-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
- * AM Waterhouse
- *******************/
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package jalview.jbgui;
-import javax.swing.*;
-import java.awt.event.*;
import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
-public class GAlignFrame extends JInternalFrame
+import jalview.schemes.*;
+
+public class GAlignFrame
+ extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenu fileMenu = new JMenu();
protected JMenu colourMenu = new JMenu();
protected JMenu calculateMenu = new JMenu();
protected JMenu webService = new JMenu();
+ protected JMenuItem webServiceNoServices;
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
protected JMenuItem invertSequenceMenuItem = new JMenuItem();
protected JMenuItem remove2RightMenuItem = new JMenuItem();
protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
protected JMenuItem sortIDMenuItem = new JMenuItem();
protected JMenuItem sortGroupMenuItem = new JMenuItem();
+ protected JMenu sortByAnnotScore = new JMenu();
protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
protected JMenuItem PCAMenuItem = new JMenuItem();
protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
- protected JMenuItem clustalAlignMenuItem = new JMenuItem();
BorderLayout borderLayout1 = new BorderLayout();
public JLabel statusBar = new JLabel();
- protected JMenu saveAlignmentMenu = new JMenu();
+ protected JMenuItem saveAs = new JMenuItem();
protected JMenu outputTextboxMenu = new JMenu();
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem hydrophobicityColour = new
+ JRadioButtonMenuItem();
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
JMenuItem htmlMenuItem = new JMenuItem();
JMenuItem overviewMenuItem = new JMenuItem();
protected JMenuItem undoMenuItem = new JMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
- protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
JMenuItem printMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
JMenuItem findMenuItem = new JMenuItem();
- JMenu searchMenu = new JMenu();
- protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
JMenuItem deleteGroups = new JMenuItem();
JMenuItem delete = new JMenuItem();
JMenuItem copy = new JMenuItem();
JMenuItem cut = new JMenuItem();
- JMenu jMenu1 = new JMenu();
+ JMenu pasteMenu = new JMenu();
JMenuItem pasteNew = new JMenuItem();
JMenuItem pasteThis = new JMenuItem();
- protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
JMenuItem createPNG = new JMenuItem();
protected JMenuItem font = new JMenuItem();
- protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
- JMenuItem jpred = new JMenuItem();
- protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- JMenuItem modifyPID = new JMenuItem();
- JMenuItem modifyConservation = new JMenuItem();
+ public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+ protected JMenuItem modifyPID = new JMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
protected JMenu sortByTreeMenu = new JMenu();
- JMenu jMenu2 = new JMenu();
- JMenu sort = new JMenu();
+ protected JMenu sort = new JMenu();
JMenu calculate = new JMenu();
- JMenuItem preferences = new JMenuItem();
- JMenuItem msaAlignMenuItem = new JMenuItem();
+ JMenu jMenu2 = new JMenu();
+ protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+ protected ButtonGroup colours = new ButtonGroup();
+ JMenuItem vamsasStore = new JMenuItem();
+ protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenuItem extractScores = new JMenuItem();
+ protected JMenu showProducts = new JMenu();
+ public JMenuItem featureSettings = new JMenuItem();
+ JMenuItem fetchSequence = new JMenuItem();
+ JMenuItem annotationColour = new JMenuItem();
+ JMenuItem associatedData = new JMenuItem();
+ protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+ JMenu addSequenceMenu = new JMenu();
+ JMenuItem addFromFile = new JMenuItem();
+ JMenuItem addFromText = new JMenuItem();
+ JMenuItem addFromURL = new JMenuItem();
+ JMenuItem exportAnnotations = new JMenuItem();
+ JMenuItem exportFeatures = new JMenuItem();
+ protected JPanel statusPanel = new JPanel();
+ GridLayout gridLayout1 = new GridLayout();
+ JMenu jMenu3 = new JMenu();
+ JMenuItem showAllSeqs = new JMenuItem();
+ JMenuItem showAllColumns = new JMenuItem();
+ JMenu hideMenu = new JMenu();
+ JMenuItem hideSelSequences = new JMenuItem();
+ JMenuItem hideSelColumns = new JMenuItem();
+ protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+ JMenuItem invertColSel = new JMenuItem();
+ protected JTabbedPane tabbedPane = new JTabbedPane();
+ JMenuItem save = new JMenuItem();
+ protected JMenuItem reload = new JMenuItem();
+ JMenuItem newView = new JMenuItem();
+ JMenuItem textColour = new JMenuItem();
+ JMenu formatMenu = new JMenu();
+ JMenu selectMenu = new JMenu();
+ protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
+ protected JMenuItem gatherViews = new JMenuItem();
+ protected JMenuItem expandViews = new JMenuItem();
+ JMenuItem pageSetup = new JMenuItem();
+ JMenuItem alignmentProperties = new JMenuItem();
public GAlignFrame()
{
-
-
try
{
jbInit();
setJMenuBar(alignFrameMenuBar);
- JMenuItem item;
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
- saveAlignmentMenu.add( item );
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- saveAs_actionPerformed(e);
- }
- });
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
+ WRITEABLE_FORMATS[i]);
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- outputTextboxMenu.add( item );
+ outputTextboxMenu.add(item);
}
-
}
- catch(Exception e)
+ catch (Exception e)
{
- e.printStackTrace();
}
- ButtonGroup colours = new ButtonGroup();
+ if (!new jalview.util.Platform().isAMac())
+ {
+ closeMenuItem.setMnemonic('C');
+ outputTextboxMenu.setMnemonic('T');
+ undoMenuItem.setMnemonic('Z');
+ redoMenuItem.setMnemonic('0');
+ copy.setMnemonic('C');
+ cut.setMnemonic('U');
+ pasteMenu.setMnemonic('P');
+ reload.setMnemonic('R');
+ }
+
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ userColours.
+ nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
+ Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(
+ radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ colourMenu.insert(radioItem, 15);
+ colours.add(radioItem);
+ }
+ }
colours.add(noColourmenuItem);
colours.add(clustalColour);
colours.add(zappoColour);
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(nucleotideColour);
+
+ setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
}
- private void jbInit() throws Exception
+
+ public void setColourSelected(String defaultColour)
+ {
+
+ if (defaultColour != null)
+ {
+ int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+
+ switch (index)
+ {
+ case ColourSchemeProperty.NONE:
+ noColourmenuItem.setSelected(true);
+ break;
+ case ColourSchemeProperty.CLUSTAL:
+ clustalColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.BLOSUM:
+ BLOSUM62Colour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.PID:
+ PIDColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.ZAPPO:
+ zappoColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.TAYLOR:
+ taylorColour.setSelected(true);
+ break;
+
+ case ColourSchemeProperty.HYDROPHOBIC:
+ hydrophobicityColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.HELIX:
+ helixColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.STRAND:
+ strandColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.TURN:
+ turnColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.BURIED:
+ buriedColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.NUCLEOTIDE:
+ nucleotideColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.USER_DEFINED:
+ userDefinedColour.setSelected(true);
+
+ break;
+ }
+ }
+
+ }
+
+ private void jbInit()
+ throws Exception
{
- fileMenu.setMnemonic('F');
fileMenu.setText("File");
- saveAlignmentMenu.setMnemonic('L');
- saveAlignmentMenu.setText("Save");
- closeMenuItem.setMnemonic('C');
+ saveAs.setText("Save As...");
+ saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+ java.awt.event.KeyEvent.SHIFT_MASK, false));
+ saveAs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ saveAs_actionPerformed(e);
+ }
+ });
closeMenuItem.setText("Close");
+ closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
closeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- closeMenuItem_actionPerformed(e);
+ closeMenuItem_actionPerformed(false);
}
});
editMenu.setText("Edit");
colourMenu.setText("Colour");
calculateMenu.setText("Calculate");
webService.setText("Web Service");
- selectAllSequenceMenuItem.setText("Select all");
+ selectAllSequenceMenuItem.setText("Select All");
selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_A, java.awt.event.KeyEvent.CTRL_MASK, false));
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ java.awt.event.KeyEvent.VK_A,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
});
deselectAllSequenceMenuItem.setText("Deselect All");
deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
- getKeyStroke(java.awt.event.
- KeyEvent.VK_ESCAPE, 0, false));
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ getKeyStroke(
+ java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
deselectAllSequenceMenuItem_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText("Invert Selection");
+ invertSequenceMenuItem.setText("Invert Sequence Selection");
+ invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
remove2LeftMenuItem.setText("Remove Left");
+ remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+ awt.event.KeyEvent.VK_L,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
remove2RightMenuItem.setText("Remove Right");
+ remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+ awt.event.KeyEvent.VK_R,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
removeGappedColumnMenuItem.setText("Remove Empty Columns");
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+ removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
+ getKeyStroke(java.awt.event.
+ KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
}
});
removeAllGapsMenuItem.setText("Remove All Gaps");
+ removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_E,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+ java.awt.event.KeyEvent.SHIFT_MASK, false));
removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
viewTextMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("Pairwise Identity");
+ sortPairwiseMenuItem.setText("by Pairwise Identity");
sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortPairwiseMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText("ID");
+ sortIDMenuItem.setText("by ID");
sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortIDMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("Group");
+ sortGroupMenuItem.setText("by Group");
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
removeRedundancyMenuItem.setText("Remove Redundancy...");
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+ removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_D,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
}
});
pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText("Principal Component Analysis...");
+ PCAMenuItem.setText("Principal Component Analysis");
PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ averageDistanceTreeMenuItem.setText(
+ "Average Distance Using % Identity");
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
averageDistanceTreeMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
neighbourTreeMenuItem_actionPerformed(e);
}
});
- clustalAlignMenuItem.setText("Clustal Alignment...");
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalAlignMenuItem_actionPerformed(e);
- }
- });
this.getContentPane().setLayout(borderLayout1);
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText("Status bar");
- outputTextboxMenu.setMnemonic('T');
outputTextboxMenu.setText("Output to Textbox");
- clustalColour.setSelected(false);
clustalColour.setText("Clustalx");
+
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
BLOSUM62Colour_actionPerformed(e);
}
});
- avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+ avDistanceTreeBlosumMenuItem.setText(
+ "Average Distance Using BLOSUM62");
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
avTreeBlosumMenuItem_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem.setText("Show Annotations");
- annotationPanelMenuItem.setState(true);
+ annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+ "SHOW_ANNOTATIONS", true));
annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText("Overview Window...");
+ overviewMenuItem.setText("Overview Window");
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
undoMenuItem.setEnabled(false);
- undoMenuItem.setMnemonic('Z');
undoMenuItem.setText("Undo");
- undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_Z, java.awt.event.KeyEvent.CTRL_MASK, false));
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_Z,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
undoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
redoMenuItem.setEnabled(false);
- redoMenuItem.setMnemonic('0');
redoMenuItem.setText("Redo");
+ redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
redoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
noColourmenuItem.setText("None");
- noColourmenuItem.setSelected(true);
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
wrapMenuItem_actionPerformed(e);
}
});
- printMenuItem.setText("Print");
+ printMenuItem.setText("Print ...");
+ printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
printMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
findMenuItem.setText("Find...");
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_F, java.awt.event.KeyEvent.CTRL_MASK, false));
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_F,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
findMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
findMenuItem_actionPerformed(e);
}
});
- searchMenu.setText("Search");
-
- abovePIDThreshold.setText("Above Identity threshold");
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent e) {
+ abovePIDThreshold.setText("Above Identity Threshold");
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
abovePIDThreshold_actionPerformed(e);
}
});
- sequenceFeatures.setText("Sequence Features");
- sequenceFeatures.addActionListener(new ActionListener()
+ showSeqFeatures.setText("Show Sequence Features");
+ showSeqFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
{
- sequenceFeatures_actionPerformed(actionEvent);
+ showSeqFeatures_actionPerformed(actionEvent);
}
});
nucleotideColour.setText("Nucleotide");
nucleotideColour_actionPerformed(e);
}
});
- deleteGroups.setSelected(false);
deleteGroups.setText("Undefine groups");
+ deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
deleteGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
copy.setText("Copy");
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_C, java.awt.event.KeyEvent.CTRL_MASK, false));
- copy.setMnemonic(KeyEvent.VK_C);
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_C,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
copy.addActionListener(new java.awt.event.ActionListener()
{
}
});
cut.setText("Cut");
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_X, java.awt.event.KeyEvent.CTRL_MASK, false));
- cut.setMnemonic(KeyEvent.VK_X);
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_X,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
cut.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
delete.setText("Delete");
+ delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_BACK_SPACE, 0, false));
delete.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
delete_actionPerformed(e);
}
});
- jMenu1.setMnemonic('V');
- jMenu1.setText("Paste");
- pasteNew.setText("to new alignment");
- pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_V, java.awt.event.KeyEvent.CTRL_MASK, false));
+ pasteMenu.setText("Paste");
+ pasteNew.setText("To New Alignment");
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+ java.awt.event.KeyEvent.SHIFT_MASK, false));
pasteNew.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
pasteNew_actionPerformed(e);
}
});
- pasteThis.setText("add to this alignment");
+ pasteThis.setText("Add To This Alignment");
+ pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
pasteThis.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
applyToAllGroups.setText("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
public void actionPerformed(ActionEvent e)
{
- createPNG_actionPerformed(e);
+ createPNG(null);
}
});
- createPNG.setActionCommand("Save as PNG Image");
+ createPNG.setActionCommand("Save As PNG Image");
createPNG.setText("PNG");
font.setText("Font...");
font.addActionListener(new java.awt.event.ActionListener()
font_actionPerformed(e);
}
});
- fullSeqId.setText("Show Full Sequence ID");
- fullSeqId.addActionListener(new java.awt.event.ActionListener()
+
+ seqLimits.setText("Show Sequence Limits");
+ seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- fullSeqId_actionPerformed(e);
+ seqLimit_actionPerformed(e);
}
});
epsFile.setText("EPS");
{
public void actionPerformed(ActionEvent e)
{
- epsFile_actionPerformed(e);
+ createEPS(null);
}
});
LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load Assocated Tree");
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent e)
- {
- LoadtreeMenuItem_actionPerformed(e);
- }
- });
- jpred.setText("JPred...");
- jpred.addActionListener(new java.awt.event.ActionListener()
+ LoadtreeMenuItem.setText("Load Associated Tree");
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- jpred_actionPerformed(e);
+ LoadtreeMenuItem_actionPerformed(e);
}
});
scaleAbove.setVisible(false);
scaleRight_actionPerformed(e);
}
});
+ centreColumnLabelsMenuItem.setVisible(true);
+ centreColumnLabelsMenuItem.setState(false);
+ centreColumnLabelsMenuItem.setText("Centre Column Labels");
+ centreColumnLabelsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ centreColumnLabels_actionPerformed(e);
+ }
+ });
+
modifyPID.setText("Modify Identity Threshold...");
modifyPID.addActionListener(new java.awt.event.ActionListener()
{
modifyConservation_actionPerformed(e);
}
});
- sortByTreeMenu.setText("Tree Order");
- jMenu2.setText("Save as");
+ sortByTreeMenu.setText("By Tree Order");
sort.setText("Sort");
+ sort.addMenuListener(new MenuListener()
+ {
+ public void menuSelected(MenuEvent e)
+ {
+ buildTreeMenu();
+ }
+
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+ sortByAnnotScore.setText("by Score");
+ sort.add(sortByAnnotScore);
+ sortByAnnotScore.addMenuListener(
+ new javax.swing.event.MenuListener() {
+
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ public void menuSelected(MenuEvent e)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ }
+ );
+ sortByAnnotScore.setVisible(false);
+
calculate.setText("Calculate Tree");
- preferences.setText("Preferences...");
- preferences.addActionListener(new ActionListener()
+
+ jMenu2.setText("Export Image");
+ padGapsMenuitem.setText("Pad Gaps");
+ padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ padGapsMenuitem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- preferences_actionPerformed(e);
+ padGapsMenuitem_actionPerformed(e);
}
});
- msaAlignMenuItem.setText("Muscle Alignment...");
- msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent e) {
- msaAlignMenuItem_actionPerformed(e);
+ vamsasStore.setVisible(false);
+ vamsasStore.setText("VAMSAS store");
+ vamsasStore.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasStore_actionPerformed(e);
}
});
+ showTranslation.setText("Translate cDNA");
+ showTranslation.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(e);
+ }
+ });
+ extractScores.setText("Extract Scores...");
+ extractScores.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ extractScores_actionPerformed(e);
+ }
+ });
+ extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction
+ showProducts.setText("Get Cross References");
+ /*showProducts.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showProducts_actionPerformed(e);
+ }
+ });*/
+ featureSettings.setText("Feature Settings...");
+ featureSettings.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ featureSettings_actionPerformed(e);
+ }
+ });
+ fetchSequence.setText("Fetch Sequence(s)...");
+ fetchSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ fetchSequence_actionPerformed(e);
+ }
+ });
+
+ annotationColour.setText("By Annotation...");
+ annotationColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed(e);
+ }
+ });
+ associatedData.setText("Load Features / Annotations");
+ associatedData.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ associatedData_actionPerformed(e);
+ }
+ });
+ autoCalculate.setText("Autocalculate Consensus");
+ autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculate.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ autoCalculate_actionPerformed(e);
+ }
+ });
+ addSequenceMenu.setText("Add Sequences");
+ addFromFile.setText("From File");
+ addFromFile.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromFile_actionPerformed(e);
+ }
+ });
+ addFromText.setText("From Textbox");
+ addFromText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromText_actionPerformed(e);
+ }
+ });
+ addFromURL.setText("From URL");
+ addFromURL.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromURL_actionPerformed(e);
+ }
+ });
+ exportFeatures.setText("Export Features...");
+ exportFeatures.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ exportFeatures_actionPerformed(e);
+ }
+ });
+ exportAnnotations.setText("Export Annotations...");
+ exportAnnotations.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ exportAnnotations_actionPerformed(e);
+ }
+ });
+ statusPanel.setLayout(gridLayout1);
+ jMenu3.setText("Show");
+ showAllSeqs.setText("All Sequences");
+ showAllSeqs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllSeqs_actionPerformed(e);
+ }
+ });
+ showAllColumns.setText("All Columns");
+ showAllColumns.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllColumns_actionPerformed(e);
+ }
+ });
+ hideMenu.setText("Hide");
+ hideSelSequences.setText("Selected Sequences");
+ hideSelSequences.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelSequences_actionPerformed(e);
+ }
+ });
+ hideSelColumns.setText("Selected Columns");
+ hideSelColumns.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelColumns_actionPerformed(e);
+ }
+ });
+ hiddenMarkers.setText("Show Hidden Markers");
+ hiddenMarkers.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hiddenMarkers_actionPerformed(e);
+ }
+ });
+ invertColSel.setText("Invert Column Selection");
+ invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.ALT_MASK,
+ false));
+ invertColSel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ invertColSel_actionPerformed(e);
+ }
+ });
+ tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+ {
+ public void stateChanged(ChangeEvent evt)
+ {
+ JTabbedPane pane = (JTabbedPane) evt.getSource();
+ int sel = pane.getSelectedIndex();
+ tabSelectionChanged(sel);
+ }
+ });
+ tabbedPane.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ tabbedPane_mousePressed(e);
+ }
+ });
+ tabbedPane.addFocusListener(new FocusAdapter()
+ {
+ public void focusGained(FocusEvent e)
+ {
+ tabbedPane_focusGained(e);
+ }
+ });
+ save.setText("Save");
+ save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ save.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ save_actionPerformed(e);
+ }
+ });
+ reload.setEnabled(false);
+ reload.setText("Reload");
+ reload.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ reload_actionPerformed(e);
+ }
+ });
+ newView.setText("New View");
+ newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+ KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ newView.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ newView_actionPerformed(e);
+ }
+ });
+ tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
+ +
+ "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
+ textColour.setText("Colour Text ...");
+ textColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed(e);
+ }
+ });
+ formatMenu.setText("Format");
+ selectMenu.setText("Select");
+ idRightAlign.setText("Right Align Sequence Id");
+ idRightAlign.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ idRightAlign_actionPerformed(e);
+ }
+ });
+ gatherViews.setEnabled(false);
+ gatherViews.setText("Gather Views");
+ gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_G, 0, false));
+ gatherViews.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ gatherViews_actionPerformed(e);
+ }
+ });
+ expandViews.setEnabled(false);
+ expandViews.setText("Expand Views");
+ expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+ event.KeyEvent.VK_X, 0, false));
+ expandViews.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ expandViews_actionPerformed(e);
+ }
+ });
+ pageSetup.setText("Page Setup ...");
+ pageSetup.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pageSetup_actionPerformed(e);
+ }
+ });
+ alignmentProperties.setText("Alignment Properties...");
+ alignmentProperties.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ alignmentProperties();
+ }
+ });
+
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(searchMenu);
+ alignFrameMenuBar.add(selectMenu);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- fileMenu.add(saveAlignmentMenu);
- fileMenu.add(jMenu2);
+ alignFrameMenuBar.add(webService);
+ fileMenu.add(fetchSequence);
+ fileMenu.add(addSequenceMenu);
+ fileMenu.add(reload);
+ fileMenu.addSeparator();
+ fileMenu.add(vamsasStore);
+ fileMenu.add(save);
+ fileMenu.add(saveAs);
fileMenu.add(outputTextboxMenu);
+ fileMenu.add(pageSetup);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
+ fileMenu.add(jMenu2);
+ fileMenu.add(exportFeatures);
+ fileMenu.add(exportAnnotations);
fileMenu.add(LoadtreeMenuItem);
+ fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
editMenu.add(cut);
editMenu.add(copy);
- editMenu.add(jMenu1);
+ editMenu.add(pasteMenu);
editMenu.add(delete);
editMenu.addSeparator();
- editMenu.add(selectAllSequenceMenuItem);
- editMenu.add(deselectAllSequenceMenuItem);
- editMenu.add(invertSequenceMenuItem);
- editMenu.add(deleteGroups);
- editMenu.addSeparator();
editMenu.add(remove2LeftMenuItem);
editMenu.add(remove2RightMenuItem);
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
- editMenu.add(preferences);
-
- searchMenu.add(findMenuItem);
- viewMenu.add(font);
- viewMenu.add(fullSeqId);
+ editMenu.add(padGapsMenuitem);
+ viewMenu.add(newView);
+ viewMenu.add(expandViews);
+ viewMenu.add(gatherViews);
viewMenu.addSeparator();
- viewMenu.add(wrapMenuItem);
- viewMenu.add(scaleAbove);
- viewMenu.add(scaleLeft);
- viewMenu.add(scaleRight);
+ viewMenu.add(jMenu3);
+ viewMenu.add(hideMenu);
viewMenu.addSeparator();
- viewMenu.add(viewBoxesMenuItem);
- viewMenu.add(viewTextMenuItem);
- viewMenu.add(colourTextMenuItem);
- viewMenu.add(renderGapsMenuItem);
viewMenu.add(annotationPanelMenuItem);
- viewMenu.add(sequenceFeatures);
+ viewMenu.addSeparator();
+ viewMenu.add(showSeqFeatures);
+ viewMenu.add(featureSettings);
+ viewMenu.addSeparator();
+ viewMenu.add(alignmentProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
colourMenu.add(applyToAllGroups);
- colourMenu.add(noColourmenuItem);
+ colourMenu.add(textColour);
colourMenu.addSeparator();
+ colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
colourMenu.add(BLOSUM62Colour);
colourMenu.add(PIDColour);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
calculateMenu.add(sort);
calculateMenu.add(calculate);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
- calculateMenu.add(webService);
- webService.add(clustalAlignMenuItem);
- webService.add(jpred);
- webService.add(msaAlignMenuItem);
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);
- jMenu1.add(pasteNew);
- jMenu1.add(pasteThis);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
+ calculateMenu.add(showTranslation);
+ calculateMenu.add(showProducts);
+ calculateMenu.add(autoCalculate);
+ calculateMenu.addSeparator();
+ calculateMenu.add(extractScores);
+ webServiceNoServices = new JMenuItem("<No Services>");
+ webService.add(webServiceNoServices);
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
sort.add(sortGroupMenuItem);
- sort.add(sortByTreeMenu);
sort.add(sortPairwiseMenuItem);
+ sort.add(sortByTreeMenu);
calculate.add(averageDistanceTreeMenuItem);
calculate.add(neighbourTreeMenuItem);
calculate.add(avDistanceTreeBlosumMenuItem);
calculate.add(njTreeBlosumMenuItem);
+ jMenu2.add(htmlMenuItem);
+ jMenu2.add(epsFile);
+ jMenu2.add(createPNG);
+ addSequenceMenu.add(addFromFile);
+ addSequenceMenu.add(addFromText);
+ addSequenceMenu.add(addFromURL);
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+ statusPanel.add(statusBar, null);
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+ jMenu3.add(showAllColumns);
+ jMenu3.add(showAllSeqs);
+ hideMenu.add(hideSelColumns);
+ hideMenu.add(hideSelSequences);
+ formatMenu.add(font);
+ formatMenu.addSeparator();
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(seqLimits);
+ formatMenu.add(idRightAlign);
+ formatMenu.add(hiddenMarkers);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelsMenuItem);
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(deleteGroups);
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void centreColumnLabels_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void showProducts_actionPerformed(ActionEvent e)
{
+ }
+ protected void buildSortByAnnotationScoresMenu()
+ {
+ }
+
+ protected void extractScores_actionPerformed(ActionEvent e)
+ {
}
protected void outputText_actionPerformed(ActionEvent e)
{
+ }
+
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
}
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ public void addFromText_actionPerformed(ActionEvent e)
{
}
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+
+ }
- protected void closeMenuItem_actionPerformed(ActionEvent e)
+ public void exportFeatures_actionPerformed(ActionEvent e)
{
}
- protected void redoMenuItem_actionPerformed(ActionEvent e)
+ public void exportAnnotations_actionPerformed(ActionEvent e)
{
}
- protected void undoMenuItem_actionPerformed(ActionEvent e)
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void closeMenuItem_actionPerformed(boolean b)
+ {
+ }
+
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
protected void wrapMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void viewTextMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void overviewMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void sortIDMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void PCAMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
+ }
+
+ protected void clustalColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void zappoColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void taylorColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void helixColour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+ protected void strandColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void turnColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void buriedColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void PIDColour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void clustalColour_actionPerformed(ActionEvent e)
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
+ }
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void zappoColour_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void printMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void taylorColour_actionPerformed(ActionEvent e)
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void findMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
+ }
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
{
+ }
+ protected void nucleotideColour_actionPerformed(ActionEvent e)
+ {
}
- protected void helixColour_actionPerformed(ActionEvent e)
+ protected void deleteGroups_actionPerformed(ActionEvent e)
{
+ }
+ protected void copy_actionPerformed(ActionEvent e)
+ {
}
- protected void strandColour_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed(ActionEvent e)
{
+ }
+ protected void delete_actionPerformed(ActionEvent e)
+ {
}
- protected void turnColour_actionPerformed(ActionEvent e)
+ protected void pasteNew_actionPerformed(ActionEvent e)
{
+ }
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
}
- protected void buriedColour_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
+ }
+ public void createPNG(java.io.File f)
+ {
}
+ protected void font_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
+ }
- protected void userDefinedColour_actionPerformed(ActionEvent e)
+ public void seqDBRef_actionPerformed(ActionEvent e)
{
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ public void createEPS(java.io.File f)
{
+ }
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ protected void jpred_actionPerformed(ActionEvent e)
{
+ }
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
}
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ }
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ protected void scaleRight_actionPerformed(ActionEvent e)
{
+ }
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed(ActionEvent e)
{
+ }
+ protected void saveAs_actionPerformed(ActionEvent e)
+ {
}
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
+ }
- protected void printMenuItem_actionPerformed(ActionEvent e)
+ public void vamsasStore_actionPerformed(ActionEvent e)
{
}
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ public void vamsasLoad_actionPerformed(ActionEvent e)
{
}
- protected void findMenuItem_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(ActionEvent e)
{
}
+ public void featureSettings_actionPerformed(ActionEvent e)
+ {
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+ }
+
+ public void fetchSequence_actionPerformed(ActionEvent e)
+ {
}
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+ public void smoothFont_actionPerformed(ActionEvent e)
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed(ActionEvent e)
{
}
- protected void deleteGroups_actionPerformed(ActionEvent e)
+ public void associatedData_actionPerformed(ActionEvent e)
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ public void autoCalculate_actionPerformed(ActionEvent e)
{
}
+ public void showAllSeqs_actionPerformed(ActionEvent e)
+ {
+
+ }
- protected void cut_actionPerformed(ActionEvent e)
+ public void showAllColumns_actionPerformed(ActionEvent e)
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ public void hideSelSequences_actionPerformed(ActionEvent e)
{
}
- protected void pasteNew_actionPerformed(ActionEvent e)
+ public void hideSelColumns_actionPerformed(ActionEvent e)
{
}
- protected void pasteThis_actionPerformed(ActionEvent e)
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ public void findPdbId_actionPerformed(ActionEvent e)
{
}
- protected void createPNG_actionPerformed(ActionEvent e)
+ public void enterPdbId_actionPerformed(ActionEvent e)
{
}
- protected void font_actionPerformed(ActionEvent e)
+ public void pdbFile_actionPerformed(ActionEvent e)
{
}
- protected void fullSeqId_actionPerformed(ActionEvent e)
+ public void invertColSel_actionPerformed(ActionEvent e)
{
}
- protected void epsFile_actionPerformed(ActionEvent e)
+ public void tabSelectionChanged(int sel)
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+ public void tabbedPane_mousePressed(MouseEvent e)
+ {
}
- protected void jpred_actionPerformed(ActionEvent e)
+ public void tabbedPane_focusGained(FocusEvent e)
+ {
+ requestFocus();
+ }
+
+ public void save_actionPerformed(ActionEvent e)
{
}
- protected void scaleAbove_actionPerformed(ActionEvent e)
+ public void reload_actionPerformed(ActionEvent e)
{
}
- protected void scaleLeft_actionPerformed(ActionEvent e)
+ public void newView_actionPerformed(ActionEvent e)
{
}
- protected void scaleRight_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed(ActionEvent e)
{
}
- protected void modifyPID_actionPerformed(ActionEvent e)
+ public void idRightAlign_actionPerformed(ActionEvent e)
{
}
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ public void expandViews_actionPerformed(ActionEvent e)
{
}
- protected void preferences_actionPerformed(ActionEvent e)
+ public void gatherViews_actionPerformed(ActionEvent e)
{
}
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
+ public void buildTreeMenu()
+ {
+
+ }
+
+ public void pageSetup_actionPerformed(ActionEvent e)
+ {
}
+ public void alignmentProperties()
+ {
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff