- public void actionPerformed(ActionEvent e)
- {
- outputText_actionPerformed(e);
- }
- });
-
- outputTextboxMenu.add(item);
- }
- closeMenuItem.addActionListener(this);
- loadApplication.addActionListener(this);
-
- loadTree.addActionListener(this);
- selectAllSequenceMenuItem.addActionListener(this);
- deselectAllSequenceMenuItem.addActionListener(this);
- invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel("Remove Left");
- remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
- remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
- removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
- removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
- sortIDMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel("by Group");
- sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");
- removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
- pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel("Principal Component Analysis");
- PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem.setLabel(
- "Average Distance Using % Identity");
- averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
- neighbourTreeMenuItem.addActionListener(this);
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setBackground(Color.white);
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText("Status bar");
- outputTextboxMenu.setLabel("Output to Textbox");
- clustalColour.setLabel("Clustalx");
-
- clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
- zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
- taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
- hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
- helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
- strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
- turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
- buriedColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
- userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62 Score");
- BLOSUM62Colour.addActionListener(this);
- avDistanceTreeBlosumMenuItem.setLabel(
- "Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
- njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel("Show Annotations");
- annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel("Colour Text");
- colourTextMenuItem.addItemListener(this);
- overviewMenuItem.setLabel("Overview Window");
- overviewMenuItem.addActionListener(this);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
- conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("None");
- noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel("Wrap");
- wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("Find...");
- findMenuItem.addActionListener(this);
- searchMenu.setLabel("Search");
-
- abovePIDThreshold.setLabel("Above Identity Threshold");
- abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
- nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
- deleteGroups.addActionListener(this);
- copy.setLabel("Copy");
- copy.addActionListener(this);
- cut.setLabel("Cut");
- cut.addActionListener(this);
- delete.setLabel("Delete");
- delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
- pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
- pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
- font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
- scaleAbove.setState(true);
- scaleAbove.setEnabled(false);
- scaleAbove.addItemListener(this);
- scaleLeft.setEnabled(false);
- scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
- scaleLeft.addItemListener(this);
- scaleRight.setEnabled(false);
- scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
- scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
- modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
- modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
- autoCalculate.addItemListener(this);
- inputText.setLabel("Input from textbox");
- inputText.addActionListener(this);
-
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
- documentation.addActionListener(this);
-
- about.setLabel("About...");
- about.addActionListener(this);
- seqLimits.setState(true);
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputTextboxMenu.add(item);
+ }
+ closeMenuItem.addActionListener(this);
+ loadApplication.addActionListener(this);
+
+ loadTree.addActionListener(this);
+ loadAnnotations.addActionListener(this);
+ outputFeatures.addActionListener(this);
+ outputAnnotations.addActionListener(this);
+ selectAllSequenceMenuItem.addActionListener(this);
+ deselectAllSequenceMenuItem.addActionListener(this);
+ invertSequenceMenuItem.addActionListener(this);
+ remove2LeftMenuItem.setLabel("Remove Left");
+ remove2LeftMenuItem.addActionListener(this);
+ remove2RightMenuItem.setLabel("Remove Right");
+ remove2RightMenuItem.addActionListener(this);
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
+ removeGappedColumnMenuItem.addActionListener(this);
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");
+ removeAllGapsMenuItem.addActionListener(this);
+ viewBoxesMenuItem.setLabel("Boxes");
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addItemListener(this);
+ viewTextMenuItem.setLabel("Text");
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addItemListener(this);
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");
+ sortPairwiseMenuItem.addActionListener(this);
+ sortIDMenuItem.setLabel("by ID");
+ sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel("by Length");
+ sortLengthMenuItem.addActionListener(this);
+ sortGroupMenuItem.setLabel("by Group");
+ sortGroupMenuItem.addActionListener(this);
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");
+ removeRedundancyMenuItem.addActionListener(this);
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
+ pairwiseAlignmentMenuItem.addActionListener(this);
+ PCAMenuItem.setLabel("Principal Component Analysis");
+ PCAMenuItem.addActionListener(this);
+ averageDistanceTreeMenuItem
+ .setLabel("Average Distance Using % Identity");
+ averageDistanceTreeMenuItem.addActionListener(this);
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
+ neighbourTreeMenuItem.addActionListener(this);
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setText("Status bar");
+ outputTextboxMenu.setLabel("Output to Textbox");
+ clustalColour.setLabel("Clustalx");
+
+ clustalColour.addActionListener(this);
+ zappoColour.setLabel("Zappo");
+ zappoColour.addActionListener(this);
+ taylorColour.setLabel("Taylor");
+ taylorColour.addActionListener(this);
+ hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.addActionListener(this);
+ helixColour.setLabel("Helix Propensity");
+ helixColour.addActionListener(this);
+ strandColour.setLabel("Strand Propensity");
+ strandColour.addActionListener(this);
+ turnColour.setLabel("Turn Propensity");
+ turnColour.addActionListener(this);
+ buriedColour.setLabel("Buried Index");
+ buriedColour.addActionListener(this);
+ userDefinedColour.setLabel("User Defined...");
+ userDefinedColour.addActionListener(this);
+ PIDColour.setLabel("Percentage Identity");
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");
+ BLOSUM62Colour.addActionListener(this);
+ avDistanceTreeBlosumMenuItem
+ .setLabel("Average Distance Using BLOSUM62");
+ avDistanceTreeBlosumMenuItem.addActionListener(this);
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
+ njTreeBlosumMenuItem.addActionListener(this);
+ annotationPanelMenuItem.setLabel("Show Annotations");
+ annotationPanelMenuItem.addItemListener(this);
+ colourTextMenuItem.setLabel("Colour Text");
+ colourTextMenuItem.addItemListener(this);
+ displayNonconservedMenuItem.setLabel("Show nonconserved");
+ displayNonconservedMenuItem.addItemListener(this);
+ alProperties.addActionListener(this);
+ overviewMenuItem.setLabel("Overview Window");
+ overviewMenuItem.addActionListener(this);
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setLabel("Undo");
+ undoMenuItem.addActionListener(this);
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setLabel("Redo");
+ redoMenuItem.addActionListener(this);
+ conservationMenuItem.setLabel("by Conservation");
+ conservationMenuItem.addItemListener(this);
+ noColourmenuItem.setLabel("None");
+ noColourmenuItem.addActionListener(this);
+ wrapMenuItem.setLabel("Wrap");
+ wrapMenuItem.addItemListener(this);
+ renderGapsMenuItem.setLabel("Show Gaps");
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addItemListener(this);
+ findMenuItem.setLabel("Find...");
+ findMenuItem.addActionListener(this);
+ abovePIDThreshold.setLabel("Above Identity Threshold");
+ abovePIDThreshold.addItemListener(this);
+ nucleotideColour.setLabel("Nucleotide");
+ nucleotideColour.addActionListener(this);
+ deleteGroups.setLabel("Undefine Groups");
+ deleteGroups.addActionListener(this);
+ grpsFromSelection.setLabel("Make Groups for selection");
+ grpsFromSelection.addActionListener(this);
+ copy.setLabel("Copy");
+ copy.addActionListener(this);
+ cut.setLabel("Cut");
+ cut.addActionListener(this);
+ delete.setLabel("Delete");
+ delete.addActionListener(this);
+ pasteMenu.setLabel("Paste");
+ pasteNew.setLabel("To New Alignment");
+ pasteNew.addActionListener(this);
+ pasteThis.setLabel("Add To This Alignment");
+ pasteThis.addActionListener(this);
+ applyToAllGroups.setLabel("Apply Colour To All Groups");
+ applyToAllGroups.setState(true);
+ applyToAllGroups.addItemListener(this);
+ font.setLabel("Font...");
+ font.addActionListener(this);
+ scaleAbove.setLabel("Scale Above");
+ scaleAbove.setState(true);
+ scaleAbove.setEnabled(false);
+ scaleAbove.addItemListener(this);
+ scaleLeft.setEnabled(false);
+ scaleLeft.setState(true);
+ scaleLeft.setLabel("Scale Left");
+ scaleLeft.addItemListener(this);
+ scaleRight.setEnabled(false);
+ scaleRight.setState(true);
+ scaleRight.setLabel("Scale Right");
+ scaleRight.addItemListener(this);
+ modifyPID.setLabel("Modify Identity Threshold...");
+ modifyPID.addActionListener(this);
+ modifyConservation.setLabel("Modify Conservation Threshold...");
+ modifyConservation.addActionListener(this);
+ sortByTreeMenu.setLabel("By Tree Order");
+ sort.setLabel("Sort");
+ calculate.setLabel("Calculate Tree");
+ autoCalculate.addItemListener(this);
+ inputText.setLabel("Input from textbox");
+ inputText.addActionListener(this);
+ centreColumnLabelFlag.setLabel("Centre column labels");
+ centreColumnLabelFlag.addItemListener(this);
+ followMouseOverFlag.setLabel("Automatic Scrolling");
+ followMouseOverFlag.addItemListener(this);
+ helpMenu.setLabel("Help");
+ documentation.setLabel("Documentation");
+ documentation.addActionListener(this);
+
+ about.setLabel("About...");
+ about.addActionListener(this);
+ seqLimits.setState(true);