X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=af7766a8ca5dd3c889081cea16ca208f95f39d07;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=1bc0b72e9a1c4d92666809c14706613e334f1771;hpb=fd29e047719a470cf304c5a41abfff5c1eac3ee8;p=jalview.git
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1bc0b72..af7766a 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see .
*/
package jalview.jbgui;
@@ -26,131 +25,288 @@ import javax.swing.event.*;
import jalview.schemes.*;
-public class GAlignFrame
- extends JInternalFrame
+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 webService = new JMenu();
+
protected JMenuItem webServiceNoServices;
+
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
+
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
+
protected JMenuItem invertSequenceMenuItem = new JMenuItem();
+
protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+
protected JMenuItem remove2RightMenuItem = new JMenuItem();
+
protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+
protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
+
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();
+
BorderLayout borderLayout1 = new BorderLayout();
+
public JLabel statusBar = new JLabel();
+
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 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();
+
public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+
public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+
JMenuItem htmlMenuItem = new JMenuItem();
+
JMenuItem overviewMenuItem = new JMenuItem();
+
protected JMenuItem undoMenuItem = new JMenuItem();
+
protected JMenuItem redoMenuItem = new JMenuItem();
+
public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+
JMenuItem printMenuItem = new JMenuItem();
+
public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+
JMenuItem findMenuItem = new JMenuItem();
+
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 pasteMenu = new JMenu();
+
JMenuItem pasteNew = new JMenuItem();
+
JMenuItem pasteThis = new JMenuItem();
+
public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+
JMenuItem createPNG = new JMenuItem();
+
protected JMenuItem font = new JMenuItem();
+
public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
JMenuItem epsFile = new JMenuItem();
+
JMenuItem LoadtreeMenuItem = 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();
+
protected JMenu sort = new JMenu();
- JMenu calculate = 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();
+
+ JMenuItem hideAllButSelection = new JMenuItem();
+
+ JMenuItem hideAllSelection = new JMenuItem();
+
+ JMenuItem showAllhidden = 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
@@ -161,8 +317,8 @@ public class GAlignFrame
// dynamically fill save as menu with available formats
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
- WRITEABLE_FORMATS[i]);
+ JMenuItem item = new JMenuItem(
+ jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
item.addActionListener(new java.awt.event.ActionListener()
{
@@ -174,8 +330,7 @@ public class GAlignFrame
outputTextboxMenu.add(item);
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
}
@@ -193,32 +348,33 @@ public class GAlignFrame
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
while (userColours.hasMoreElements())
{
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.
- nextElement().toString());
+ userColours.nextElement().toString());
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
- if (evt.isControlDown() || SwingUtilities.isRightMouseButton(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);
+ 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());
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
colourMenu.remove(radioItem);
}
else
@@ -259,7 +415,8 @@ public class GAlignFrame
colours.add(BLOSUM62Colour);
colours.add(nucleotideColour);
- setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+ setColourSelected(jalview.bin.Cache
+ .getDefault("DEFAULT_COLOUR", "None"));
}
@@ -268,85 +425,87 @@ public class GAlignFrame
if (defaultColour != null)
{
- int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+ int index = ColourSchemeProperty
+ .getColourIndexFromName(defaultColour);
switch (index)
{
- case ColourSchemeProperty.NONE:
- noColourmenuItem.setSelected(true);
- break;
- case ColourSchemeProperty.CLUSTAL:
- clustalColour.setSelected(true);
+ case ColourSchemeProperty.CLUSTAL:
+ clustalColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.BLOSUM:
- BLOSUM62Colour.setSelected(true);
+ case ColourSchemeProperty.BLOSUM:
+ BLOSUM62Colour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.PID:
- PIDColour.setSelected(true);
+ case ColourSchemeProperty.PID:
+ PIDColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.ZAPPO:
- zappoColour.setSelected(true);
+ case ColourSchemeProperty.ZAPPO:
+ zappoColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.TAYLOR:
- taylorColour.setSelected(true);
- break;
+ case ColourSchemeProperty.TAYLOR:
+ taylorColour.setSelected(true);
+ break;
- case ColourSchemeProperty.HYDROPHOBIC:
- hydrophobicityColour.setSelected(true);
+ case ColourSchemeProperty.HYDROPHOBIC:
+ hydrophobicityColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.HELIX:
- helixColour.setSelected(true);
+ case ColourSchemeProperty.HELIX:
+ helixColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.STRAND:
- strandColour.setSelected(true);
+ case ColourSchemeProperty.STRAND:
+ strandColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.TURN:
- turnColour.setSelected(true);
+ case ColourSchemeProperty.TURN:
+ turnColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.BURIED:
- buriedColour.setSelected(true);
+ case ColourSchemeProperty.BURIED:
+ buriedColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.NUCLEOTIDE:
- nucleotideColour.setSelected(true);
+ case ColourSchemeProperty.NUCLEOTIDE:
+ nucleotideColour.setSelected(true);
- break;
+ break;
- case ColourSchemeProperty.USER_DEFINED:
- userDefinedColour.setSelected(true);
+ case ColourSchemeProperty.USER_DEFINED:
+ userDefinedColour.setSelected(true);
- break;
+ break;
+ case ColourSchemeProperty.NONE:
+ default:
+ noColourmenuItem.setSelected(true);
+ break;
+
}
}
}
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
fileMenu.setText("File");
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.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)
@@ -355,8 +514,9 @@ public class GAlignFrame
}
});
closeMenuItem.setText("Close");
- closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ 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)
@@ -370,86 +530,116 @@ public class GAlignFrame
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);
- }
- });
+ 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);
- }
- });
+ 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()
+ 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)
{
- invertSequenceMenuItem_actionPerformed(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);
- }
- });
+ 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);
- }
- });
+ 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);
- }
- });
+ 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);
- }
- });
+ 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()
@@ -468,14 +658,25 @@ public class GAlignFrame
viewTextMenuItem_actionPerformed(e);
}
});
+ showNonconservedMenuItem.setText("Show nonconserved");
+ showNonconservedMenuItem.setState(false);
+ showNonconservedMenuItem
+ .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);
- }
- });
+ 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()
{
@@ -484,6 +685,15 @@ public class GAlignFrame
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()
{
@@ -493,26 +703,26 @@ public class GAlignFrame
}
});
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);
- }
- });
+ 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);
- }
- });
+ 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()
{
@@ -521,24 +731,25 @@ public class GAlignFrame
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem.setText(
- "Average Distance Using % Identity");
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
- ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_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);
- }
- });
+ 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);
@@ -572,13 +783,14 @@ public class GAlignFrame
}
});
hydrophobicityColour.setText("Hydrophobicity");
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
+ 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()
{
@@ -635,43 +847,45 @@ public class GAlignFrame
BLOSUM62Colour_actionPerformed(e);
}
});
- avDistanceTreeBlosumMenuItem.setText(
- "Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
- ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
+ 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);
- }
- });
+ 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);
- }
- });
+ "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);
- }
- });
+ 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()
{
@@ -691,8 +905,8 @@ public class GAlignFrame
undoMenuItem.setEnabled(false);
undoMenuItem.setText("Undo");
undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_Z,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
undoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -702,8 +916,9 @@ public class GAlignFrame
});
redoMenuItem.setEnabled(false);
redoMenuItem.setText("Redo");
- redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ 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)
@@ -712,13 +927,14 @@ public class GAlignFrame
}
});
conservationMenuItem.setText("By Conservation");
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed(e);
- }
- });
+ 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()
{
@@ -736,8 +952,9 @@ public class GAlignFrame
}
});
printMenuItem.setText("Print ...");
- printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ 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)
@@ -747,17 +964,18 @@ public class GAlignFrame
});
renderGapsMenuItem.setText("Show Gaps");
renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- renderGapsMenuItem_actionPerformed(e);
- }
- });
+ 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));
+ java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
findMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -781,6 +999,86 @@ public class GAlignFrame
showSeqFeatures_actionPerformed(actionEvent);
}
});
+ /*
+ * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+ * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
+ * void actionPerformed(ActionEvent actionEvent) {
+ * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
+ */
+ showDbRefsMenuitem.setText("Show Database Refs");
+ showDbRefsMenuitem.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showDbRefs_actionPerformed(e);
+ }
+
+ });
+ showNpFeatsMenuitem.setText("Show Non-Positional Features");
+ showNpFeatsMenuitem.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showNpFeats_actionPerformed(e);
+ }
+
+ });
+ showGroupConservation.setText("Group Conservation");
+ showGroupConservation.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConservation_actionPerformed(e);
+ }
+
+ });
+
+ showGroupConsensus.setText("Group Consensus");
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConsensus_actionPerformed(e);
+ }
+
+ });
+ showConsensusHistogram.setText("Show Consensus Histogram");
+ showConsensusHistogram.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showConsensusHistogram_actionPerformed(e);
+ }
+
+ });
+ showSequenceLogo.setText("Show Consensus Logo");
+ showSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ applyAutoAnnotationSettings.setText("Apply to all groups");
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ applyAutoAnnotationSettings_actionPerformed(e);
+ }
+
+ });
+
nucleotideColour.setText("Nucleotide");
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
@@ -790,8 +1088,9 @@ public class GAlignFrame
}
});
deleteGroups.setText("Undefine groups");
- deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ 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)
@@ -801,8 +1100,8 @@ public class GAlignFrame
});
copy.setText("Copy");
copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
copy.addActionListener(new java.awt.event.ActionListener()
{
@@ -813,8 +1112,8 @@ public class GAlignFrame
});
cut.setText("Cut");
cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_X,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
cut.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -823,8 +1122,8 @@ public class GAlignFrame
}
});
delete.setText("Delete");
- delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_BACK_SPACE, 0, false));
+ 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)
@@ -835,9 +1134,9 @@ public class GAlignFrame
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));
+ 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)
@@ -847,8 +1146,8 @@ public class GAlignFrame
});
pasteThis.setText("Add To This Alignment");
pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask(), false));
pasteThis.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -940,14 +1239,27 @@ public class GAlignFrame
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
centreColumnLabelsMenuItem.setText("Centre Column Labels");
- centreColumnLabelsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- centreColumnLabels_actionPerformed(e);
+ followHighlight_actionPerformed();
}
+
});
-
+
modifyPID.setText("Modify Identity Threshold...");
modifyPID.addActionListener(new java.awt.event.ActionListener()
{
@@ -957,13 +1269,14 @@ public class GAlignFrame
}
});
modifyConservation.setText("Modify Conservation Threshold...");
- modifyConservation.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- modifyConservation_actionPerformed(e);
- }
- });
+ 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()
@@ -983,30 +1296,30 @@ public class GAlignFrame
});
sortByAnnotScore.setText("by Score");
sort.add(sortByAnnotScore);
- sortByAnnotScore.addMenuListener(
- new javax.swing.event.MenuListener() {
-
- public void menuCanceled(MenuEvent e)
- {
- }
+ sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+ {
- public void menuDeselected(MenuEvent e)
- {
- }
+ public void menuCanceled(MenuEvent e)
+ {
+ }
- public void menuSelected(MenuEvent e)
- {
- buildSortByAnnotationScoresMenu();
- }
- }
- );
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ public void menuSelected(MenuEvent e)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ });
sortByAnnotScore.setVisible(false);
-
- calculate.setText("Calculate Tree");
+
+ calculateTree.setText("Calculate Tree");
jMenu2.setText("Export Image");
padGapsMenuitem.setText("Pad Gaps");
- padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ padGapsMenuitem.setState(jalview.bin.Cache
+ .getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1039,16 +1352,15 @@ public class GAlignFrame
extractScores_actionPerformed(e);
}
});
- extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction
+ 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);
- }
- });*/
+ /*
+ * showProducts.addActionListener(new ActionListener() {
+ *
+ * public void actionPerformed(ActionEvent e) {
+ * showProducts_actionPerformed(e); } });
+ */
featureSettings.setText("Feature Settings...");
featureSettings.addActionListener(new ActionListener()
{
@@ -1083,7 +1395,8 @@ public class GAlignFrame
}
});
autoCalculate.setText("Autocalculate Consensus");
- autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculate.setState(jalview.bin.Cache.getDefault(
+ "AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1135,6 +1448,7 @@ public class GAlignFrame
statusPanel.setLayout(gridLayout1);
jMenu3.setText("Show");
showAllSeqs.setText("All Sequences");
+ showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
showAllSeqs.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1143,6 +1457,7 @@ public class GAlignFrame
}
});
showAllColumns.setText("All Columns");
+ showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
showAllColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1152,6 +1467,7 @@ public class GAlignFrame
});
hideMenu.setText("Hide");
hideSelSequences.setText("Selected Sequences");
+ hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
hideSelSequences.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1160,6 +1476,7 @@ public class GAlignFrame
}
});
hideSelColumns.setText("Selected Columns");
+ hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
hideSelColumns.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1167,6 +1484,34 @@ public class GAlignFrame
hideSelColumns_actionPerformed(e);
}
});
+ hideAllSelection.setText("Selected Region");
+ hideAllSelection.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllSelection_actionPerformed(e);
+ }
+ });
+ // TODO: should be hidden if no selection exists.
+ hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
+ hideAllButSelection.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllButSelection_actionPerformed(e);
+ }
+ });
+ showAllhidden.setText("All Sequences and Columns");
+ showAllhidden
+ .setToolTipText("H toggles visibility of hidden or selected regions.");
+ showAllhidden.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllhidden_actionPerformed(e);
+ }
+ });
+
hiddenMarkers.setText("Show Hidden Markers");
hiddenMarkers.addActionListener(new ActionListener()
{
@@ -1176,11 +1521,10 @@ public class GAlignFrame
}
});
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.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)
@@ -1212,8 +1556,9 @@ public class GAlignFrame
}
});
save.setText("Save");
- save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ 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)
@@ -1231,8 +1576,9 @@ public class GAlignFrame
}
});
newView.setText("New View");
- newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ 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)
@@ -1241,8 +1587,7 @@ public class GAlignFrame
}
});
tabbedPane.setToolTipText(" Right-click to rename tab"
- +
- "
Press X to eXpand tabs, G to reGroup.");
+ + "
Press X to eXpand tabs, G to reGroup.