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Commit 79927114 authored by tjc's avatar tjc
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include qualifier values for entire gene model if the active feature is part of a gene model 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10243 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent dab29535
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uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+ 271
− 131
View file @ 79927114
......@@ -39,9 +39,12 @@ import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.Vector;
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JCheckBox;
......@@ -52,6 +55,9 @@ import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.SwingConstants;
import javax.swing.border.Border;
import javax.swing.border.EtchedBorder;
import javax.swing.border.TitledBorder;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
......@@ -131,12 +137,12 @@ class TransferAnnotationTool extends JFrame
framePanel.setPreferredSize(new Dimension(600,600));
final Vector geneNameCheckBoxes = new Vector();
final Hashtable qualifierCheckBoxes = new Hashtable();
final Vector qualifierPanels = new Vector();
addMainPanel(feature, pane, qualifierCheckBoxes,
addMainPanel(feature, pane, qualifierPanels,
geneNameCheckBoxes, geneNames);
addBottomButtons(qualifierCheckBoxes, geneNameCheckBoxes,
framePanel, feature, entryGroup);
addBottomButtons(qualifierPanels, geneNameCheckBoxes,
framePanel, entryGroup);
pack();
setVisible(true);
......@@ -153,7 +159,7 @@ class TransferAnnotationTool extends JFrame
*/
private void addMainPanel(final Feature feature,
final JPanel pane,
final Hashtable qualifierCheckBoxes,
final Vector qualifierPanels,
final Vector geneNameCheckBoxes,
final List geneNames)
{
......@@ -165,24 +171,66 @@ class TransferAnnotationTool extends JFrame
c.gridy = 0;
c.ipadx = 0;
JLabel geneLabel = new JLabel(feature.getIDString() + " Qualifiers");
JLabel geneLabel = new JLabel("Qualifier(s)");
geneLabel.setFont(geneLabel.getFont().deriveFont(Font.BOLD));
pane.add(geneLabel, c);
c.gridy = 0;
c.ipadx = 0;
c.gridx = 0;
JLabel label = new JLabel("Gene List");
label.setFont(label.getFont().deriveFont(Font.BOLD));
pane.add(label, c);
c.gridx = 2;
c.gridy = ++nrows;
c.gridy = ++nrows;
c.anchor = GridBagConstraints.WEST;
final QualifierVector qualifiers = feature.getQualifiers();
for(int i = 0; i < qualifiers.size(); i++)
addQualifierPanel(feature, qualifierPanels, c, nrows, pane);
nrows+=2;
if(feature.getEmblFeature() instanceof GFFStreamFeature)
{
nrows = addQualifierComponents(pane, (Qualifier) qualifiers.get(i),
qualifierCheckBoxes, c, nrows);
GFFStreamFeature gffFeature =
((GFFStreamFeature) feature.getEmblFeature());
if (gffFeature.getChadoGene() != null)
{
String id = GeneUtils.getUniqueName(gffFeature);
ChadoCanonicalGene chadoGene = gffFeature.getChadoGene();
Feature gene = (Feature) chadoGene.getGene().getUserData();
if(!id.equals( GeneUtils.getUniqueName(((GFFStreamFeature)chadoGene.getGene())) ))
addQualifierPanel(gene, qualifierPanels, c, nrows, pane);
nrows+=2;
String transcriptName =
chadoGene.getTranscriptFromName(GeneUtils.getUniqueName(gffFeature));
if(transcriptName != null)
{
GFFStreamFeature transcript =
(GFFStreamFeature) chadoGene.getFeatureFromId(transcriptName);
addQualifierPanel((Feature)transcript.getUserData(),
qualifierPanels, c, nrows, pane);
nrows+=2;
Set children = chadoGene.getChildren(transcript);
Iterator it = children.iterator();
while(it.hasNext())
{
GFFStreamFeature kid = (GFFStreamFeature)it.next();
if(id.equals( GeneUtils.getUniqueName(((GFFStreamFeature)kid)) ))
continue;
addQualifierPanel((Feature)kid.getUserData(), qualifierPanels,
c, nrows, pane);
nrows+=2;
}
}
}
}
c.gridx = 0;
......@@ -212,13 +260,17 @@ class TransferAnnotationTool extends JFrame
{
public void actionPerformed(ActionEvent e)
{
Enumeration enumQualifiers = qualifierCheckBoxes.keys();
for(int i=0; i<qualifierPanels.size(); i++)
{
QualifierPanel qP = (QualifierPanel)qualifierPanels.get(i);
Enumeration enumQualifiers = qP.getQualifierCheckBoxes().keys();
while(enumQualifiers.hasMoreElements())
{
JCheckBox cb = (JCheckBox) enumQualifiers.nextElement();
cb.setSelected(!cb.isSelected());
}
}
}
});
pane.add(toggle, c);
......@@ -269,6 +321,40 @@ class TransferAnnotationTool extends JFrame
pane.add(xBox, c);
}
/**
* Add a panel to display a given features qualifiers.
* @param f
* @param qualifierPanels
* @param c
* @param nrows
* @param pane
*/
private void addQualifierPanel(Feature f,
Vector qualifierPanels,
GridBagConstraints c,
int nrows,
JPanel pane)
{
QualifierPanel qPanel = new QualifierPanel(f,f.getKey().getKeyString());
if(qPanel.nrows == 0)
return;
c.fill = GridBagConstraints.HORIZONTAL;
c.anchor = GridBagConstraints.WEST;
c.weightx = 100;
qualifierPanels.add(qPanel);
c.gridy = ++nrows;
JLabel l = new JLabel(f.getIDString());
l.setFont(l.getFont().deriveFont(Font.BOLD));
l.setForeground(STEEL_BLUE);
pane.add(l, c);
c.gridy = ++nrows;
pane.add(qPanel, c);
c.weightx = 0.d;
}
/**
* Add panel for the transfer and close button.
......@@ -278,10 +364,9 @@ class TransferAnnotationTool extends JFrame
* @param feature
* @param entryGroup
*/
private void addBottomButtons(final Hashtable qualifierCheckBoxes,
private void addBottomButtons(final Vector qualifierPanels,
final Vector geneNameCheckBoxes,
final JPanel framePanel,
final Feature feature,
final EntryGroup entryGroup)
{
final JCheckBox sameKeyCheckBox = new JCheckBox("Add to feature of same key", true);
......@@ -296,10 +381,24 @@ class TransferAnnotationTool extends JFrame
{
public void actionPerformed(ActionEvent e)
{
transferAnnotation(qualifierCheckBoxes, geneNameCheckBoxes, feature,
entryGroup, sameKeyCheckBox.isSelected(),
if(overwriteCheckBox.isSelected())
{
int res = JOptionPane.showConfirmDialog(TransferAnnotationTool.this,
"Overwrite selected annotation?",
"Overwrite", JOptionPane.OK_CANCEL_OPTION);
if(res == JOptionPane.CANCEL_OPTION)
return;
}
for(int i = 0; i < qualifierPanels.size(); i++)
{
QualifierPanel qP = (QualifierPanel) qualifierPanels.get(i);
transferAnnotation(qP.getQualifierCheckBoxes(),
geneNameCheckBoxes, qP.getFeature(), entryGroup,
sameKeyCheckBox.isSelected(),
overwriteCheckBox.isSelected());
}
}
});
Box yBox = Box.createVerticalBox();
yBox.add(transfer);
......@@ -324,105 +423,6 @@ class TransferAnnotationTool extends JFrame
}
/**
* 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
* @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 JPanel pane)
{
butt.setMargin(new Insets(0, 0, 0, 0));
butt.setHorizontalAlignment(SwingConstants.RIGHT);
butt.setHorizontalTextPosition(SwingConstants.RIGHT);
butt.setBorderPainted(false);
butt.setFont(butt.getFont().deriveFont(Font.BOLD));
butt.setForeground(STEEL_BLUE);
butt.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (butt.getText().equals("+"))
butt.setText("-");
else
butt.setText("+");
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++)
{
JCheckBox cb = new JCheckBox((String) values.get(i),
qualifierNameCheckBox.isSelected());
cb.setFont(cb.getFont().deriveFont(Font.ITALIC));
qualifierValueBox.add(cb);
qualifierValuesCheckBox.add(cb);
}
return qualifierValuesCheckBox;
}
/**
* Returns true if this qualifier is non-transferable
* @param qualifierName
......@@ -501,14 +501,6 @@ 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));
......@@ -724,6 +716,154 @@ class TransferAnnotationTool extends JFrame
return newarray;
}
class QualifierPanel extends JPanel
{
private Hashtable qualifierCheckBoxes = new Hashtable();
private Feature feature;
protected int nrows = 0;
public QualifierPanel(Feature feature, String title)
{
super(new GridBagLayout());
this.feature = feature;
TitledBorder titleBorder = BorderFactory.createTitledBorder(
BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), title);
titleBorder.setTitleJustification(TitledBorder.LEFT);
titleBorder.setTitleColor(STEEL_BLUE);
setBorder(titleBorder);
GridBagConstraints c = new GridBagConstraints();
c.anchor = GridBagConstraints.WEST;
c.ipadx = 0;
final QualifierVector qualifiers = feature.getQualifiers();
for(int i = 0; i < qualifiers.size(); i++)
{
nrows =
addQualifierComponents((Qualifier) qualifiers.get(i),
qualifierCheckBoxes, c, nrows);
}
setMinimumSize(new Dimension(
titleBorder.getMinimumSize(this).width,
getMinimumSize().height));
}
/**
* Add a qualifier to the list of transferable annotation
* @param pane
* @param qualifier
* @param qualifierCheckBoxes
* @param c
* @param nrows
* @return
*/
private int addQualifierComponents(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;
c.fill = GridBagConstraints.NONE;
c.weightx = 0.d;
Box qualifierValueBox = Box.createVerticalBox();
JButton detailsShowHide = new JButton("+");
final Vector qualifierValuesCheckBox = setExpanderButton(detailsShowHide,
qualifier, qualifierValueBox, qualifierNameCheckBox);
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());
}
}
});
add(detailsShowHide, c);
c.fill = GridBagConstraints.HORIZONTAL;
c.weightx = 100;
c.gridx = 2;
add(qualifierNameCheckBox, c);
qualifierCheckBoxes.put(qualifierNameCheckBox, qualifierValuesCheckBox);
c.gridy = ++nrows;
add(qualifierValueBox, c);
c.gridy = ++nrows;
return nrows;
}
/**
* 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)
{
butt.setMargin(new Insets(0, 0, 0, 0));
butt.setHorizontalAlignment(SwingConstants.RIGHT);
butt.setHorizontalTextPosition(SwingConstants.RIGHT);
butt.setBorderPainted(false);
butt.setFont(butt.getFont().deriveFont(Font.BOLD));
butt.setForeground(STEEL_BLUE);
butt.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
if (butt.getText().equals("+"))
butt.setText("-");
else
butt.setText("+");
qualifierValueBox.setVisible(butt.getText().equals("-"));
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());
cb.setFont(cb.getFont().deriveFont(Font.ITALIC));
qualifierValueBox.add(cb);
qualifierValuesCheckBox.add(cb);
}
return qualifierValuesCheckBox;
}
protected Hashtable getQualifierCheckBoxes()
{
return qualifierCheckBoxes;
}
protected Feature getFeature()
{
return feature;
}
}
/**
* Test if the feature is nominated to have annotation transferred
* to it. For genes in a chado database it looks at the gene name
......
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