diff --git a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
index 3561ea1c6bb251502cbbcf51fb17bac8772138ad..a26385842af36ad223097b0cc3eca29f282a668f 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
@@ -17,7 +17,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java,v 1.1 2008-06-03 10:34:59 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java,v 1.2 2008-09-19 12:39:35 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder.gff;
@@ -69,8 +69,10 @@ public class PropertiesPanel extends JPanel
private static final long serialVersionUID = 1L;
private QualifierVector gffQualifiers;
private JTextField uniquenameTextField;
+ private JTextField primaryNameTextField;
private JCheckBox obsoleteField;
private Feature feature;
+ /** controls if this panel is automatically closed or open */
private boolean empty = true;
/** track if feature isObsolete flag has changed */
private boolean obsoleteChanged = false;
@@ -89,6 +91,7 @@ public class PropertiesPanel extends JPanel
public boolean isPropertiesTag(final Qualifier qualifier, final Feature feature)
{
if(qualifier.getName().equals("ID") ||
+ qualifier.getName().equals("Name") ||
qualifier.getName().equals("feature_id") ||
qualifier.getName().equals("Parent") ||
qualifier.getName().equals("Derives_from") ||
@@ -107,6 +110,7 @@ public class PropertiesPanel extends JPanel
int nrows = 0;
Qualifier idQualifier = gffQualifiers.getQualifierByName("ID");
+ Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name");
Qualifier parentQualifier = gffQualifiers.getQualifierByName("Parent");
Qualifier derivesFromQualifier = gffQualifiers.getQualifierByName("Derives_from");
Qualifier timeQualifier = gffQualifiers.getQualifierByName("timelastmodified");
@@ -165,7 +169,7 @@ public class PropertiesPanel extends JPanel
if(idQualifier != null)
{
final String uniquename = (String)idQualifier.getValues().get(0);
- JLabel idField = new JLabel("Internal ID");
+ JLabel idField = new JLabel("ID");
uniquenameTextField = new JTextField(uniquename);
cellDimension = new Dimension(uniquenameTextField.getPreferredSize().width+10,
@@ -176,16 +180,15 @@ public class PropertiesPanel extends JPanel
uniquenameTextField.setMaximumSize(cellDimension);
c.gridx = 3;
- c.gridy = 0;
+ c.gridy = nrows;
c.ipadx = 5;
c.fill = GridBagConstraints.NONE;
- c.anchor = GridBagConstraints.NORTHEAST;
+ c.anchor = GridBagConstraints.SOUTHEAST;
gridPanel.add(idField, c);
c.gridx = 4;
- c.gridy = 0;
c.ipadx = 0;
c.fill = GridBagConstraints.HORIZONTAL;
- c.anchor = GridBagConstraints.NORTHWEST;
+ c.anchor = GridBagConstraints.SOUTHWEST;
gridPanel.add(uniquenameTextField, c);
Qualifier featIdQualifier = gffQualifiers.getQualifierByName("feature_id");
@@ -199,6 +202,41 @@ public class PropertiesPanel extends JPanel
}
+
+ if(!feature.getKey().getKeyString().equals(DatabaseDocument.EXONMODEL))
+ {
+ primaryNameTextField = new JTextField();
+ if(nameQualifier != null)
+ {
+ primaryNameTextField.setText((String)nameQualifier.getValues().get(0));
+ empty = false;
+ }
+
+ JLabel idField = new JLabel("Primary Name");
+ if(cellDimension == null)
+ cellDimension = new Dimension(primaryNameTextField.getPreferredSize().width+10,
+ idField.getPreferredSize().height+10);
+
+ if(feature.getKey().getKeyString().indexOf("exon") > -1)
+ primaryNameTextField.setEditable(false);
+ primaryNameTextField.setMaximumSize(cellDimension);
+
+ c.gridx = 3;
+ c.gridy = nrows;
+ c.ipadx = 5;
+ c.fill = GridBagConstraints.NONE;
+ c.anchor = GridBagConstraints.EAST;
+ gridPanel.add(idField, c);
+ c.gridx = 4;
+ c.gridy = nrows;
+ c.ipadx = 0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.anchor = GridBagConstraints.NORTHWEST;
+ gridPanel.add(primaryNameTextField, c);
+ nrows++;
+ }
+
+
if(parentQualifier != null)
{
StringVector parents = parentQualifier.getValues();
@@ -219,7 +257,7 @@ public class PropertiesPanel extends JPanel
c.gridy = nrows;
c.ipadx = 5;
c.fill = GridBagConstraints.NONE;
- c.anchor = GridBagConstraints.NORTHEAST;
+ c.anchor = GridBagConstraints.EAST;
gridPanel.add(parentField, c);
c.gridx = 4;
c.gridy = nrows;
@@ -252,7 +290,7 @@ public class PropertiesPanel extends JPanel
c.gridy = nrows;
c.ipadx = 5;
c.fill = GridBagConstraints.NONE;
- c.anchor = GridBagConstraints.NORTHEAST;
+ c.anchor = GridBagConstraints.EAST;
gridPanel.add(derivesFromsField, c);
c.gridx = 4;
c.gridy = nrows;
@@ -264,7 +302,6 @@ public class PropertiesPanel extends JPanel
}
}
-
if(timeQualifier != null)
{
String time = (String)timeQualifier.getValues().get(0);
@@ -285,7 +322,7 @@ public class PropertiesPanel extends JPanel
c.gridy = nrows;
c.ipadx = 5;
c.fill = GridBagConstraints.NONE;
- c.anchor = GridBagConstraints.NORTHEAST;
+ c.anchor = GridBagConstraints.EAST;
gridPanel.add(timeField, c);
c.gridx = 4;
c.gridy = nrows;
@@ -301,6 +338,7 @@ public class PropertiesPanel extends JPanel
{
boolean isObsolete = Boolean.parseBoolean((String) obsoleteQualifier.getValues().get(0));
obsoleteField = new JCheckBox("is obsolete", isObsolete);
+ obsoleteField.setOpaque(false);
obsoleteField.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -322,15 +360,13 @@ public class PropertiesPanel extends JPanel
nrows++;
}
-
-
gffBox.add(gridPanel);
// add/remove buttons
Box xBox = Box.createHorizontalBox();
-
- final JButton addSynonym = new JButton("ADD");
+
+ final JButton addSynonym = new JButton("ADD SYNONYM");
addSynonym.setOpaque(false);
addSynonym.setToolTipText("Add id or synonym");
addSynonym.addActionListener(new ActionListener()
@@ -343,7 +379,7 @@ public class PropertiesPanel extends JPanel
xBox.add(addSynonym);
xBox.add(Box.createHorizontalStrut(10));
- final JButton removeSynonym = new JButton("REMOVE");
+ final JButton removeSynonym = new JButton("REMOVE SYNONYM");
removeSynonym.setOpaque(false);
removeSynonym.setToolTipText("Remove id or synonym");
removeSynonym.addActionListener(new ActionListener()
@@ -404,6 +440,20 @@ public class PropertiesPanel extends JPanel
}
}
+ Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name");
+ if( (nameQualifier != null &&
+ !((String)(nameQualifier.getValues().get(0))).equals(primaryNameTextField.getText())) ||
+ primaryNameTextField != null)
+ {
+ gffQualifiers.remove(nameQualifier);
+
+ if(!primaryNameTextField.getText().equals(""))
+ {
+ nameQualifier = new Qualifier("Name", primaryNameTextField.getText());
+ gffQualifiers.addElement(nameQualifier);
+ }
+ }
+
Qualifier isObsoleteQualifier = gffQualifiers.getQualifierByName("isObsolete");
if(isObsoleteQualifier != null)
{
@@ -629,7 +679,7 @@ public class PropertiesPanel extends JPanel
GridBagConstraints c = new GridBagConstraints();
c.gridx = 0;
c.gridy = nrows;
- c.ipady = 6;
+ c.ipady = 3;
c.gridwidth = 2;
c.anchor = GridBagConstraints.CENTER;
c.fill = GridBagConstraints.HORIZONTAL;