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Commit ff4be7c8 authored by tjc's avatar tjc
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further development - addition of overwrite function and changes to the look of the tool 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10218 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+ 154
− 49
View file @ ff4be7c8
/* 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;
}
}
}
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