diff --git a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
index e7bd8cfda2ae24bef62e55e0f542d9ff13b5fa94..51e1e63740796da258cba1a7f448d56782d65668 100644
--- a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+++ b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
@@ -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)
{
@@ -165,26 +171,68 @@ 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;
c.gridy = 2;
c.gridheight = nrows;
@@ -212,11 +260,15 @@ class TransferAnnotationTool extends JFrame
{
public void actionPerformed(ActionEvent e)
{
- Enumeration enumQualifiers = qualifierCheckBoxes.keys();
- while(enumQualifiers.hasMoreElements())
+ for(int i=0; i<qualifierPanels.size(); i++)
{
- JCheckBox cb = (JCheckBox) enumQualifiers.nextElement();
- cb.setSelected(!cb.isSelected());
+ QualifierPanel qP = (QualifierPanel)qualifierPanels.get(i);
+ Enumeration enumQualifiers = qP.getQualifierCheckBoxes().keys();
+ while(enumQualifiers.hasMoreElements())
+ {
+ JCheckBox cb = (JCheckBox) enumQualifiers.nextElement();
+ cb.setSelected(!cb.isSelected());
+ }
}
}
});
@@ -268,6 +320,40 @@ class TransferAnnotationTool extends JFrame
c.gridx = 0;
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;
+ }
/**
@@ -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 JPanel framePanel,
final EntryGroup entryGroup)
{
final JCheckBox sameKeyCheckBox = new JCheckBox("Add to feature of same key", true);
@@ -296,9 +381,23 @@ class TransferAnnotationTool extends JFrame
{
public void actionPerformed(ActionEvent e)
{
- transferAnnotation(qualifierCheckBoxes, geneNameCheckBoxes, feature,
- entryGroup, sameKeyCheckBox.isSelected(),
- overwriteCheckBox.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();
@@ -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
@@ -500,15 +500,7 @@ class TransferAnnotationTool extends JFrame
"No genes selected.",
"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