import java.awt.event.*;
import javax.swing.*;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.analysis.*;
import jalview.commands.*;
JMenuItem sequenceSelDetails = new JMenuItem();
SequenceI sequence;
-
+ JMenuItem createGroupMenuItem = new JMenuItem();
JMenuItem unGroupMenuItem = new JMenuItem();
JMenuItem outline = new JMenuItem();
JMenu pdbMenu = new JMenu();
JMenuItem pdbFromFile = new JMenuItem();
-
+ // JBPNote: Commented these out - Should add these services via the web services menu system.
+ // JMenuItem ContraFold = new JMenuItem();
+
+ // JMenuItem RNAFold = new JMenuItem();
+
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
}
SequenceGroup sg = ap.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
if (sg != null && sg.getSize() > 0)
- {
+ {
groupName.setText("Name: " + sg.getName());
groupName.setText("Edit name and description of current group.");
purinePyrimidineColour.setSelected(true);
}
- else if (sg.cs instanceof RNAInteractionColourScheme)
- {
- RNAInteractionColour.setSelected(true);
- }
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
editMenu.setVisible(false);
}
- if (!ap.av.getAlignment().getGroups().contains(sg))
+ if (!isDefinedGroup)
{
+ createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
+ jMenu1.setText("Edit New Group");
+ } else {
+ createGroupMenuItem.setVisible(false);
+ unGroupMenuItem.setVisible(true);
+ jMenu1.setText("Edit Group");
}
if (seq == null)
unGroupMenuItem_actionPerformed();
}
});
+ createGroupMenuItem.setText("Create Group");
+ createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
outline.setText("Border colour");
outline.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- try {
- pdbFromFile_actionPerformed();
- } catch (ExceptionFileFormatOrSyntax e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (ParserConfigurationException e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (SAXException e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (ExceptionPermissionDenied e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (ExceptionLoadingFailed e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (InterruptedException e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (ExceptionUnmatchedClosingParentheses e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
+ pdbFromFile_actionPerformed();
}
});
+// RNAFold.setText("From RNA Fold with predict2D");
+// RNAFold.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e)
+// {
+// try {
+// RNAFold_actionPerformed();
+// } catch (Exception e1) {
+// // TODO Auto-generated catch block
+// e1.printStackTrace();
+// }
+// }
+// });
+// ContraFold.setText("From Contra Fold with predict2D");
+// ContraFold.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e)
+// {
+// try {
+// ContraFold_actionPerformed();
+// } catch (Exception e1) {
+// // TODO Auto-generated catch block
+// e1.printStackTrace();
+// }
+// }
+// });
enterPDB.setText("Enter PDB Id");
enterPDB.addActionListener(new ActionListener()
{
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
if (ap.getAlignment().isNucleotide()) {
- colourMenu.add(RNAInteractionColour);
+ // JBPNote - commented since the colourscheme isn't functional
+ // colourMenu.add(RNAInteractionColour);
colourMenu.add(purinePyrimidineColour);
}
// colourMenu.add(covariationColour);
editMenu.add(lowerCase);
editMenu.add(toggle);
pdbMenu.add(pdbFromFile);
+ // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
+ // pdbMenu.add(RNAFold);
+ // pdbMenu.add(ContraFold);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
- jMenu1.add(unGroupMenuItem);
jMenu1.add(colourMenu);
jMenu1.add(showBoxes);
jMenu1.add(showText);
}
});
- RNAInteractionColour.setText("RNA Interaction type");
- RNAInteractionColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- RNAInteractionColour_actionPerformed();
- }
- });
+
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
refresh();
}
- protected void RNAInteractionColour_actionPerformed()
- {
- getGroup().cs = new RNAInteractionColourScheme();
- refresh();
- }
+
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
sg.cs = acg;
refresh();
ap.av.setSelectionGroup(null);
refresh();
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ refresh();
+ }
/**
* DOCUMENT ME!
oal = null;
}
- public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public void pdbFromFile_actionPerformed()
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
}
}
-
+ // JBNote: commented out - these won't be instantiated here...!
+// public void RNAFold_actionPerformed() throws Exception
+// {
+// Predict2D P2D = new Predict2D();
+// P2D.getStructure2DFromRNAFold("toto");
+// }
+//
+// public void ContraFold_actionPerformed() throws Exception
+// {
+// Predict2D P2D = new Predict2D();
+// P2D.getStructure2DFromContraFold("toto");
+// }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,