- sf = new SequenceFeature(type, desc, "", start, end);\r
- sf.setFeatureGroup(featureGroup);\r
+ sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
PIDColour_actionPerformed();\r
else if(evt.getSource()==BLOSUM62Colour)\r
BLOSUM62Colour_actionPerformed();\r
PIDColour_actionPerformed();\r
else if(evt.getSource()==BLOSUM62Colour)\r
BLOSUM62Colour_actionPerformed();\r
else if(evt.getSource()==sortPairwiseMenuItem)\r
sortPairwiseMenuItem_actionPerformed();\r
else if(evt.getSource()==sortIDMenuItem)\r
else if(evt.getSource()==sortPairwiseMenuItem)\r
sortPairwiseMenuItem_actionPerformed();\r
else if(evt.getSource()==sortIDMenuItem)\r
protected Menu colourMenu = new Menu("Colour");\r
protected Menu calculateMenu = new Menu("Calculate");\r
protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
protected Menu colourMenu = new Menu("Colour");\r
protected Menu calculateMenu = new Menu("Calculate");\r
protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
- protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem invertSequenceMenuItem = new MenuItem();\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
protected MenuItem remove2LeftMenuItem = new MenuItem();\r
protected MenuItem remove2RightMenuItem = new MenuItem();\r
protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
protected MenuItem remove2LeftMenuItem = new MenuItem();\r
protected MenuItem remove2RightMenuItem = new MenuItem();\r
protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
invertSequenceMenuItem.addActionListener(this);\r
remove2LeftMenuItem.setLabel("Remove Left");\r
remove2LeftMenuItem.addActionListener(this);\r
invertSequenceMenuItem.addActionListener(this);\r
remove2LeftMenuItem.setLabel("Remove Left");\r
remove2LeftMenuItem.addActionListener(this);\r
sequenceFeatures.setLabel("Sequence Features");\r
sequenceFeatures.addItemListener(this);\r
sequenceFeatures.setState(false);\r
sequenceFeatures.setLabel("Sequence Features");\r
sequenceFeatures.addItemListener(this);\r
sequenceFeatures.setState(false);\r
colourMenu.add(modifyConservation);\r
colourMenu.add(abovePIDThreshold);\r
colourMenu.add(modifyPID);\r
colourMenu.add(modifyConservation);\r
colourMenu.add(abovePIDThreshold);\r
colourMenu.add(modifyPID);\r
calculateMenu.add(calculate);\r
calculateMenu.addSeparator();\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
calculateMenu.add(calculate);\r
calculateMenu.addSeparator();\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
viewPopup, colourPopup, calculatePopup, helpPopup;\r
MenuItem featureSettings = new MenuItem();\r
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
viewPopup, colourPopup, calculatePopup, helpPopup;\r
MenuItem featureSettings = new MenuItem();\r
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r