diff --git a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
index f26be8d7f165198f9d3106572d574e001840457a..3e227ac939ec121ea6283dbe59223b929ebce0f4 100644
--- a/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
+++ b/uk/ac/sanger/artemis/components/TransferAnnotationTool.java
@@ -55,7 +55,6 @@ 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;
@@ -109,7 +108,7 @@ class TransferAnnotationTool extends JFrame
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(TransferAnnotationTool.class);
- private Color STEEL_BLUE = new Color(25, 25, 112);
+ protected static Color STEEL_BLUE = new Color(25, 25, 112);
/**
* Tool for transferring annotation from one feature to other feature(s)
@@ -389,6 +388,7 @@ class TransferAnnotationTool extends JFrame
return;
}
+ setCursor(new Cursor(Cursor.WAIT_CURSOR));
for(int i = 0; i < qualifierPanels.size(); i++)
{
QualifierPanel qP = (QualifierPanel) qualifierPanels.get(i);
@@ -399,6 +399,7 @@ class TransferAnnotationTool extends JFrame
if(res == -1)
break;
}
+ setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});
Box yBox = Box.createVerticalBox();
@@ -429,7 +430,7 @@ class TransferAnnotationTool extends JFrame
* @param qualifierName
* @return
*/
- private boolean isNonTransferable(String qualifierName)
+ protected static boolean isNonTransferable(String qualifierName)
{
for(int i=0; i<NON_TRANSFERABLE_QUALIFIERS.length; i++)
{
@@ -449,7 +450,8 @@ class TransferAnnotationTool extends JFrame
* @param sameKey
* @param overwrite
*/
- private int transferAnnotation(final Hashtable qualifierCheckBoxes,
+ protected static int transferAnnotation(
+ final Hashtable qualifierCheckBoxes,
final Vector geneNameCheckBoxes,
final Feature orginatingFeature,
final EntryGroup entryGroup,
@@ -496,15 +498,12 @@ class TransferAnnotationTool extends JFrame
if(count < 1)
{
- setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
- JOptionPane.showMessageDialog(this,
+ JOptionPane.showMessageDialog(null,
"No genes selected.",
"Warning", JOptionPane.WARNING_MESSAGE);
return -1;
}
- setCursor(new Cursor(Cursor.WAIT_CURSOR));
-
String geneNames[] = new String[count];
count = 0;
for(int i =0; i<geneNameCheckBoxes.size(); i++)
@@ -583,10 +582,9 @@ class TransferAnnotationTool extends JFrame
// GeneEdit.showGeneEditor(null, geneNames[i], newDbEntry);
}
}
- setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
if(genesNotFound != null)
- JOptionPane.showMessageDialog(this,
+ JOptionPane.showMessageDialog(null,
"Gene(s) Not Found:\n"+genesNotFound.toString(),
"Gene(s) Not Found", JOptionPane.WARNING_MESSAGE);
return 0;
@@ -602,7 +600,7 @@ class TransferAnnotationTool extends JFrame
* @param geneNames
* @return
*/
- private String[] transfer(final FeatureVector features,
+ private static String[] transfer(final FeatureVector features,
final QualifierVector qualifiersToTransfer,
final String key,
final boolean sameKey,
@@ -661,7 +659,7 @@ class TransferAnnotationTool extends JFrame
* @return
* @throws InvalidRelationException
*/
- private Qualifier getQualifierWithoutDuplicateValues(
+ private static Qualifier getQualifierWithoutDuplicateValues(
final Qualifier qualifier,
final StringVector values) throws InvalidRelationException
{
@@ -692,7 +690,7 @@ class TransferAnnotationTool extends JFrame
* @param str
* @return
*/
- private String[] removeArrayElement(final String strArr[], final String str)
+ private static String[] removeArrayElement(final String strArr[], final String str)
{
String[] newarray = new String[strArr.length - 1];
int count = 0;
@@ -718,221 +716,223 @@ class TransferAnnotationTool extends JFrame
return newarray;
}
- class QualifierPanel extends JPanel
+
+
+}
+
+class QualifierPanel extends JPanel
+{
+ private Hashtable qualifierCheckBoxes = new Hashtable();
+ private Feature feature;
+ protected int nrows = 0;
+
+ public QualifierPanel(Feature feature, String title)
{
- private Hashtable qualifierCheckBoxes = new Hashtable();
- private Feature feature;
- protected int nrows = 0;
+ super(new GridBagLayout());
+
+ this.feature = feature;
+
+ TitledBorder titleBorder = BorderFactory.createTitledBorder(
+ BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), title);
+ titleBorder.setTitleJustification(TitledBorder.LEFT);
+ titleBorder.setTitleColor(TransferAnnotationTool.STEEL_BLUE);
+ setBorder(titleBorder);
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.WEST;
+ c.ipadx = 0;
+ final QualifierVector qualifiers = feature.getQualifiers();
- public QualifierPanel(Feature feature, String title)
+ for(int i = 0; i < qualifiers.size(); i++)
{
- 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));
+ nrows =
+ addQualifierComponents((Qualifier) qualifiers.get(i),
+ qualifierCheckBoxes, c, nrows);
}
- /**
- * 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;
+ 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(TransferAnnotationTool.isNonTransferable(qualifier.getName()))
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 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()
{
- 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 itemStateChanged(ItemEvent e)
{
- public void actionPerformed(ActionEvent e)
+ for(int i=0; i<qualifierValuesCheckBox.size(); i++)
{
- if (butt.getText().equals("+"))
- butt.setText("-");
- else
- butt.setText("+");
-
- qualifierValueBox.setVisible(butt.getText().equals("-"));
- revalidate();
+ JCheckBox cb = (JCheckBox) qualifierValuesCheckBox.get(i);
+ cb.setSelected(qualifierNameCheckBox.isSelected());
}
- });
-
- // 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;
- }
+ }
+ });
+ add(detailsShowHide, c);
- protected Feature getFeature()
- {
- return feature;
- }
+ 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;
}
/**
- * Test if the feature is nominated to have annotation transferred
- * to it. For genes in a chado database it looks at the gene name
- * and transcript name.
+ * 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
*/
- class TransferFeaturePredicate implements FeaturePredicate
+ private Vector setExpanderButton(final JButton butt,
+ final Qualifier qualifier,
+ final Box qualifierValueBox,
+ final JCheckBox qualifierNameCheckBox)
{
- private String geneName;
- private String key;
- private boolean sameKey;
- private boolean isDatabaseEntry;
- private String[] geneNames;
-
- public TransferFeaturePredicate(final String key,
- final boolean sameKey,
- final boolean isDatabaseEntry,
- final String[] geneNames)
+ 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(TransferAnnotationTool.STEEL_BLUE);
+
+ butt.addActionListener(new ActionListener()
{
- this.key = key;
- this.sameKey = sameKey;
- this.isDatabaseEntry = isDatabaseEntry;
- this.geneNames = geneNames;
- }
+ public void actionPerformed(ActionEvent e)
+ {
+ if (butt.getText().equals("+"))
+ butt.setText("-");
+ else
+ butt.setText("+");
- public boolean testPredicate(Feature targetFeature)
+ 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++)
{
- String targetKey = targetFeature.getKey().getKeyString();
- if (sameKey && !targetKey.equals(key))
- return false;
+ 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;
+ }
+}
- Vector chadoNames = null;
- if (isDatabaseEntry)
- {
- GFFStreamFeature gffFeature =
- ((GFFStreamFeature) targetFeature.getEmblFeature());
- if (gffFeature.getChadoGene() != null)
- {
- chadoNames = new Vector();
-
- ChadoCanonicalGene chadoGene = gffFeature.getChadoGene();
- chadoNames.add(chadoGene.getGeneUniqueName());
- List transcripts = chadoGene.getTranscripts();
- for(int i=0;i<transcripts.size();i++)
- {
- GFFStreamFeature feature = (GFFStreamFeature) transcripts.get(i);
- chadoNames.add(GeneUtils.getUniqueName(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
+ * and transcript name.
+ */
+class TransferFeaturePredicate implements FeaturePredicate
+{
+ private String geneName;
+ private String key;
+ private boolean sameKey;
+ private boolean isDatabaseEntry;
+ private String[] geneNames;
+
+ public TransferFeaturePredicate(final String key,
+ final boolean sameKey,
+ final boolean isDatabaseEntry,
+ final String[] geneNames)
+ {
+ this.key = key;
+ this.sameKey = sameKey;
+ this.isDatabaseEntry = isDatabaseEntry;
+ this.geneNames = geneNames;
+ }
- String thisFeatureSystematicName = targetFeature.getSystematicName();
- for (int i = 0; i < geneNames.length; i++)
+ public boolean testPredicate(Feature targetFeature)
+ {
+ String targetKey = targetFeature.getKey().getKeyString();
+ if (sameKey && !targetKey.equals(key))
+ return false;
+
+ Vector chadoNames = null;
+ if (isDatabaseEntry)
+ {
+ GFFStreamFeature gffFeature =
+ ((GFFStreamFeature) targetFeature.getEmblFeature());
+ if (gffFeature.getChadoGene() != null)
{
- if(geneNames[i].equals(thisFeatureSystematicName) ||
- (chadoNames != null && chadoNames.contains(geneNames[i])))
+ chadoNames = new Vector();
+
+ ChadoCanonicalGene chadoGene = gffFeature.getChadoGene();
+ chadoNames.add(chadoGene.getGeneUniqueName());
+ List transcripts = chadoGene.getTranscripts();
+ for(int i=0;i<transcripts.size();i++)
{
- geneName = geneNames[i];
- return true;
+ GFFStreamFeature feature = (GFFStreamFeature) transcripts.get(i);
+ chadoNames.add(GeneUtils.getUniqueName(feature));
}
}
- return false;
}
- protected String getGeneName()
+ String thisFeatureSystematicName = targetFeature.getSystematicName();
+ for (int i = 0; i < geneNames.length; i++)
{
- return geneName;
+ if(geneNames[i].equals(thisFeatureSystematicName) ||
+ (chadoNames != null && chadoNames.contains(geneNames[i])))
+ {
+ geneName = geneNames[i];
+ return true;
+ }
}
+ return false;
+ }
+
+ protected String getGeneName()
+ {
+ return geneName;
}
-
}