/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
protected JMenuItem sortIDMenuItem = new JMenuItem();
+ protected JMenuItem sortLengthMenuItem = new JMenuItem();
+
protected JMenuItem sortGroupMenuItem = new JMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
+
JMenuItem htmlMenuItem = new JMenuItem();
JMenuItem overviewMenuItem = new JMenuItem();
public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
protected JMenu sort = new JMenu();
- JMenu calculate = new JMenu();
+ protected JMenu calculateTree = new JMenu();
JMenu jMenu2 = new JMenu();
protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
+
protected JMenuItem gatherViews = new JMenuItem();
protected JMenuItem expandViews = new JMenuItem();
JMenuItem alignmentProperties = new JMenuItem();
JMenu tooltipSettingsMenu = new JMenu();
-
+
+ private JMenuItem justifyLeftMenuItem=new JMenuItem();
+
+ private JMenuItem justifyRightMenuItem=new JMenuItem();
+
+ JMenu autoAnnMenu = new JMenu();
+ protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showSequenceLogo=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
+
+ private JMenuItem grpsFromSelection = new JMenuItem();
public GAlignFrame()
{
try
invertSequenceMenuItem_actionPerformed(e);
}
});
+ grpsFromSelection.setText("Make Groups for selection");
+ grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ makeGrpsFromSelection_actionPerformed(e);
+ }
+ });
+
remove2LeftMenuItem.setText("Remove Left");
remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
removeAllGapsMenuItem_actionPerformed(e);
}
});
+ justifyLeftMenuItem.setText("Left Justify Alignment");
+ justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyLeftMenuItem_actionPerformed(e);
+ }
+ });
+ justifyRightMenuItem.setText("Right Justify Alignment");
+ justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyRightMenuItem_actionPerformed(e);
+ }
+ });
viewBoxesMenuItem.setText("Boxes");
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
viewTextMenuItem_actionPerformed(e);
}
});
+ showUnconservedMenuItem.setText("Show Unconserved");
+ showUnconservedMenuItem.setState(false);
+ showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showUnconservedMenuItem_actionPerformed(e);
+ }
+ });
sortPairwiseMenuItem.setText("by Pairwise Identity");
sortPairwiseMenuItem
.addActionListener(new java.awt.event.ActionListener()
sortIDMenuItem_actionPerformed(e);
}
});
+ sortLengthMenuItem.setText("By Length");
+ sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortLengthMenuItem_actionPerformed(e);
+ }
+ });
sortGroupMenuItem.setText("by Group");
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
showSeqFeatures_actionPerformed(actionEvent);
}
});
+/*
+ * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+ showSeqFeaturesHeight.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ showSeqFeaturesHeight_actionPerformed(actionEvent);
+ }
+ }); */
showDbRefsMenuitem.setText("Show Database Refs");
showDbRefsMenuitem.addActionListener(new ActionListener()
{
}
});
+ showGroupConservation.setText("Group Conservation");
+ showGroupConservation.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConservation_actionPerformed(e);
+ }
+
+ });
+
+ showGroupConsensus.setText("Group Consensus");
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConsensus_actionPerformed(e);
+ }
+
+ });
+ showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showConsensusHistogram_actionPerformed(e);
+ }
+
+ });
+ showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ applyAutoAnnotationSettings.setText("Apply to all groups");
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ applyAutoAnnotationSettings_actionPerformed(e);
+ }
+
+ });
+
nucleotideColour.setText("Nucleotide");
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
centreColumnLabels_actionPerformed(e);
}
});
+ followHighlightMenuItem.setVisible(true);
+ followHighlightMenuItem.setState(true);
+ followHighlightMenuItem.setText("Automatic Scrolling");
+ followHighlightMenuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ followHighlight_actionPerformed();
+ }
+
+ });
+
modifyPID.setText("Modify Identity Threshold...");
modifyPID.addActionListener(new java.awt.event.ActionListener()
{
});
sortByAnnotScore.setVisible(false);
- calculate.setText("Calculate Tree");
+ calculateTree.setText("Calculate Tree");
jMenu2.setText("Export Image");
padGapsMenuitem.setText("Pad Gaps");
}
});
tooltipSettingsMenu.setText("Sequence ID Tooltip");
+ autoAnnMenu.setText("Autocalculated Annotation");
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
+ // dont add these yet in the CVS build - they cannot be undone!
+ editMenu.add(justifyLeftMenuItem);
+ editMenu.add(justifyRightMenuItem);
+ editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
viewMenu.add(newView);
viewMenu.add(expandViews);
viewMenu.add(jMenu3);
viewMenu.add(hideMenu);
viewMenu.addSeparator();
+ viewMenu.add(followHighlightMenuItem);
viewMenu.add(annotationPanelMenuItem);
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ viewMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(showSeqFeatures);
+ //viewMenu.add(showSeqFeaturesHeight);
+
viewMenu.add(featureSettings);
tooltipSettingsMenu.add(showDbRefsMenuitem);
tooltipSettingsMenu.add(showNpFeatsMenuitem);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
calculateMenu.add(sort);
- calculateMenu.add(calculate);
+ calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
sort.add(sortByTreeMenu);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
+ calculateTree.add(averageDistanceTreeMenuItem);
+ calculateTree.add(neighbourTreeMenuItem);
+ calculateTree.add(avDistanceTreeBlosumMenuItem);
+ calculateTree.add(njTreeBlosumMenuItem);
jMenu2.add(htmlMenuItem);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
formatMenu.add(colourTextMenuItem);
formatMenu.add(renderGapsMenuItem);
formatMenu.add(centreColumnLabelsMenuItem);
+ formatMenu.add(showUnconservedMenuItem);
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
selectMenu.add(deleteGroups);
+ selectMenu.add(grpsFromSelection);
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSeqFeaturesHeight_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void followHighlight_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
}
protected void showNpFeats_actionPerformed(ActionEvent e)
{
}
+ protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
}
git://source.jalview.org / jalview.git / blobdiff