import java.awt.event.*;\r
import java.awt.*;\r
\r
+import jalview.gui.Preferences;\r
+import jalview.schemes.ColourSchemeProperty;\r
+\r
public class GAlignFrame extends JInternalFrame\r
{\r
protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
protected JMenu fileMenu = new JMenu();\r
protected JMenuItem closeMenuItem = new JMenuItem();\r
protected JMenu editMenu = new JMenu();\r
- protected JMenu fontMenu = 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 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 JMenuItem fontNameMenuItem = new JMenuItem();\r
- protected JMenuItem fontSizeMenuItem = new JMenuItem();\r
- protected JMenuItem fontStyleMenuItem = new JMenuItem();\r
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
protected 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 JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
- protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
+ protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
JMenuItem htmlMenuItem = new JMenuItem();\r
JMenuItem overviewMenuItem = new JMenuItem();\r
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem pdbTest = new JMenuItem();\r
JMenuItem printMenuItem = new JMenuItem();\r
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
JMenuItem findMenuItem = new JMenuItem();\r
protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
JMenuItem deleteGroups = new JMenuItem();\r
+ JMenuItem delete = new JMenuItem();\r
+ JMenuItem copy = new JMenuItem();\r
+ JMenuItem cut = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
+ JMenuItem pasteNew = new JMenuItem();\r
+ JMenuItem pasteThis = new JMenuItem();\r
+ protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
+ JMenuItem createPNG = new JMenuItem();\r
+ protected JMenuItem font = new JMenuItem();\r
+ protected 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
+ protected JMenu sortByTreeMenu = new JMenu();\r
+ JMenu jMenu2 = new JMenu();\r
+ JMenu sort = new JMenu();\r
+ JMenu calculate = new JMenu();\r
+ JMenuItem msaAlignMenuItem = new JMenuItem();\r
public GAlignFrame()\r
{\r
+ ButtonGroup colours = new ButtonGroup();\r
+ colours.add(noColourmenuItem);\r
+ colours.add(clustalColour);\r
+ colours.add(zappoColour);\r
+ colours.add(taylorColour);\r
+ colours.add(hydrophobicityColour);\r
+ colours.add(helixColour);\r
+ colours.add(strandColour);\r
+ colours.add(turnColour);\r
+ colours.add(buriedColour);\r
+ colours.add(userDefinedColour);\r
+ colours.add(PIDColour);\r
+ colours.add(BLOSUM62Colour);\r
+ colours.add(nucleotideColour);\r
+\r
+ noColourmenuItem.setSelected(true);\r
+ String defaultColour = Preferences.defaultColour;\r
+ if(defaultColour!=null)\r
+ {\r
+ int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
+ switch(index)\r
+ {\r
+ case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;\r
+ case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;\r
+ case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;\r
+ case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;\r
+ case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;\r
+ case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;\r
+ case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;\r
+ case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;\r
+ case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;\r
+ case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;\r
+ case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;\r
+ }\r
+ }\r
\r
\r
try\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
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
+ item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
saveAlignmentMenu.add( item );\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
});\r
\r
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
+ item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
e.printStackTrace();\r
}\r
\r
- ButtonGroup colours = new ButtonGroup();\r
- colours.add(noColourmenuItem);\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- colours.add(strandColour);\r
- colours.add(turnColour);\r
- colours.add(buriedColour);\r
- colours.add(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
- colours.add(nucleotideColour);\r
}\r
private void jbInit() 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");\r
closeMenuItem.setMnemonic('C');\r
closeMenuItem.setText("Close");\r
closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
}\r
});\r
editMenu.setText("Edit");\r
- fontMenu.setText("Font");\r
viewMenu.setText("View");\r
colourMenu.setText("Colour");\r
calculateMenu.setText("Calculate");\r
- alignMenu.setText("Web Service");\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.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
{\r
public void actionPerformed(ActionEvent e)\r
selectAllSequenceMenuItem_actionPerformed(e);\r
}\r
});\r
- deselectAllSequenceMenuItem.setText("Clear selection");\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
{\r
public void actionPerformed(ActionEvent e)\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.setText("Remove Empty Columns");\r
removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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
- fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fontNameMenuItem_actionPerformed(e);\r
- }\r
- });\r
- fontSizeMenuItem.setText("10");\r
- fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fontSizeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- fontStyleMenuItem.setText("Plain");\r
- fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- fontStyleMenuItem_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("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("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("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.setText("Remove Redundancy...");\r
removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
removeRedundancyMenuItem_actionPerformed(e);\r
}\r
});\r
- pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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.setText("Average Distance Using % Identity...");\r
averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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.setText("Clustal Alignment...");\r
clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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.setText("Average Distance using BLOSUM62...");\r
avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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.gui.Preferences.showAnnotation );\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(java.awt.\r
+ event.KeyEvent.VK_Z, 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
wrapMenuItem_actionPerformed(e);\r
}\r
});\r
- pdbTest.setText("PDB Test Viewer");\r
- pdbTest.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbTest_actionPerformed(e);\r
- }\r
- });\r
printMenuItem.setText("Print");\r
printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\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(java.awt.\r
+ event.KeyEvent.VK_F, 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.setText("Above Identity threshold");\r
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
public void actionPerformed(ActionEvent e) {\r
abovePIDThreshold_actionPerformed(e);\r
}\r
});\r
- sequenceFeatures.setSelected(true);\r
sequenceFeatures.setText("Sequence Features");\r
sequenceFeatures.addActionListener(new ActionListener()\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
deleteGroups_actionPerformed(e);\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.setMnemonic(KeyEvent.VK_C);\r
+\r
+ copy.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(e);\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.setMnemonic(KeyEvent.VK_X);\r
+ cut.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setText("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ delete_actionPerformed(e);\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.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setText("add to this alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setText("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ applyToAllGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ createPNG.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ createPNG_actionPerformed(e);\r
+ }\r
+ });\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
+ {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+ fullSeqId.setText("Show Full Sequence ID");\r
+ fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ fullSeqId_actionPerformed(e);\r
+ }\r
+ });\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
+ }\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
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ jpred_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("Tree Order");\r
+ jMenu2.setText("Save as");\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
+ });\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(fontMenu);\r
alignFrameMenuBar.add(viewMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(alignMenu);\r
fileMenu.add(saveAlignmentMenu);\r
+ fileMenu.add(jMenu2);\r
fileMenu.add(outputTextboxMenu);\r
- fileMenu.add(htmlMenuItem);\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.addSeparator();\r
- editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(jMenu1);\r
+ editMenu.add(delete);\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
searchMenu.add(findMenuItem);\r
- fontMenu.add(fontNameMenuItem);\r
- fontMenu.add(fontSizeMenuItem);\r
- fontMenu.add(fontStyleMenuItem);\r
+ viewMenu.add(font);\r
+ viewMenu.add(fullSeqId);\r
+ viewMenu.addSeparator();\r
viewMenu.add(wrapMenuItem);\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(consensusGraphMenuItem);\r
- viewMenu.add(overviewMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
viewMenu.add(sequenceFeatures);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
colourMenu.add(noColourmenuItem);\r
+ colourMenu.addSeparator();\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
- alignMenu.add(pdbTest);\r
+ calculateMenu.add(webService);\r
+ webService.add(clustalAlignMenuItem);\r
+ webService.add(jpred);\r
+ webService.add(msaAlignMenuItem);\r
this.getContentPane().add(statusBar, BorderLayout.SOUTH);\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
\r
-\r
-\r
-\r
protected void closeMenuItem_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
\r
-\r
- protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
\r
}\r
\r
- protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
\r
protected void wrapMenuItem_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
}\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 pdbTest_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
\r
protected void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
}\r
\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
+ {\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
+\r
+ protected void epsFile_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+\r
+ }\r
+\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void preferences_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff