thisFeature.getQualifierByName(newQualifier.getName()).getValues();
-
- final Qualifier newQualifierTmp =
- getQualifierWithoutDuplicateValues(newQualifier, oldValues);
- if(newQualifierTmp == null)
- continue;
- thisFeature.addQualifierValues(newQualifierTmp);
+ if(overwrite)
+ thisFeature.setQualifier(newQualifier);
+ else
+ {
+ final StringVector oldValues;
+ if (thisFeature.getQualifierByName(newQualifier.getName()) == null)
+ oldValues = null;
+ else
+ oldValues = thisFeature.getQualifierByName(
+ newQualifier.getName()).getValues();
+
+ final Qualifier newQualifierTmp = getQualifierWithoutDuplicateValues(
+ newQualifier, oldValues);
+ if (newQualifierTmp == null)
+ continue;
+ thisFeature.addQualifierValues(newQualifierTmp);
+ }
}
catch (Exception e1)
{
@@ -647,4 +751,5 @@ class TransferAnnotationTool extends JFrame
return geneName;
}
}
+
}