-/********************\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 colourMenu = new JMenu();\r
protected JMenu calculateMenu = new JMenu();\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 remove2RightMenuItem = new JMenuItem();\r
protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
protected JMenuItem removeAllGapsMenuItem = 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 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 annotationPanelMenuItem = 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 fullSeqId = new JCheckBoxMenuItem();\r
JMenuItem epsFile = new JMenuItem();\r
JMenuItem LoadtreeMenuItem = new JMenuItem();\r
- JMenuItem jpred = new JMenuItem();\r
- protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
- protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
- JMenuItem modifyPID = new JMenuItem();\r
- JMenuItem modifyConservation = 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
- JMenu jMenu2 = new JMenu();\r
- JMenu sort = new JMenu();\r
+ protected JMenu sort = new JMenu();\r
JMenu calculate = new JMenu();\r
- JMenuItem msaAlignMenuItem = new JMenuItem();\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
+ protected JMenuItem featureSettings = 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");\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
webService.setText("Web Service");\r
selectAllSequenceMenuItem.setText("Select all");\r
selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\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
});\r
deselectAllSequenceMenuItem.setText("Deselect All");\r
deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
- getKeyStroke(java.awt.event.\r
- KeyEvent.VK_ESCAPE, 0, false));\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\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
}\r
});\r
removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
viewTextMenuItem_actionPerformed(e);\r
}\r
});\r
- sortPairwiseMenuItem.setText("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("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("Group");\r
+ sortGroupMenuItem.setText("by Group");\r
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
removeRedundancyMenuItem.setText("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
}\r
});\r
pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\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 Using % Identity...");\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 Using % Identity...");\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 to Textbox");\r
- clustalColour.setSelected(false);\r
clustalColour.setText("Clustalx");\r
+\r
clustalColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
BLOSUM62Colour_actionPerformed(e);\r
}\r
});\r
- avDistanceTreeBlosumMenuItem.setText("Average Distance 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 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
});\r
annotationPanelMenuItem.setActionCommand("");\r
annotationPanelMenuItem.setText("Show Annotations");\r
- annotationPanelMenuItem.setState(true);\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
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(java.awt.\r
- event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\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
}\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
}\r
});\r
findMenuItem.setText("Find...");\r
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
- event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\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 Identity 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
nucleotideColour_actionPerformed(e);\r
}\r
});\r
- deleteGroups.setSelected(false);\r
deleteGroups.setText("Undefine groups");\r
deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
});\r
copy.setText("Copy");\r
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
- KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\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(java.awt.event.\r
- KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
- KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\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
{\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.setActionCommand("Save As PNG Image");\r
createPNG.setText("PNG");\r
font.setText("Font...");\r
font.addActionListener(new java.awt.event.ActionListener()\r
}\r
});\r
fullSeqId.setText("Show Full Sequence ID");\r
+ fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true));\r
fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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
- public void actionPerformed(ActionEvent e)\r
- {\r
- LoadtreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- jpred.setText("JPred...");\r
- jpred.addActionListener(new java.awt.event.ActionListener()\r
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- jpred_actionPerformed(e);\r
+ LoadtreeMenuItem_actionPerformed(e);\r
}\r
});\r
scaleAbove.setVisible(false);\r
modifyConservation_actionPerformed(e);\r
}\r
});\r
- sortByTreeMenu.setText("Tree Order");\r
- jMenu2.setText("Save as");\r
+ sortByTreeMenu.setText("By Tree Order");\r
sort.setText("Sort");\r
calculate.setText("Calculate Tree");\r
- msaAlignMenuItem.setText("Muscle Alignment...");\r
- msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- msaAlignMenuItem_actionPerformed(e);\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
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(viewMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(webService);\r
+ fileMenu.add(vamsasStore);\r
fileMenu.add(saveAlignmentMenu);\r
fileMenu.add(jMenu2);\r
fileMenu.add(outputTextboxMenu);\r
editMenu.add(copy);\r
editMenu.add(jMenu1);\r
editMenu.add(delete);\r
+ editMenu.addSeparator();\r
editMenu.add(selectAllSequenceMenuItem);\r
editMenu.add(deselectAllSequenceMenuItem);\r
editMenu.add(invertSequenceMenuItem);\r
editMenu.add(removeGappedColumnMenuItem);\r
editMenu.add(removeAllGapsMenuItem);\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(fullSeqId);\r
viewMenu.add(scaleAbove);\r
viewMenu.add(scaleLeft);\r
viewMenu.add(scaleRight);\r
- viewMenu.addSeparator();\r
viewMenu.add(viewBoxesMenuItem);\r
viewMenu.add(viewTextMenuItem);\r
viewMenu.add(colourTextMenuItem);\r
viewMenu.add(renderGapsMenuItem);\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.add(noColourmenuItem);\r
colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
colourMenu.add(PIDColour);\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
calculateMenu.add(PCAMenuItem);\r
calculateMenu.addSeparator();\r
- calculateMenu.add(webService);\r
- webService.add(clustalAlignMenuItem);\r
- webService.add(jpred);\r
- webService.add(msaAlignMenuItem);\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
- jMenu2.add(htmlMenuItem);\r
- jMenu2.add(epsFile);\r
- jMenu2.add(createPNG);\r
sort.add(sortIDMenuItem);\r
sort.add(sortGroupMenuItem);\r
- sort.add(sortByTreeMenu);\r
sort.add(sortPairwiseMenuItem);\r
calculate.add(averageDistanceTreeMenuItem);\r
calculate.add(neighbourTreeMenuItem);\r
calculate.add(avDistanceTreeBlosumMenuItem);\r
calculate.add(njTreeBlosumMenuItem);\r
- }\r
-\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
- {\r
-\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
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 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
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
-\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
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
-\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
\r
-\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
protected void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
-\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
{\r
-\r
}\r
\r
protected void nucleotideColour_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
- protected void copy_actionPerformed(ActionEvent e)\r
+ protected void copy_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
-\r
protected void cut_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void delete_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void pasteNew_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void pasteThis_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
+ public void createPNG(java.io.File f)\r
{\r
-\r
}\r
\r
protected void font_actionPerformed(ActionEvent e)\r
{\r
-\r
}\r
\r
protected void fullSeqId_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ public void createEPS(java.io.File f)\r
+ {\r
}\r
\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ }\r
\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
}\r
\r
- protected void jpred_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 scaleAbove_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 scaleLeft_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 scaleRight_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 modifyPID_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 modifyConservation_actionPerformed(ActionEvent e)\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void preferences_actionPerformed(ActionEvent e)\r
+ public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ public void tabSelected()\r
+ {\r
\r
}\r
\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff