-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
- * AM Waterhouse\r
- *******************/\r
-\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.jbgui;\r
\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
import java.awt.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+\r
+import jalview.schemes.*;\r
\r
-public class GAlignFrame extends JInternalFrame\r
+public class GAlignFrame\r
+ extends JInternalFrame\r
{\r
protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
protected JMenu fileMenu = new JMenu();\r
protected JMenu viewMenu = new JMenu();\r
protected JMenu colourMenu = new JMenu();\r
protected JMenu calculateMenu = new JMenu();\r
- protected JMenu alignMenu = new JMenu();\r
- protected JMenuItem groupsMenuItem = new JMenuItem();\r
+ protected JMenu webService = new JMenu();\r
+ protected JMenuItem webServiceNoServices;\r
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
- protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
protected JMenuItem sortIDMenuItem = new JMenuItem();\r
protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
- protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
protected JMenuItem PCAMenuItem = new JMenuItem();\r
protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
BorderLayout borderLayout1 = new BorderLayout();\r
public JLabel statusBar = new JLabel();\r
- protected JMenu saveAlignmentMenu = new JMenu();\r
+ protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
protected JMenu outputTextboxMenu = new JMenu();\r
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem hydrophobicityColour = new\r
+ JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
JMenuItem htmlMenuItem = new JMenuItem();\r
JMenuItem overviewMenuItem = new JMenuItem();\r
protected JMenuItem undoMenuItem = new JMenuItem();\r
protected JMenuItem redoMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
- protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
JMenuItem printMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
JMenuItem findMenuItem = new JMenuItem();\r
JMenu searchMenu = new JMenu();\r
- protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
JMenuItem deleteGroups = new JMenuItem();\r
JMenuItem delete = new JMenuItem();\r
JMenu jMenu1 = new JMenu();\r
JMenuItem pasteNew = new JMenuItem();\r
JMenuItem pasteThis = new JMenuItem();\r
- protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
JMenuItem createPNG = new JMenuItem();\r
protected JMenuItem font = new JMenuItem();\r
- protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
JMenuItem epsFile = new JMenuItem();\r
+ JMenuItem LoadtreeMenuItem = new JMenuItem();\r
+ public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
+ protected JMenuItem modifyPID = new JMenuItem();\r
+ protected JMenuItem modifyConservation = new JMenuItem();\r
+ protected JMenu sortByTreeMenu = new JMenu();\r
+ protected JMenu sort = new JMenu();\r
+ JMenu calculate = new JMenu();\r
+ JMenu jMenu2 = new JMenu();\r
+ JMenuItem padGapsMenuitem = new JMenuItem();\r
+ protected ButtonGroup colours = new ButtonGroup();\r
+ JMenuItem vamsasStore = new JMenuItem();\r
+ protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
+ protected JTabbedPane tabbedPane = new JTabbedPane();\r
+ public JMenuItem featureSettings = new JMenuItem();\r
+ public JCheckBoxMenuItem seqDBRef = new JCheckBoxMenuItem();\r
+ JMenuItem fetchSequence = new JMenuItem();\r
+\r
public GAlignFrame()\r
{\r
\r
jbInit();\r
setJMenuBar(alignFrameMenuBar);\r
\r
- JMenuItem item;\r
// dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
- saveAlignmentMenu.add( item );\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveAs_actionPerformed(e);\r
- }\r
- });\r
-\r
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
+ {\r
+ JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
+ elementAt(\r
+ i));\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
\r
- outputTextboxMenu.add( item );\r
+ outputTextboxMenu.add(item);\r
}\r
-\r
}\r
- catch(Exception e)\r
+ catch (Exception e)\r
{\r
- e.printStackTrace();\r
}\r
\r
- ButtonGroup colours = new ButtonGroup();\r
+\r
+ if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+ nextElement().toString());\r
+ radioItem.setName("USER_DEFINED");\r
+ radioItem.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
+ "Remove from default list?",\r
+ "Remove user defined colour",\r
+ JOptionPane.YES_NO_OPTION);\r
+ if(option == JOptionPane.YES_OPTION)\r
+ {\r
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
+ colourMenu.remove(radioItem);\r
+ }\r
+ else\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ }\r
+ }\r
+ });\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ colourMenu.insert(radioItem, 15);\r
+ colours.add(radioItem);\r
+ }\r
+ }\r
colours.add(noColourmenuItem);\r
colours.add(clustalColour);\r
colours.add(zappoColour);\r
colours.add(PIDColour);\r
colours.add(BLOSUM62Colour);\r
colours.add(nucleotideColour);\r
+\r
+ setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
+\r
+\r
}\r
- private void jbInit() throws Exception\r
+\r
+ public void setColourSelected(String defaultColour)\r
+ {\r
+\r
+ if (defaultColour != null)\r
+ {\r
+ int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
+\r
+ switch (index)\r
+ {\r
+ case ColourSchemeProperty.NONE:\r
+ noColourmenuItem.setSelected(true);\r
+ break;\r
+ case ColourSchemeProperty.CLUSTAL:\r
+ clustalColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BLOSUM:\r
+ BLOSUM62Colour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.PID:\r
+ PIDColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.ZAPPO:\r
+ zappoColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.TAYLOR:\r
+ taylorColour.setSelected(true);\r
+ break;\r
+\r
+ case ColourSchemeProperty.HYDROPHOBIC:\r
+ hydrophobicityColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.HELIX:\r
+ helixColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.STRAND:\r
+ strandColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.TURN:\r
+ turnColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BURIED:\r
+ buriedColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.NUCLEOTIDE:\r
+ nucleotideColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.USER_DEFINED:\r
+ userDefinedColour.setSelected(true);\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
{\r
fileMenu.setMnemonic('F');\r
fileMenu.setText("File");\r
saveAlignmentMenu.setMnemonic('L');\r
- saveAlignmentMenu.setText("Save alignment to local file");\r
+ saveAlignmentMenu.setText("Save As");\r
+ saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+ awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
+ saveAlignmentMenu.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ saveAlignmentMenu_actionPerformed(e);\r
+ }\r
+ });\r
closeMenuItem.setMnemonic('C');\r
closeMenuItem.setText("Close");\r
closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
viewMenu.setText("View");\r
colourMenu.setText("Colour");\r
calculateMenu.setText("Calculate");\r
- alignMenu.setText("Web Service");\r
- groupsMenuItem.setVisible(false);\r
- groupsMenuItem.setText("Groups");\r
- groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupsMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ webService.setText("Web Service");\r
selectAllSequenceMenuItem.setText("Select all");\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_A,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
selectAllSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- deselectAllSequenceMenuItem.setText("Clear selection");\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ deselectAllSequenceMenuItem.setText("Deselect All");\r
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
+ getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
deselectAllSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- invertSequenceMenuItem.setText("Invert sequence selection");\r
+ invertSequenceMenuItem.setText("Invert Selection");\r
invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
invertSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- deselectAllColumnsMenuItem.setText("Deselect all columns");\r
- deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deselectAllColumnsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
+ remove2LeftMenuItem.setText("Remove Left");\r
remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
remove2LeftMenuItem_actionPerformed(e);\r
}\r
});\r
- remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
+ remove2RightMenuItem.setText("Remove Right");\r
remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
remove2RightMenuItem_actionPerformed(e);\r
}\r
});\r
- removeGappedColumnMenuItem.setText("Remove gapped columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
removeGappedColumnMenuItem_actionPerformed(e);\r
}\r
});\r
- removeAllGapsMenuItem.setText("Remove all gaps");\r
+ removeAllGapsMenuItem.setText("Remove All Gaps");\r
removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
removeAllGapsMenuItem_actionPerformed(e);\r
}\r
});\r
- setGapCharMenuItem.setText("Set gap character to \".\"");\r
- setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- setGapCharMenuItem_actionPerformed(e);\r
- }\r
- });\r
viewBoxesMenuItem.setText("Boxes");\r
viewBoxesMenuItem.setState(true);\r
viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
viewTextMenuItem_actionPerformed(e);\r
}\r
});\r
- sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
+ sortPairwiseMenuItem.setText("by Pairwise Identity");\r
sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
sortPairwiseMenuItem_actionPerformed(e);\r
}\r
});\r
- sortIDMenuItem.setText("Sort by ID");\r
+ sortIDMenuItem.setText("by ID");\r
sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
sortIDMenuItem_actionPerformed(e);\r
}\r
});\r
- sortGroupMenuItem.setText("Sort by group");\r
+ sortGroupMenuItem.setText("by Group");\r
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
sortGroupMenuItem_actionPerformed(e);\r
}\r
});\r
- sortTreeOrderMenuItem.setText("Sort by tree order");\r
- sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortTreeOrderMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeRedundancyMenuItem.setText("Remove redundancy");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ removeRedundancyMenuItem.setText("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
removeRedundancyMenuItem_actionPerformed(e);\r
}\r
});\r
- pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
pairwiseAlignmentMenuItem_actionPerformed(e);\r
}\r
});\r
- PCAMenuItem.setText("Principal component analysis");\r
+ PCAMenuItem.setText("Principal Component Analysis");\r
PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
PCAMenuItem_actionPerformed(e);\r
}\r
});\r
- averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ averageDistanceTreeMenuItem.setText(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
averageDistanceTreeMenuItem_actionPerformed(e);\r
}\r
});\r
- neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
neighbourTreeMenuItem_actionPerformed(e);\r
}\r
});\r
- clustalAlignMenuItem.setText("Clustal alignment");\r
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ this.getContentPane().setLayout(borderLayout1);\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void ancestorAdded(AncestorEvent event)\r
+ {\r
+ alignFrameMenuBar_ancestorAdded(event);\r
+ }\r
+\r
+ public void ancestorRemoved(AncestorEvent event)\r
+ {\r
+ }\r
+\r
+ public void ancestorMoved(AncestorEvent event)\r
{\r
- clustalAlignMenuItem_actionPerformed(e);\r
}\r
});\r
- this.getContentPane().setLayout(borderLayout1);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setBackground(Color.white);\r
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
statusBar.setText("Status bar");\r
outputTextboxMenu.setMnemonic('T');\r
- outputTextboxMenu.setText("Output alignment via textbox");\r
- clustalColour.setSelected(false);\r
- clustalColour.setText("Clustalx colours");\r
+ outputTextboxMenu.setText("Output to Textbox");\r
+ clustalColour.setText("Clustalx");\r
+\r
clustalColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
clustalColour_actionPerformed(e);\r
}\r
});\r
- zappoColour.setText("Zappo colour scheme");\r
+ zappoColour.setText("Zappo");\r
zappoColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
zappoColour_actionPerformed(e);\r
}\r
});\r
- taylorColour.setText("Taylor colour scheme");\r
+ taylorColour.setText("Taylor");\r
taylorColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
taylorColour_actionPerformed(e);\r
}\r
});\r
- hydrophobicityColour.setText("By hydrophobicity");\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
hydrophobicityColour_actionPerformed(e);\r
}\r
});\r
- helixColour.setText("Helix propensity");\r
+ helixColour.setText("Helix Propensity");\r
helixColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
helixColour_actionPerformed(e);\r
}\r
});\r
- strandColour.setText("Strand propensity");\r
+ strandColour.setText("Strand Propensity");\r
strandColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
strandColour_actionPerformed(e);\r
}\r
});\r
- turnColour.setText("Turn propensity");\r
+ turnColour.setText("Turn Propensity");\r
turnColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
turnColour_actionPerformed(e);\r
}\r
});\r
- buriedColour.setText("Buried index");\r
+ buriedColour.setText("Buried Index");\r
buriedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
buriedColour_actionPerformed(e);\r
}\r
});\r
- userDefinedColour.setText("User defined colours");\r
+ userDefinedColour.setText("User Defined...");\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
PIDColour_actionPerformed(e);\r
}\r
});\r
- BLOSUM62Colour.setText("BLOSUM62 score");\r
+ BLOSUM62Colour.setText("BLOSUM62 Score");\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
BLOSUM62Colour_actionPerformed(e);\r
}\r
});\r
- avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ avDistanceTreeBlosumMenuItem.setText(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
avTreeBlosumMenuItem_actionPerformed(e);\r
}\r
});\r
- njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
njTreeBlosumMenuItem_actionPerformed(e);\r
}\r
});\r
- consensusGraphMenuItem.setActionCommand("");\r
- consensusGraphMenuItem.setText("Consensus graph");\r
- consensusGraphMenuItem.setState(true);\r
- consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setText("Show Annotations");\r
+ annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
+ annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- consensusGraphMenuItem_actionPerformed(e);\r
+ annotationPanelMenuItem_actionPerformed(e);\r
}\r
});\r
- colourTextMenuItem.setText("Colour text");\r
+ colourTextMenuItem.setText("Colour Text");\r
colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
colourTextMenuItem_actionPerformed(e);\r
}\r
});\r
- htmlMenuItem.setText("Output as HTML");\r
+ htmlMenuItem.setText("HTML");\r
htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
htmlMenuItem_actionPerformed(e);\r
}\r
});\r
- overviewMenuItem.setText("Overview window");\r
+ overviewMenuItem.setText("Overview Window");\r
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
undoMenuItem.setEnabled(false);\r
undoMenuItem.setMnemonic('Z');\r
undoMenuItem.setText("Undo");\r
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_Z,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
redoMenuItem_actionPerformed(e);\r
}\r
});\r
- conservationMenuItem.setText("By conservation");\r
+ conservationMenuItem.setText("By Conservation");\r
conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
noColourmenuItem.setText("None");\r
- noColourmenuItem.setSelected(true);\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
noColourmenuItem_actionPerformed(e);\r
}\r
});\r
- wrapMenuItem.setText("Wrap alignment");\r
+ wrapMenuItem.setText("Wrap");\r
wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
printMenuItem_actionPerformed(e);\r
}\r
});\r
- renderGapsMenuItem.setText("Render gaps");\r
+ renderGapsMenuItem.setText("Show Gaps");\r
renderGapsMenuItem.setState(true);\r
renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
renderGapsMenuItem_actionPerformed(e);\r
}\r
});\r
- findMenuItem.setText("Find");\r
+ findMenuItem.setText("Find...");\r
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_F,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
});\r
searchMenu.setText("Search");\r
\r
- abovePIDThreshold.setText("Above PID threshold");\r
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
+ abovePIDThreshold.setText("Above Identity Threshold");\r
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
abovePIDThreshold_actionPerformed(e);\r
}\r
});\r
sequenceFeatures_actionPerformed(actionEvent);\r
}\r
});\r
- nucleotideColour.setText("Nucleotide colours");\r
+ nucleotideColour.setText("Nucleotide");\r
nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
nucleotideColour_actionPerformed(e);\r
}\r
});\r
- deleteGroups.setSelected(false);\r
- deleteGroups.setText("Delete all groups");\r
+ deleteGroups.setText("Undefine groups");\r
deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
copy.setText("Copy");\r
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_C,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
copy.setMnemonic(KeyEvent.VK_C);\r
\r
copy.addActionListener(new java.awt.event.ActionListener()\r
}\r
});\r
cut.setText("Cut");\r
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_X,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
cut.setMnemonic(KeyEvent.VK_X);\r
cut.addActionListener(new java.awt.event.ActionListener()\r
{\r
});\r
jMenu1.setMnemonic('V');\r
jMenu1.setText("Paste");\r
- pasteNew.setText("to new alignment");\r
+ pasteNew.setText("To New Alignment");\r
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_V,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
pasteNew.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
pasteNew_actionPerformed(e);\r
}\r
});\r
- pasteThis.setText("add to this alignment");\r
+ pasteThis.setText("Add To This Alignment");\r
pasteThis.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
pasteThis_actionPerformed(e);\r
}\r
});\r
- applyToAllGroups.setText("Apply colour to all groups");\r
+ applyToAllGroups.setText("Apply Colour To All Groups");\r
applyToAllGroups.setState(true);\r
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
{\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- createPNG_actionPerformed(e);\r
+ createPNG(null);\r
}\r
});\r
- createPNG.setActionCommand("Save as PNG Image");\r
- createPNG.setText("Save as PNG Image");\r
- font.setText("Change Font");\r
+ createPNG.setActionCommand("Save As PNG Image");\r
+ createPNG.setText("PNG");\r
+ font.setText("Font...");\r
font.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
font_actionPerformed(e);\r
}\r
});\r
- fullSeqId.setText("Show full sequence id");\r
- fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
+\r
+ seqLimits.setText("Show Sequence Limits");\r
+ seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
+ seqLimits.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- fullSeqId_actionPerformed(e);\r
+ seqLimit_actionPerformed(e);\r
}\r
});\r
- epsFile.setText("Save as EPS file");\r
+ epsFile.setText("EPS");\r
epsFile.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- epsFile_actionPerformed(e);\r
+ createEPS(null);\r
+ }\r
+ });\r
+ LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
+ LoadtreeMenuItem.setText("Load Assocated Tree");\r
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ LoadtreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleAbove.setVisible(false);\r
+ scaleAbove.setText("Scale Above");\r
+ scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ scaleAbove_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleLeft.setVisible(false);\r
+ scaleLeft.setSelected(true);\r
+ scaleLeft.setText("Scale Left");\r
+ scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ scaleLeft_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleRight.setVisible(false);\r
+ scaleRight.setSelected(true);\r
+ scaleRight.setText("Scale Right");\r
+ scaleRight.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ scaleRight_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyPID.setText("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setText("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setText("By Tree Order");\r
+ sort.setText("Sort");\r
+ calculate.setText("Calculate Tree");\r
+\r
+ jMenu2.setText("Export");\r
+ padGapsMenuitem.setText("Pad Gaps");\r
+ padGapsMenuitem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ padGapsMenuitem_actionPerformed(e);\r
+ }\r
+ });\r
+ vamsasStore.setText("VAMSAS store");\r
+ vamsasStore.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ vamsasStore_actionPerformed(e);\r
+ }\r
+ });\r
+ showTranslation.setText("Translate cDNA");\r
+ showTranslation.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showTranslation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ tabbedPane.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent ece)\r
+ {\r
+\r
+ tabSelected();\r
+ }\r
+ });\r
+ featureSettings.setEnabled(false);\r
+ featureSettings.setText("Feature Settings...");\r
+ featureSettings.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ featureSettings_actionPerformed(e);\r
+ }\r
+ });\r
+ seqDBRef.setState( jalview.bin.Cache.getDefault("SHOW_DBPREFIX",true));\r
+ seqDBRef.setText("Show Full Sequence Id");\r
+ seqDBRef.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ seqDBRef_actionPerformed(e);\r
+ }\r
+ });\r
+ fetchSequence.setText("Fetch Sequence...");\r
+ fetchSequence.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ fetchSequence_actionPerformed(e);\r
}\r
});\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(viewMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(alignMenu);\r
+ alignFrameMenuBar.add(webService);\r
+ fileMenu.add(fetchSequence);\r
+ fileMenu.add(vamsasStore);\r
fileMenu.add(saveAlignmentMenu);\r
+ fileMenu.add(jMenu2);\r
fileMenu.add(outputTextboxMenu);\r
- fileMenu.add(htmlMenuItem);\r
- fileMenu.add(epsFile);\r
- fileMenu.add(createPNG);\r
fileMenu.add(printMenuItem);\r
fileMenu.addSeparator();\r
+ fileMenu.add(LoadtreeMenuItem);\r
+ fileMenu.addSeparator();\r
fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
editMenu.add(copy);\r
editMenu.add(jMenu1);\r
- editMenu.add(cut);\r
editMenu.add(delete);\r
editMenu.addSeparator();\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(deselectAllSequenceMenuItem);\r
editMenu.add(selectAllSequenceMenuItem);\r
+ editMenu.add(deselectAllSequenceMenuItem);\r
editMenu.add(invertSequenceMenuItem);\r
editMenu.add(deleteGroups);\r
- editMenu.add(groupsMenuItem);\r
editMenu.addSeparator();\r
- editMenu.add(deselectAllColumnsMenuItem);\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(remove2RightMenuItem);\r
- editMenu.addSeparator();\r
editMenu.add(removeGappedColumnMenuItem);\r
editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(setGapCharMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ editMenu.addSeparator();\r
+ editMenu.add(padGapsMenuitem);\r
searchMenu.add(findMenuItem);\r
viewMenu.add(font);\r
- viewMenu.add(fullSeqId);\r
+ viewMenu.addSeparator();\r
viewMenu.add(wrapMenuItem);\r
+ viewMenu.add(seqDBRef);\r
+ viewMenu.add(seqLimits);\r
+ viewMenu.add(scaleAbove);\r
+ viewMenu.add(scaleLeft);\r
+ viewMenu.add(scaleRight);\r
viewMenu.add(viewBoxesMenuItem);\r
viewMenu.add(viewTextMenuItem);\r
viewMenu.add(colourTextMenuItem);\r
viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(consensusGraphMenuItem);\r
- viewMenu.add(overviewMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
colourMenu.add(zappoColour);\r
colourMenu.add(taylorColour);\r
colourMenu.add(hydrophobicityColour);\r
colourMenu.add(buriedColour);\r
colourMenu.add(nucleotideColour);\r
colourMenu.add(userDefinedColour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(BLOSUM62Colour);\r
colourMenu.addSeparator();\r
- colourMenu.add(abovePIDThreshold);\r
colourMenu.add(conservationMenuItem);\r
- calculateMenu.add(sortPairwiseMenuItem);\r
- calculateMenu.add(sortIDMenuItem);\r
- calculateMenu.add(sortGroupMenuItem);\r
- calculateMenu.add(sortTreeOrderMenuItem);\r
- calculateMenu.add(removeRedundancyMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
calculateMenu.addSeparator();\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
calculateMenu.add(PCAMenuItem);\r
calculateMenu.addSeparator();\r
- calculateMenu.add(averageDistanceTreeMenuItem);\r
- calculateMenu.add(neighbourTreeMenuItem);\r
- calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
- calculateMenu.add(njTreeBlosumMenuItem);\r
- alignMenu.add(clustalAlignMenuItem);\r
+ calculateMenu.add(showTranslation);\r
+ webServiceNoServices=new JMenuItem("<No Services>");\r
+ webService.add(webServiceNoServices);\r
this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
jMenu1.add(pasteNew);\r
jMenu1.add(pasteThis);\r
- }\r
-\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
- {\r
-\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ jMenu2.add(htmlMenuItem);\r
+ jMenu2.add(epsFile);\r
+ jMenu2.add(createPNG);\r
}\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
-\r
-\r
-\r
protected void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void undoMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
- protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
- }\r
-\r
-\r
- protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
}\r
\r
protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
- }\r
-\r
- protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
}\r
\r
-\r
-\r
-\r
-\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
-\r
- protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
- }\r
-\r
- protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
}\r
\r
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
-\r
protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
-\r
-\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void zappoColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void taylorColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void helixColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void strandColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void turnColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void buriedColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
-\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void PIDColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ protected void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
+ public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ }\r
\r
- protected void printMenuItem_actionPerformed(ActionEvent e)\r
+ protected void nucleotideColour_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ protected void copy_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void findMenuItem_actionPerformed(ActionEvent e)\r
+ protected void delete_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
+ public void createPNG(java.io.File f)\r
+ {\r
}\r
\r
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
+ protected void font_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void nucleotideColour_actionPerformed(ActionEvent e)\r
+ public void seqDBRef_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
+\r
+ public void createEPS(java.io.File f)\r
{\r
+ }\r
\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void copy_actionPerformed(ActionEvent e)\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void cut_actionPerformed(ActionEvent e)\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void delete_actionPerformed(ActionEvent e)\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void preferences_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+ {\r
}\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
+ protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ protected void ClustalRealign_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void font_actionPerformed(ActionEvent e)\r
+ public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ public void tabSelected()\r
{\r
\r
}\r
\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
+ {\r
\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff