-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
+/*
+ * 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
+ * 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.*;
+
+import jalview.schemes.*;
public class GAlignFrame extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
+
protected JMenu fileMenu = new JMenu();
+
protected JMenuItem closeMenuItem = new JMenuItem();
+
protected JMenu editMenu = new JMenu();
+
protected JMenu viewMenu = new JMenu();
+
protected JMenu colourMenu = new JMenu();
+
protected JMenu calculateMenu = new JMenu();
- protected JMenu alignMenu = 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 deselectAllColumnsMenuItem = new JMenuItem();
+
protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+
protected JMenuItem remove2RightMenuItem = new JMenuItem();
+
protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+
protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
- protected JMenuItem setGapCharMenuItem = 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 sortLengthMenuItem = 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();
- protected JMenuItem msaAlignMenuItem = 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 helixColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem PIDColour = 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();
+
+ public JCheckBoxMenuItem showUnconservedMenuItem = 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();
+ public JCheckBoxMenuItem showSeqFeaturesHeight = 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();
- public GAlignFrame()
- {
+ protected JMenu sort = new JMenu();
+
+ protected JMenu calculateTree = new JMenu();
+
+ JMenu jMenu2 = new JMenu();
+
+ protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showDbRefsMenuitem = 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 JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
+
+ protected JMenuItem gatherViews = new JMenuItem();
+
+ protected JMenuItem expandViews = new JMenuItem();
+
+ JMenuItem pageSetup = 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
{
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)
+
+ if (!new jalview.util.Platform().isAMac())
{
- e.printStackTrace();
+ closeMenuItem.setMnemonic('C');
+ outputTextboxMenu.setMnemonic('T');
+ undoMenuItem.setMnemonic('Z');
+ redoMenuItem.setMnemonic('0');
+ copy.setMnemonic('C');
+ cut.setMnemonic('U');
+ pasteMenu.setMnemonic('P');
+ reload.setMnemonic('R');
}
- ButtonGroup colours = new ButtonGroup();
+ 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"));
+
}
+
+ 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 alignment to local file");
- 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");
+ viewMenu.setText("View");
+ colourMenu.setText("Colour");
+ calculateMenu.setText("Calculate");
+ webService.setText("Web Service");
+ selectAllSequenceMenuItem.setText("Select All");
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ selectAllSequenceMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ selectAllSequenceMenuItem_actionPerformed(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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ deselectAllSequenceMenuItem_actionPerformed(e);
+ }
+ });
+ 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)
+ {
+ 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()
+ .getMenuShortcutKeyMask(), false));
+ remove2LeftMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ remove2LeftMenuItem_actionPerformed(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)
+ {
+ remove2RightMenuItem_actionPerformed(e);
+ }
+ });
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");
+ 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)
+ {
+ removeGappedColumnMenuItem_actionPerformed(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)
+ {
+ 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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ viewBoxesMenuItem_actionPerformed(e);
+ }
+ });
+ viewTextMenuItem.setText("Text");
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ 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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortPairwiseMenuItem_actionPerformed(e);
+ }
+ });
+ sortIDMenuItem.setText("by ID");
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ 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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sortGroupMenuItem_actionPerformed(e);
+ }
+ });
+ removeRedundancyMenuItem.setText("Remove Redundancy...");
+ 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)
+ {
+ removeRedundancyMenuItem_actionPerformed(e);
+ }
+ });
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
+ pairwiseAlignmentMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed(e);
+ }
+ });
+ 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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ averageDistanceTreeMenuItem_actionPerformed(e);
+ }
+ });
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
+ neighbourTreeMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ neighbourTreeMenuItem_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.setText("Output to Textbox");
+ clustalColour.setText("Clustalx");
+
+ clustalColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed(e);
+ }
+ });
+ zappoColour.setText("Zappo");
+ zappoColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed(e);
}
});
- editMenu.setText("Edit");
- viewMenu.setText("View");
- colourMenu.setText("Colour");
- calculateMenu.setText("Calculate");
- alignMenu.setText("Web Service");
- selectAllSequenceMenuItem.setText("Select all");
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ taylorColour.setText("Taylor");
+ taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- selectAllSequenceMenuItem_actionPerformed(e);
+ taylorColour_actionPerformed(e);
}
});
- deselectAllSequenceMenuItem.setText("Clear selection");
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed(e);
+ }
+ });
+ helixColour.setText("Helix Propensity");
+ helixColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- deselectAllSequenceMenuItem_actionPerformed(e);
+ helixColour_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText("Invert sequence selection");
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ strandColour.setText("Strand Propensity");
+ strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- invertSequenceMenuItem_actionPerformed(e);
+ strandColour_actionPerformed(e);
}
});
- deselectAllColumnsMenuItem.setText("Deselect all columns");
- deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ turnColour.setText("Turn Propensity");
+ turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- deselectAllColumnsMenuItem_actionPerformed(e);
+ turnColour_actionPerformed(e);
}
});
- remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+ buriedColour.setText("Buried Index");
+ buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- remove2LeftMenuItem_actionPerformed(e);
+ buriedColour_actionPerformed(e);
}
});
- remove2RightMenuItem.setText("Remove sequence -> right of selected column");
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
+ userDefinedColour.setText("User Defined...");
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- remove2RightMenuItem_actionPerformed(e);
+ userDefinedColour_actionPerformed(e);
}
});
- removeGappedColumnMenuItem.setText("Remove gapped columns");
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+ PIDColour.setText("Percentage Identity");
+ PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- removeGappedColumnMenuItem_actionPerformed(e);
+ PIDColour_actionPerformed(e);
}
});
- removeAllGapsMenuItem.setText("Remove all gaps");
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ BLOSUM62Colour.setText("BLOSUM62 Score");
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- removeAllGapsMenuItem_actionPerformed(e);
+ BLOSUM62Colour_actionPerformed(e);
}
});
- setGapCharMenuItem.setText("Set gap character to \".\"");
- setGapCharMenuItem.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
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ njTreeBlosumMenuItem_actionPerformed(e);
+ }
+ });
+ annotationPanelMenuItem.setActionCommand("");
+ annotationPanelMenuItem.setText("Show Annotations");
+ annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+ "SHOW_ANNOTATIONS", true));
+ annotationPanelMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationPanelMenuItem_actionPerformed(e);
+ }
+ });
+ colourTextMenuItem.setText("Colour Text");
+ colourTextMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ colourTextMenuItem_actionPerformed(e);
+ }
+ });
+ htmlMenuItem.setText("HTML");
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- setGapCharMenuItem_actionPerformed(e);
+ htmlMenuItem_actionPerformed(e);
}
});
- viewBoxesMenuItem.setText("Boxes");
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ overviewMenuItem.setText("Overview Window");
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- viewBoxesMenuItem_actionPerformed(e);
+ overviewMenuItem_actionPerformed(e);
}
});
- viewTextMenuItem.setText("Text");
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText("Undo");
+ 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)
{
- viewTextMenuItem_actionPerformed(e);
+ undoMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("Sort by pairwise identity");
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
+ redoMenuItem.setEnabled(false);
+ 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)
{
- sortPairwiseMenuItem_actionPerformed(e);
+ redoMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText("Sort by ID");
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ conservationMenuItem.setText("By Conservation");
+ conservationMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(e);
+ }
+ });
+ noColourmenuItem.setText("None");
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- sortIDMenuItem_actionPerformed(e);
+ noColourmenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("Sort by group");
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ wrapMenuItem.setText("Wrap");
+ wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- sortGroupMenuItem_actionPerformed(e);
+ wrapMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText("Remove redundancy");
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- removeRedundancyMenuItem_actionPerformed(e);
+ printMenuItem_actionPerformed(e);
}
});
- pairwiseAlignmentMenuItem.setText("Pairwise alignments");
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+ renderGapsMenuItem.setText("Show Gaps");
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ renderGapsMenuItem_actionPerformed(e);
+ }
+ });
+ findMenuItem.setText("Find...");
+ 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)
{
- pairwiseAlignmentMenuItem_actionPerformed(e);
+ findMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText("Principal component analysis");
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+ abovePIDThreshold.setText("Above Identity Threshold");
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- PCAMenuItem_actionPerformed(e);
+ abovePIDThreshold_actionPerformed(e);
+ }
+ });
+ showSeqFeatures.setText("Show Sequence Features");
+ showSeqFeatures.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ showSeqFeatures_actionPerformed(actionEvent);
}
});
- averageDistanceTreeMenuItem.setText("Average distance tree using PID");
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+/*
+ * 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()
{
+
public void actionPerformed(ActionEvent e)
{
- averageDistanceTreeMenuItem_actionPerformed(e);
+ showDbRefs_actionPerformed(e);
}
+
});
- neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showNpFeatsMenuitem.setText("Show Non-Positional Features");
+ showNpFeatsMenuitem.addActionListener(new ActionListener()
{
+
public void actionPerformed(ActionEvent e)
{
- neighbourTreeMenuItem_actionPerformed(e);
+ showNpFeats_actionPerformed(e);
}
+
});
- clustalAlignMenuItem.setText("Clustal alignment");
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showGroupConservation.setText("Group Conservation");
+ showGroupConservation.addActionListener(new ActionListener()
{
+
public void actionPerformed(ActionEvent e)
{
- clustalAlignMenuItem_actionPerformed(e);
+ showGroupConservation_actionPerformed(e);
}
+
});
- msaAlignMenuItem.setText("Muscle alignment");
- msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ showGroupConsensus.setText("Group Consensus");
+ showGroupConsensus.addActionListener(new ActionListener()
{
+
public void actionPerformed(ActionEvent e)
{
- msaAlignMenuItem_actionPerformed(e);
+ showGroupConsensus_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 alignment via textbox");
- clustalColour.setSelected(false);
- clustalColour.setText("Clustalx colours");
- clustalColour.addActionListener(new java.awt.event.ActionListener()
+ showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.addActionListener(new ActionListener()
{
+
public void actionPerformed(ActionEvent e)
{
- clustalColour_actionPerformed(e);
+ showConsensusHistogram_actionPerformed(e);
}
+
});
- zappoColour.setText("Zappo colour scheme");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
+ showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.addActionListener(new ActionListener()
{
+
public void actionPerformed(ActionEvent e)
{
- zappoColour_actionPerformed(e);
+ showSequenceLogo_actionPerformed(e);
}
+
});
- taylorColour.setText("Taylor colour scheme");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
+ applyAutoAnnotationSettings.setText("Apply to all groups");
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
{
+
public void actionPerformed(ActionEvent e)
{
- taylorColour_actionPerformed(e);
+ applyAutoAnnotationSettings_actionPerformed(e);
}
+
});
- hydrophobicityColour.setText("By hydrophobicity");
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+
+ nucleotideColour.setText("Nucleotide");
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- hydrophobicityColour_actionPerformed(e);
+ nucleotideColour_actionPerformed(e);
}
});
- helixColour.setText("Helix propensity");
- helixColour.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- helixColour_actionPerformed(e);
+ deleteGroups_actionPerformed(e);
}
});
- strandColour.setText("Strand propensity");
- strandColour.addActionListener(new java.awt.event.ActionListener()
+ copy.setText("Copy");
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
+
+ copy.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- strandColour_actionPerformed(e);
+ copy_actionPerformed(e);
}
});
- turnColour.setText("Turn propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
+ cut.setText("Cut");
+ 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)
{
- turnColour_actionPerformed(e);
+ cut_actionPerformed(e);
}
});
- buriedColour.setText("Buried index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- buriedColour_actionPerformed(e);
+ delete_actionPerformed(e);
}
});
- userDefinedColour.setText("User defined colours");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- userDefinedColour_actionPerformed(e);
+ pasteNew_actionPerformed(e);
}
});
- PIDColour.setText("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- PIDColour_actionPerformed(e);
+ pasteThis_actionPerformed(e);
}
});
- BLOSUM62Colour.setText("BLOSUM62 score");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ applyToAllGroups.setText("Apply Colour To All Groups");
+ applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- BLOSUM62Colour_actionPerformed(e);
+ applyToAllGroups_actionPerformed(e);
+ }
+ });
+ createPNG.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createPNG(null);
}
});
- avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+ createPNG.setActionCommand("Save As PNG Image");
+ createPNG.setText("PNG");
+ font.setText("Font...");
+ font.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- avTreeBlosumMenuItem_actionPerformed(e);
+ font_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
- njTreeBlosumMenuItem.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)
{
- njTreeBlosumMenuItem_actionPerformed(e);
+ seqLimit_actionPerformed(e);
}
});
- annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText("Annotation Panel");
- annotationPanelMenuItem.setState(true);
- annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
+ epsFile.setText("EPS");
+ epsFile.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- annotationPanelMenuItem_actionPerformed(e);
+ createEPS(null);
}
});
- colourTextMenuItem.setText("Colour text");
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
+ LoadtreeMenuItem.setText("Load Associated Tree");
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- colourTextMenuItem_actionPerformed(e);
+ LoadtreeMenuItem_actionPerformed(e);
}
});
- htmlMenuItem.setText("Output as HTML");
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ scaleAbove.setVisible(false);
+ scaleAbove.setText("Scale Above");
+ scaleAbove.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- htmlMenuItem_actionPerformed(e);
+ scaleAbove_actionPerformed(e);
}
});
- overviewMenuItem.setText("Overview window");
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+ scaleLeft.setVisible(false);
+ scaleLeft.setSelected(true);
+ scaleLeft.setText("Scale Left");
+ scaleLeft.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- overviewMenuItem_actionPerformed(e);
+ scaleLeft_actionPerformed(e);
}
});
- undoMenuItem.setEnabled(false);
- undoMenuItem.setMnemonic('Z');
- undoMenuItem.setText("Undo");
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ scaleRight.setVisible(false);
+ scaleRight.setSelected(true);
+ scaleRight.setText("Scale Right");
+ scaleRight.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- undoMenuItem_actionPerformed(e);
+ scaleRight_actionPerformed(e);
}
});
- redoMenuItem.setEnabled(false);
- redoMenuItem.setMnemonic('0');
- redoMenuItem.setText("Redo");
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ 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);
+ }
+ });
+ followHighlightMenuItem.setVisible(true);
+ followHighlightMenuItem.setState(true);
+ followHighlightMenuItem.setText("Automatic Scrolling");
+ followHighlightMenuItem.addActionListener(new ActionListener()
{
+
public void actionPerformed(ActionEvent e)
{
- redoMenuItem_actionPerformed(e);
+ followHighlight_actionPerformed();
}
+
});
- conservationMenuItem.setText("By conservation");
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ modifyPID.setText("Modify Identity Threshold...");
+ modifyPID.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed(e);
+ modifyPID_actionPerformed(e);
}
});
- noColourmenuItem.setText("None");
- noColourmenuItem.setSelected(true);
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ modifyConservation.setText("Modify Conservation Threshold...");
+ modifyConservation
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed(e);
+ }
+ });
+ 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);
+
+ calculateTree.setText("Calculate Tree");
+
+ 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)
{
- noColourmenuItem_actionPerformed(e);
+ padGapsMenuitem_actionPerformed(e);
}
});
- wrapMenuItem.setText("Wrap alignment");
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+ vamsasStore.setVisible(false);
+ vamsasStore.setText("VAMSAS store");
+ vamsasStore.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- wrapMenuItem_actionPerformed(e);
+ vamsasStore_actionPerformed(e);
}
});
- printMenuItem.setText("Print");
- printMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showTranslation.setText("Translate cDNA");
+ showTranslation.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- printMenuItem_actionPerformed(e);
+ showTranslation_actionPerformed(e);
}
});
- renderGapsMenuItem.setText("Render gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ extractScores.setText("Extract Scores...");
+ extractScores.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- renderGapsMenuItem_actionPerformed(e);
+ extractScores_actionPerformed(e);
}
});
- findMenuItem.setText("Find");
- findMenuItem.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- findMenuItem_actionPerformed(e);
+ featureSettings_actionPerformed(e);
+ }
+ });
+ fetchSequence.setText("Fetch Sequence(s)...");
+ fetchSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ fetchSequence_actionPerformed(e);
}
});
- searchMenu.setText("Search");
- abovePIDThreshold.setText("Above PID threshold");
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent e) {
- abovePIDThreshold_actionPerformed(e);
+ annotationColour.setText("By Annotation...");
+ annotationColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed(e);
}
});
- sequenceFeatures.setText("Sequence Features");
- sequenceFeatures.addActionListener(new ActionListener()
+ associatedData.setText("Load Features / Annotations");
+ associatedData.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent actionEvent)
+ public void actionPerformed(ActionEvent e)
{
- sequenceFeatures_actionPerformed(actionEvent);
+ associatedData_actionPerformed(e);
}
});
- nucleotideColour.setText("Nucleotide colours");
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ autoCalculate.setText("Autocalculate Consensus");
+ autoCalculate.setState(jalview.bin.Cache.getDefault(
+ "AUTO_CALC_CONSENSUS", true));
+ autoCalculate.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- nucleotideColour_actionPerformed(e);
+ autoCalculate_actionPerformed(e);
}
});
- deleteGroups.setSelected(false);
- deleteGroups.setText("Delete all groups");
- deleteGroups.addActionListener(new java.awt.event.ActionListener()
+ addSequenceMenu.setText("Add Sequences");
+ addFromFile.setText("From File");
+ addFromFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- deleteGroups_actionPerformed(e);
+ addFromFile_actionPerformed(e);
}
});
- copy.setText("Copy");
- copy.setMnemonic(KeyEvent.VK_C);
-
- copy.addActionListener(new java.awt.event.ActionListener()
+ addFromText.setText("From Textbox");
+ addFromText.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- copy_actionPerformed(e);
+ addFromText_actionPerformed(e);
}
});
- cut.setText("Cut");
- cut.setMnemonic(KeyEvent.VK_X);
- cut.addActionListener(new java.awt.event.ActionListener()
+ addFromURL.setText("From URL");
+ addFromURL.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- cut_actionPerformed(e);
+ addFromURL_actionPerformed(e);
}
});
- delete.setText("Delete");
- delete.addActionListener(new java.awt.event.ActionListener()
+ exportFeatures.setText("Export Features...");
+ exportFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- delete_actionPerformed(e);
+ exportFeatures_actionPerformed(e);
}
});
- jMenu1.setMnemonic('V');
- jMenu1.setText("Paste");
- pasteNew.setText("to new alignment");
- pasteNew.addActionListener(new java.awt.event.ActionListener()
+ exportAnnotations.setText("Export Annotations...");
+ exportAnnotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- pasteNew_actionPerformed(e);
+ exportAnnotations_actionPerformed(e);
}
});
- pasteThis.setText("add to this alignment");
- pasteThis.addActionListener(new java.awt.event.ActionListener()
+ statusPanel.setLayout(gridLayout1);
+ jMenu3.setText("Show");
+ showAllSeqs.setText("All Sequences");
+ showAllSeqs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- pasteThis_actionPerformed(e);
+ showAllSeqs_actionPerformed(e);
}
});
- applyToAllGroups.setText("Apply colour to all groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+ showAllColumns.setText("All Columns");
+ showAllColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- applyToAllGroups_actionPerformed(e);
+ showAllColumns_actionPerformed(e);
}
});
- createPNG.addActionListener(new java.awt.event.ActionListener()
+ hideMenu.setText("Hide");
+ hideSelSequences.setText("Selected Sequences");
+ hideSelSequences.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- createPNG_actionPerformed(e);
+ hideSelSequences_actionPerformed(e);
}
});
- createPNG.setActionCommand("Save as PNG Image");
- createPNG.setText("Save as PNG Image");
- font.setText("Change Font");
- font.addActionListener(new java.awt.event.ActionListener()
+ hideSelColumns.setText("Selected Columns");
+ hideSelColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- font_actionPerformed(e);
+ hideSelColumns_actionPerformed(e);
}
});
- fullSeqId.setText("Show full sequence id");
- fullSeqId.addActionListener(new java.awt.event.ActionListener()
+ hiddenMarkers.setText("Show Hidden Markers");
+ hiddenMarkers.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- fullSeqId_actionPerformed(e);
+ hiddenMarkers_actionPerformed(e);
}
});
- epsFile.setText("Save as EPS file");
- epsFile.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- epsFile_actionPerformed(e);
+ invertColSel_actionPerformed(e);
}
});
- LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load assocated tree");
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ 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)
{
- LoadtreeMenuItem_actionPerformed(e);
+ newView_actionPerformed(e);
}
});
- jpred.setText("JPred");
- jpred.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- jpred_actionPerformed(e);
+ textColour_actionPerformed(e);
}
});
- scaleAbove.setVisible(false);
- scaleAbove.setText("Scale above alignment");
- scaleAbove.addActionListener(new java.awt.event.ActionListener()
+ formatMenu.setText("Format");
+ selectMenu.setText("Select");
+ idRightAlign.setText("Right Align Sequence Id");
+ idRightAlign.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- scaleAbove_actionPerformed(e);
+ idRightAlign_actionPerformed(e);
}
});
- scaleLeft.setVisible(false);
- scaleLeft.setSelected(true);
- scaleLeft.setText("Scale left of sequence");
- scaleLeft.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- scaleLeft_actionPerformed(e);
+ gatherViews_actionPerformed(e);
}
});
- scaleRight.setVisible(false);
- scaleRight.setSelected(true);
- scaleRight.setText("Scale right of sequence");
- scaleRight.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- scaleRight_actionPerformed(e);
+ expandViews_actionPerformed(e);
}
});
- modifyPID.setText("Modify PID Threshold");
- modifyPID.addActionListener(new java.awt.event.ActionListener()
+ pageSetup.setText("Page Setup ...");
+ pageSetup.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- modifyPID_actionPerformed(e);
+ pageSetup_actionPerformed(e);
}
});
- modifyConservation.setText("Modify Conservation Threshold");
- modifyConservation.addActionListener(new java.awt.event.ActionListener()
+ alignmentProperties.setText("Alignment Properties...");
+ alignmentProperties.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent e)
+ public void actionPerformed(ActionEvent actionEvent)
{
- modifyConservation_actionPerformed(e);
+ alignmentProperties();
}
});
- sortByTreeMenu.setText("Sort by tree order");
+ tooltipSettingsMenu.setText("Sequence ID Tooltip");
+ autoAnnMenu.setText("Autocalculated Annotation");
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(searchMenu);
+ alignFrameMenuBar.add(selectMenu);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(alignMenu);
- fileMenu.add(saveAlignmentMenu);
+ 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(htmlMenuItem);
- fileMenu.add(epsFile);
- fileMenu.add(createPNG);
+ 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(copy);
- editMenu.add(jMenu1);
- editMenu.add(cut);
- editMenu.add(delete);
- editMenu.addSeparator();
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
+ editMenu.add(cut);
+ editMenu.add(copy);
+ editMenu.add(pasteMenu);
+ editMenu.add(delete);
editMenu.addSeparator();
- editMenu.add(deselectAllSequenceMenuItem);
- editMenu.add(selectAllSequenceMenuItem);
- editMenu.add(invertSequenceMenuItem);
- editMenu.add(deleteGroups);
- editMenu.addSeparator();
- editMenu.add(deselectAllColumnsMenuItem);
editMenu.add(remove2LeftMenuItem);
editMenu.add(remove2RightMenuItem);
- editMenu.addSeparator();
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
- editMenu.add(setGapCharMenuItem);
- searchMenu.add(findMenuItem);
- viewMenu.add(font);
- viewMenu.add(fullSeqId);
+ 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(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(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);
+ viewMenu.add(tooltipSettingsMenu);
+ viewMenu.addSeparator();
+ viewMenu.add(alignmentProperties);
+ viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
- viewMenu.add(sequenceFeatures);
colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
colourMenu.add(zappoColour);
colourMenu.add(taylorColour);
colourMenu.add(hydrophobicityColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(userDefinedColour);
- colourMenu.add(PIDColour);
- colourMenu.add(BLOSUM62Colour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
- calculateMenu.add(sortPairwiseMenuItem);
- calculateMenu.add(sortIDMenuItem);
- calculateMenu.add(sortGroupMenuItem);
- calculateMenu.add(sortByTreeMenu);
- calculateMenu.add(removeRedundancyMenuItem);
+ colourMenu.add(annotationColour);
+ calculateMenu.add(sort);
+ calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
- calculateMenu.add(averageDistanceTreeMenuItem);
- calculateMenu.add(neighbourTreeMenuItem);
- calculateMenu.add(avDistanceTreeBlosumMenuItem);
- calculateMenu.add(njTreeBlosumMenuItem);
- alignMenu.add(clustalAlignMenuItem);
- alignMenu.add(msaAlignMenuItem);
- alignMenu.add(jpred);
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);
- jMenu1.add(pasteNew);
- jMenu1.add(pasteThis);
+ 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(sortLengthMenuItem);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortPairwiseMenuItem);
+ sort.add(sortByTreeMenu);
+ calculateTree.add(averageDistanceTreeMenuItem);
+ calculateTree.add(neighbourTreeMenuItem);
+ calculateTree.add(avDistanceTreeBlosumMenuItem);
+ calculateTree.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);
+ formatMenu.add(showUnconservedMenuItem);
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(grpsFromSelection);
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
-
+ // TODO Auto-generated method stub
+
}
- protected void outputText_actionPerformed(ActionEvent e)
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
+ }
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
}
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ 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 closeMenuItem_actionPerformed(ActionEvent e)
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
+ }
+ protected void followHighlight_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
}
- protected void redoMenuItem_actionPerformed(ActionEvent e)
+ protected void showNpFeats_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
+ }
+ protected void showDbRefs_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
}
- protected void undoMenuItem_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)
+ {
+ }
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ public void addFromFile_actionPerformed(ActionEvent e)
{
}
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ public void addFromText_actionPerformed(ActionEvent e)
{
}
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ public void addFromURL_actionPerformed(ActionEvent e)
{
}
-
- protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
+ public void exportFeatures_actionPerformed(ActionEvent e)
{
}
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ public void exportAnnotations_actionPerformed(ActionEvent e)
{
}
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
-
}
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ protected void closeMenuItem_actionPerformed(boolean b)
{
+ }
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void setGapCharMenuItem_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 sortLengthMenuItem_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 njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ protected void clustalColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void zappoColour_actionPerformed(ActionEvent e)
+ {
}
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ protected void taylorColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void helixColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void strandColour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+ protected void turnColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void buriedColour_actionPerformed(ActionEvent e)
+ {
}
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void PIDColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void clustalColour_actionPerformed(ActionEvent e)
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void zappoColour_actionPerformed(ActionEvent e)
+ protected void printMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void taylorColour_actionPerformed(ActionEvent e)
+ protected void findMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
}
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
+ {
+ }
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ protected void nucleotideColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
}
- protected void helixColour_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void cut_actionPerformed(ActionEvent e)
{
+ }
+ protected void delete_actionPerformed(ActionEvent e)
+ {
}
- protected void strandColour_actionPerformed(ActionEvent e)
+ protected void pasteNew_actionPerformed(ActionEvent e)
{
+ }
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
}
- protected void turnColour_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
+ }
+ public void createPNG(java.io.File f)
+ {
}
- protected void buriedColour_actionPerformed(ActionEvent e)
+ protected void font_actionPerformed(ActionEvent e)
{
+ }
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
}
+ public void seqDBRef_actionPerformed(ActionEvent e)
+ {
+ }
- protected void userDefinedColour_actionPerformed(ActionEvent e)
+ public void createEPS(java.io.File f)
{
+ }
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ protected void jpred_actionPerformed(ActionEvent e)
{
+ }
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void scaleRight_actionPerformed(ActionEvent e)
{
+ }
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
}
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ }
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed(ActionEvent e)
{
+ }
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ public void vamsasStore_actionPerformed(ActionEvent e)
{
}
+ public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
- protected void printMenuItem_actionPerformed(ActionEvent e)
+ }
+
+ public void showTranslation_actionPerformed(ActionEvent e)
{
}
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ public void featureSettings_actionPerformed(ActionEvent e)
{
}
- protected void findMenuItem_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed(ActionEvent e)
{
}
+ public void smoothFont_actionPerformed(ActionEvent e)
+ {
+
+ }
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+ public void annotationColour_actionPerformed(ActionEvent e)
+ {
}
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+ public void associatedData_actionPerformed(ActionEvent e)
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ public void autoCalculate_actionPerformed(ActionEvent e)
{
}
- protected void deleteGroups_actionPerformed(ActionEvent e)
+ public void showAllSeqs_actionPerformed(ActionEvent e)
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ public void showAllColumns_actionPerformed(ActionEvent e)
{
}
+ public void hideSelSequences_actionPerformed(ActionEvent e)
+ {
- protected void cut_actionPerformed(ActionEvent e)
+ }
+
+ public void hideSelColumns_actionPerformed(ActionEvent e)
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
{
}
- protected void pasteNew_actionPerformed(ActionEvent e)
+ public void findPdbId_actionPerformed(ActionEvent e)
{
}
- protected void pasteThis_actionPerformed(ActionEvent e)
+ public void enterPdbId_actionPerformed(ActionEvent e)
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ public void pdbFile_actionPerformed(ActionEvent e)
{
}
- protected void createPNG_actionPerformed(ActionEvent e)
+ public void invertColSel_actionPerformed(ActionEvent e)
{
}
- protected void font_actionPerformed(ActionEvent e)
+ public void tabSelectionChanged(int sel)
{
}
- protected void fullSeqId_actionPerformed(ActionEvent e)
+ public void tabbedPane_mousePressed(MouseEvent e)
{
}
- protected void epsFile_actionPerformed(ActionEvent e)
+ public void tabbedPane_focusGained(FocusEvent e)
+ {
+ requestFocus();
+ }
+
+ public void save_actionPerformed(ActionEvent e)
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+ public void reload_actionPerformed(ActionEvent e)
+ {
}
- protected void jpred_actionPerformed(ActionEvent e)
+ public void newView_actionPerformed(ActionEvent e)
{
}
- protected void scaleAbove_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed(ActionEvent e)
{
}
- protected void scaleLeft_actionPerformed(ActionEvent e)
+ public void idRightAlign_actionPerformed(ActionEvent e)
{
}
- protected void scaleRight_actionPerformed(ActionEvent e)
+ public void expandViews_actionPerformed(ActionEvent e)
{
}
- protected void modifyPID_actionPerformed(ActionEvent e)
+ public void gatherViews_actionPerformed(ActionEvent e)
{
}
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ public void buildTreeMenu()
{
}
+ public void pageSetup_actionPerformed(ActionEvent e)
+ {
+ }
+ public void alignmentProperties()
+ {
+ }
}
git://source.jalview.org / jalview.git / blobdiff