X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbappletgui%2FGAlignFrame.java;h=7775b65cac77cb6441adc13ee9e04e27344d485e;hb=a3601f26e2c2be8af72dcfb23d8f2d9bebd89d0a;hp=4c95334b48d1617ae98b84cfe1bd672262da0843;hpb=b92b967816da8ca0252b221589988f9c2d83ca46;p=jalview.git diff --git a/src/jalview/jbappletgui/GAlignFrame.java b/src/jalview/jbappletgui/GAlignFrame.java index 4c95334..7775b65 100755 --- a/src/jalview/jbappletgui/GAlignFrame.java +++ b/src/jalview/jbappletgui/GAlignFrame.java @@ -1,1114 +1,831 @@ -/******************** - * 2004 Jalview Reengineered - * Barton Group - * Dundee University - * - * AM Waterhouse - *******************/ - +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program is free software; you can redistribute it and/or +* modify it under the terms of the GNU General Public License +* as published by the Free Software Foundation; either version 2 +* of the License, or (at your option) any later version. +* +* This program is distributed in the hope that it will be useful, +* but WITHOUT ANY WARRANTY; without even the implied warranty of +* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +* GNU General Public License for more details. +* +* You should have received a copy of the GNU General Public License +* along with this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.jbappletgui; -import java.awt.event.*; import java.awt.*; - -public class GAlignFrame extends Frame -{ - protected MenuBar alignFrameMenuBar = new MenuBar(); - protected Menu fileMenu = new Menu(); - protected MenuItem closeMenuItem = new MenuItem(); - protected Menu editMenu = new Menu(); - protected Menu viewMenu = new Menu(); - protected Menu colourMenu = new Menu(); - protected Menu calculateMenu = new Menu(); - protected MenuItem selectAllSequenceMenuItem = new MenuItem(); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem(); - protected MenuItem invertSequenceMenuItem = new MenuItem(); - protected MenuItem remove2LeftMenuItem = new MenuItem(); - protected MenuItem remove2RightMenuItem = new MenuItem(); - protected MenuItem removeGappedColumnMenuItem = new MenuItem(); - protected MenuItem removeAllGapsMenuItem = new MenuItem(); - protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - protected MenuItem sortPairwiseMenuItem = new MenuItem(); - protected MenuItem sortIDMenuItem = new MenuItem(); - protected MenuItem sortGroupMenuItem = new MenuItem(); - protected MenuItem removeRedundancyMenuItem = new MenuItem(); - protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - protected MenuItem PCAMenuItem = new MenuItem(); - protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); - protected MenuItem neighbourTreeMenuItem = new MenuItem(); - BorderLayout borderLayout1 = new BorderLayout(); - public Label statusBar = new Label(); - protected Menu outputTextboxMenu = new Menu(); - protected MenuItem clustalColour = new MenuItem(); - protected MenuItem zappoColour = new MenuItem(); - protected MenuItem taylorColour = new MenuItem(); - protected MenuItem hydrophobicityColour = new MenuItem(); - protected MenuItem helixColour = new MenuItem(); - protected MenuItem strandColour = new MenuItem(); - protected MenuItem turnColour = new MenuItem(); - protected MenuItem buriedColour = new MenuItem(); - protected MenuItem userDefinedColour = new MenuItem(); - protected MenuItem PIDColour = new MenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); - MenuItem njTreeBlosumMenuItem = new MenuItem(); - MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - MenuItem overviewMenuItem = new MenuItem(); - protected MenuItem undoMenuItem = new MenuItem(); - protected MenuItem redoMenuItem = new MenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); - protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); - MenuItem findMenuItem = new MenuItem(); - Menu searchMenu = new Menu(); - protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - protected MenuItem nucleotideColour = new MenuItem(); - MenuItem deleteGroups = new MenuItem(); - MenuItem delete = new MenuItem(); - MenuItem copy = new MenuItem(); - MenuItem cut = new MenuItem(); - Menu Menu1 = new Menu(); - MenuItem pasteNew = new MenuItem(); - MenuItem pasteThis = new MenuItem(); - protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - protected MenuItem font = new MenuItem(); - protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); - MenuItem modifyPID = new MenuItem(); - MenuItem modifyConservation = new MenuItem(); - protected Menu sortByTreeMenu = new Menu(); - Menu sort = new Menu(); - Menu calculate = new Menu(); - MenuItem inputText = new MenuItem(); - Menu helpMenu = new Menu(); - MenuItem documentation = new MenuItem(); - MenuItem about = new MenuItem(); - public GAlignFrame() - { - try - { - jbInit(); - setMenuBar(alignFrameMenuBar); - - MenuItem item; - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) { - item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i)); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - saveAs_actionPerformed(e); - } - }); - - item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i)); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - outputText_actionPerformed(e); - } - }); - - outputTextboxMenu.add( item ); - } - - } - catch(Exception e) - { - e.printStackTrace(); - } - - } - private void jbInit() throws Exception - { - fileMenu.setLabel("File"); - closeMenuItem.setLabel("Close"); - closeMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - closeMenuItem_actionPerformed(e); - } - }); - editMenu.setLabel("Edit"); - viewMenu.setLabel("View"); - colourMenu.setLabel("Colour"); - calculateMenu.setLabel("Calculate"); - selectAllSequenceMenuItem.setLabel("Select all"); - selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - selectAllSequenceMenuItem_actionPerformed(e); - } - }); - deselectAllSequenceMenuItem.setLabel("Deselect All"); - deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deselectAllSequenceMenuItem_actionPerformed(e); - } - }); - invertSequenceMenuItem.setLabel("Invert Selection"); - invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - invertSequenceMenuItem_actionPerformed(e); - } - }); - remove2LeftMenuItem.setLabel("Remove Left"); - remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - remove2LeftMenuItem_actionPerformed(e); - } - }); - remove2RightMenuItem.setLabel("Remove Right"); - remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - remove2RightMenuItem_actionPerformed(e); - } - }); - removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - removeGappedColumnMenuItem_actionPerformed(e); - } - }); - removeAllGapsMenuItem.setLabel("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - removeAllGapsMenuItem_actionPerformed(e); - } - }); - viewBoxesMenuItem.setLabel("Boxes"); - viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - viewBoxesMenuItem_actionPerformed(null); - } - }); - viewTextMenuItem.setLabel("Text"); - viewTextMenuItem.setState(true); - viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - viewTextMenuItem_actionPerformed(null); - } - }); - sortPairwiseMenuItem.setLabel("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortPairwiseMenuItem_actionPerformed(e); - } - }); - sortIDMenuItem.setLabel("by ID"); - sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortIDMenuItem_actionPerformed(e); - } - }); - sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortGroupMenuItem_actionPerformed(e); - } - }); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - removeRedundancyMenuItem_actionPerformed(e); - } - }); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pairwiseAlignmentMenuItem_actionPerformed(e); - } - }); - PCAMenuItem.setLabel("Principal Component Analysis..."); - PCAMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - PCAMenuItem_actionPerformed(e); - } - }); - averageDistanceTreeMenuItem.setLabel("Average Distance Using % Identity..."); - averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - averageDistanceTreeMenuItem_actionPerformed(e); - } - }); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity..."); - neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - neighbourTreeMenuItem_actionPerformed(e); - } - }); - 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(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); - zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(e); - } - }); - taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(e); - } - }); - hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); - helixColour.setLabel("Helix Propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(e); - } - }); - strandColour.setLabel("Strand Propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(e); - } - }); - turnColour.setLabel("Turn Propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(e); - } - }); - buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(e); - } - }); - userDefinedColour.setLabel("User Defined..."); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); - PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(e); - } - }); - BLOSUM62Colour.setLabel("BLOSUM62 Score"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(e); - } - }); - avDistanceTreeBlosumMenuItem.setLabel("Average Distance using BLOSUM62..."); - avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - avTreeBlosumMenuItem_actionPerformed(e); - } - }); - njTreeBlosumMenuItem.setLabel("Neighbour Joining using BLOSUM62..."); - njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - njTreeBlosumMenuItem_actionPerformed(e); - } - }); - annotationPanelMenuItem.setActionCommand(""); - annotationPanelMenuItem.setState(true); - annotationPanelMenuItem.setLabel("Show Annotations"); - annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - annotationPanelMenuItem_actionPerformed(null); - } - }); - colourTextMenuItem.setLabel("Colour Text"); - colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - colourTextMenuItem_actionPerformed(null); - } - }); - overviewMenuItem.setLabel("Overview Window..."); - overviewMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - overviewMenuItem_actionPerformed(e); - } - }); - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - undoMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - undoMenuItem_actionPerformed(e); - } - }); - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - redoMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - redoMenuItem_actionPerformed(e); - } - }); - conservationMenuItem.setLabel("by Conservation"); - conservationMenuItem.addItemListener(new java.awt.event.ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - conservationMenuItem_actionPerformed(null); - } - }); - noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); - wrapMenuItem.setLabel("Wrap"); - wrapMenuItem.addItemListener(new java.awt.event.ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - wrapMenuItem_actionPerformed(null); - } - }); - renderGapsMenuItem.setLabel("Show Gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() - { - - public void itemStateChanged(ItemEvent e) - { - - renderGapsMenuItem_actionPerformed(null); - } - }); - findMenuItem.setLabel("Find..."); - findMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - findMenuItem_actionPerformed(e); - } - }); - searchMenu.setLabel("Search"); - - abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - abovePIDThreshold_actionPerformed(null); - } - }); - nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - nucleotideColour_actionPerformed(e); - } - }); - deleteGroups.setLabel("Undefine groups"); - deleteGroups.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deleteGroups_actionPerformed(e); - } - }); - copy.setLabel("Copy"); - copy.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copy_actionPerformed(e); - } - }); - cut.setLabel("Cut"); - cut.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - cut_actionPerformed(e); - } - }); - delete.setLabel("Delete"); - delete.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - delete_actionPerformed(e); - } - }); - Menu1.setLabel("Paste"); - pasteNew.setLabel("to new alignment"); - pasteNew.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pasteNew_actionPerformed(e); - } - }); - pasteThis.setLabel("add to this alignment"); - pasteThis.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pasteThis_actionPerformed(e); - } - }); - applyToAllGroups.setLabel("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(new java.awt.event.ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - applyToAllGroups_actionPerformed(null); - } - }); - font.setLabel("Font..."); - font.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - font_actionPerformed(e); - } - }); - fullSeqId.setLabel("Show Full Sequence ID"); - fullSeqId.setState(true); - fullSeqId.addItemListener(new java.awt.event.ItemListener() - { - - public void itemStateChanged(ItemEvent e) - { - fullSeqId_actionPerformed(null); - } - }); - scaleAbove.setLabel("Scale Above"); - scaleAbove.setState(true); - scaleAbove.addItemListener(new java.awt.event.ItemListener() - { - - public void itemStateChanged(ItemEvent e) - { - - scaleAbove_actionPerformed(null); - } - }); - scaleLeft.setEnabled(false); - scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(new java.awt.event.ItemListener() - { - - public void itemStateChanged(ItemEvent e) - { - - scaleLeft_actionPerformed(null); - } - }); - scaleRight.setEnabled(false); - scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(new java.awt.event.ItemListener() - { - - public void itemStateChanged(ItemEvent e) - { - - scaleRight_actionPerformed(null); - } - }); - modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - modifyPID_actionPerformed(e); - } - }); - modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - modifyConservation_actionPerformed(e); - } - }); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); - inputText.setLabel("Input from textbox"); - inputText.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - inputText_actionPerformed(e); - } - }); - - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); - documentation.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - documentation_actionPerformed(e); - } - }); - - about.setLabel("About..."); - about.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - about_actionPerformed(e); - } - }); - - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(helpMenu); - fileMenu.add(inputText); - fileMenu.add(outputTextboxMenu); - fileMenu.addSeparator(); - fileMenu.add(closeMenuItem); - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.add(cut); - editMenu.add(copy); - editMenu.add(Menu1); - editMenu.add(delete); - editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(deleteGroups); - editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); - searchMenu.add(findMenuItem); - viewMenu.add(font); - viewMenu.addSeparator(); - viewMenu.add(wrapMenuItem); - viewMenu.add(scaleAbove); - viewMenu.add(scaleLeft); - viewMenu.add(scaleRight); - viewMenu.addSeparator(); - viewMenu.add(fullSeqId); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(annotationPanelMenuItem); - viewMenu.addSeparator(); - viewMenu.add(overviewMenuItem); - colourMenu.add(applyToAllGroups); - colourMenu.addSeparator(); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideColour); - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); - calculateMenu.add(sort); - calculateMenu.add(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - this.add(statusBar, BorderLayout.SOUTH); - Menu1.add(pasteNew); - Menu1.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortByTreeMenu); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); - helpMenu.add(documentation); - helpMenu.add(about); - } - - protected void saveAs_actionPerformed(ActionEvent e) - { - - } - - protected void outputText_actionPerformed(ActionEvent e) - { - - } - - protected void htmlMenuItem_actionPerformed(ActionEvent e) - { - - } - - - protected void closeMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void redoMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void undoMenuItem_actionPerformed(ActionEvent e) - { - - } - - - protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void remove2RightMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) - { - - } - - - protected void wrapMenuItem_actionPerformed(ActionEvent e) - { - - } - - - protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void viewTextMenuItem_actionPerformed(ActionEvent e) - { - - } - - - protected void colourTextMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void overviewMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void sortIDMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void sortGroupMenuItem_actionPerformed(ActionEvent e) - { - - } - - - protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void PCAMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - - } - - - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - - } - - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - - } - - - - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) - { - - } - - - - - protected void clustalColour_actionPerformed(ActionEvent e) - { - - } - - protected void zappoColour_actionPerformed(ActionEvent e) - { - - } - - protected void taylorColour_actionPerformed(ActionEvent e) - { - - } - - - protected void hydrophobicityColour_actionPerformed(ActionEvent e) - { - - } - - protected void helixColour_actionPerformed(ActionEvent e) - { - - } - - protected void strandColour_actionPerformed(ActionEvent e) - { - - } - - protected void turnColour_actionPerformed(ActionEvent e) - { - - } - - protected void buriedColour_actionPerformed(ActionEvent e) - { - - } - +import java.awt.event.*; - protected void userDefinedColour_actionPerformed(ActionEvent e) - { +public class GAlignFrame extends Frame { + protected MenuBar alignFrameMenuBar = new MenuBar(); + protected Menu fileMenu = new Menu(); + protected MenuItem closeMenuItem = new MenuItem(); + protected Menu editMenu = new Menu(); + protected Menu viewMenu = new Menu(); + protected Menu colourMenu = new Menu(); + protected Menu calculateMenu = new Menu(); + protected MenuItem selectAllSequenceMenuItem = new MenuItem(); + protected MenuItem deselectAllSequenceMenuItem = new MenuItem(); + protected MenuItem invertSequenceMenuItem = new MenuItem(); + protected MenuItem remove2LeftMenuItem = new MenuItem(); + protected MenuItem remove2RightMenuItem = new MenuItem(); + protected MenuItem removeGappedColumnMenuItem = new MenuItem(); + protected MenuItem removeAllGapsMenuItem = new MenuItem(); + protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + protected MenuItem sortPairwiseMenuItem = new MenuItem(); + protected MenuItem sortIDMenuItem = new MenuItem(); + protected MenuItem sortGroupMenuItem = new MenuItem(); + protected MenuItem removeRedundancyMenuItem = new MenuItem(); + protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + protected MenuItem PCAMenuItem = new MenuItem(); + protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); + protected MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + protected Menu outputTextboxMenu = new Menu(); + protected MenuItem clustalColour = new MenuItem(); + protected MenuItem zappoColour = new MenuItem(); + protected MenuItem taylorColour = new MenuItem(); + protected MenuItem hydrophobicityColour = new MenuItem(); + protected MenuItem helixColour = new MenuItem(); + protected MenuItem strandColour = new MenuItem(); + protected MenuItem turnColour = new MenuItem(); + protected MenuItem buriedColour = new MenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + protected MenuItem PIDColour = new MenuItem(); + protected MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem overviewMenuItem = new MenuItem(); + protected MenuItem undoMenuItem = new MenuItem(); + protected MenuItem redoMenuItem = new MenuItem(); + protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); + Menu searchMenu = new Menu(); + protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + protected MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu Menu1 = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); + protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + protected MenuItem font = new MenuItem(); + protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + protected Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); + + public GAlignFrame() { + try { + jbInit(); + setMenuBar(alignFrameMenuBar); + + MenuItem item; + + // dynamically fill save as menu with available formats + for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) { + item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt( + i)); + item.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + saveAs_actionPerformed(e); + } + }); + + item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt( + i)); + item.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + } catch (Exception e) { + e.printStackTrace(); + } + } - } + private void jbInit() throws Exception { + fileMenu.setLabel("File"); + closeMenuItem.setLabel("Close"); + closeMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + closeMenuItem_actionPerformed(e); + } + }); + editMenu.setLabel("Edit"); + viewMenu.setLabel("View"); + colourMenu.setLabel("Colour"); + calculateMenu.setLabel("Calculate"); + selectAllSequenceMenuItem.setLabel("Select all"); + selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + selectAllSequenceMenuItem_actionPerformed(e); + } + }); + deselectAllSequenceMenuItem.setLabel("Deselect All"); + deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + deselectAllSequenceMenuItem_actionPerformed(e); + } + }); + invertSequenceMenuItem.setLabel("Invert Selection"); + invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + invertSequenceMenuItem_actionPerformed(e); + } + }); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + remove2LeftMenuItem_actionPerformed(e); + } + }); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + remove2RightMenuItem_actionPerformed(e); + } + }); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + removeGappedColumnMenuItem_actionPerformed(e); + } + }); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + removeAllGapsMenuItem_actionPerformed(e); + } + }); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + viewBoxesMenuItem_actionPerformed(null); + } + }); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + viewTextMenuItem_actionPerformed(null); + } + }); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + sortPairwiseMenuItem_actionPerformed(e); + } + }); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + sortIDMenuItem_actionPerformed(e); + } + }); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + sortGroupMenuItem_actionPerformed(e); + } + }); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + removeRedundancyMenuItem_actionPerformed(e); + } + }); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + pairwiseAlignmentMenuItem_actionPerformed(e); + } + }); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + PCAMenuItem_actionPerformed(e); + } + }); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + averageDistanceTreeMenuItem_actionPerformed(e); + } + }); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + neighbourTreeMenuItem_actionPerformed(e); + } + }); + 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(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + clustalColour_actionPerformed(e); + } + }); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + zappoColour_actionPerformed(e); + } + }); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + taylorColour_actionPerformed(e); + } + }); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + hydrophobicityColour_actionPerformed(e); + } + }); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + helixColour_actionPerformed(e); + } + }); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + strandColour_actionPerformed(e); + } + }); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + turnColour_actionPerformed(e); + } + }); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + buriedColour_actionPerformed(e); + } + }); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + userDefinedColour_actionPerformed(e); + } + }); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + PIDColour_actionPerformed(e); + } + }); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + BLOSUM62Colour_actionPerformed(e); + } + }); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + avTreeBlosumMenuItem_actionPerformed(e); + } + }); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + njTreeBlosumMenuItem_actionPerformed(e); + } + }); + annotationPanelMenuItem.setActionCommand(""); + annotationPanelMenuItem.setState(true); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + annotationPanelMenuItem_actionPerformed(null); + } + }); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + colourTextMenuItem_actionPerformed(null); + } + }); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + overviewMenuItem_actionPerformed(e); + } + }); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + undoMenuItem_actionPerformed(e); + } + }); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + redoMenuItem_actionPerformed(e); + } + }); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + conservationMenuItem_actionPerformed(null); + } + }); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + noColourmenuItem_actionPerformed(e); + } + }); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + wrapMenuItem_actionPerformed(null); + } + }); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + renderGapsMenuItem_actionPerformed(null); + } + }); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + findMenuItem_actionPerformed(e); + } + }); + searchMenu.setLabel("Search"); + + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + abovePIDThreshold_actionPerformed(null); + } + }); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + nucleotideColour_actionPerformed(e); + } + }); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + deleteGroups_actionPerformed(e); + } + }); + copy.setLabel("Copy"); + copy.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + copy_actionPerformed(e); + } + }); + cut.setLabel("Cut"); + cut.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + cut_actionPerformed(e); + } + }); + delete.setLabel("Delete"); + delete.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + delete_actionPerformed(e); + } + }); + Menu1.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + pasteNew_actionPerformed(e); + } + }); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + pasteThis_actionPerformed(e); + } + }); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + applyToAllGroups_actionPerformed(null); + } + }); + font.setLabel("Font..."); + font.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + font_actionPerformed(e); + } + }); + fullSeqId.setLabel("Show Full Sequence ID"); + fullSeqId.setState(true); + fullSeqId.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + fullSeqId_actionPerformed(null); + } + }); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + scaleAbove_actionPerformed(null); + } + }); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + scaleLeft_actionPerformed(null); + } + }); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + scaleRight_actionPerformed(null); + } + }); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + modifyPID_actionPerformed(e); + } + }); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + modifyConservation_actionPerformed(e); + } + }); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + inputText_actionPerformed(e); + } + }); + + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + documentation_actionPerformed(e); + } + }); + + about.setLabel("About..."); + about.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + about_actionPerformed(e); + } + }); + + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(searchMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(helpMenu); + fileMenu.add(inputText); + fileMenu.add(outputTextboxMenu); + fileMenu.addSeparator(); + fileMenu.add(closeMenuItem); + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(Menu1); + editMenu.add(delete); + editMenu.addSeparator(); + editMenu.add(selectAllSequenceMenuItem); + editMenu.add(deselectAllSequenceMenuItem); + editMenu.add(invertSequenceMenuItem); + editMenu.add(deleteGroups); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + searchMenu.add(findMenuItem); + viewMenu.add(font); + viewMenu.addSeparator(); + viewMenu.add(wrapMenuItem); + viewMenu.add(scaleAbove); + viewMenu.add(scaleLeft); + viewMenu.add(scaleRight); + viewMenu.addSeparator(); + viewMenu.add(fullSeqId); + viewMenu.add(viewBoxesMenuItem); + viewMenu.add(viewTextMenuItem); + viewMenu.add(colourTextMenuItem); + viewMenu.add(renderGapsMenuItem); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + this.add(statusBar, BorderLayout.SOUTH); + Menu1.add(pasteNew); + Menu1.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); + } - protected void PIDColour_actionPerformed(ActionEvent e) - { + protected void saveAs_actionPerformed(ActionEvent e) { + } - } + protected void outputText_actionPerformed(ActionEvent e) { + } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) - { + protected void htmlMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void closeMenuItem_actionPerformed(ActionEvent e) { + } + protected void redoMenuItem_actionPerformed(ActionEvent e) { + } - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { + protected void undoMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { + } - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { + protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) { + } + protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) { + } - protected void printMenuItem_actionPerformed(ActionEvent e) - { + protected void remove2RightMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { + } - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) - { + protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void wrapMenuItem_actionPerformed(ActionEvent e) { + } - protected void findMenuItem_actionPerformed(ActionEvent e) - { + protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void viewTextMenuItem_actionPerformed(ActionEvent e) { + } + protected void colourTextMenuItem_actionPerformed(ActionEvent e) { + } - protected void abovePIDThreshold_actionPerformed(ActionEvent e) { + protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void overviewMenuItem_actionPerformed(ActionEvent e) { + } - public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) - { + protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void sortIDMenuItem_actionPerformed(ActionEvent e) { + } - protected void nucleotideColour_actionPerformed(ActionEvent e) - { + protected void sortGroupMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { + } - protected void deleteGroups_actionPerformed(ActionEvent e) - { + protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void PCAMenuItem_actionPerformed(ActionEvent e) { + } - protected void copy_actionPerformed(ActionEvent e) - { + protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { + } + protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { + } - protected void cut_actionPerformed(ActionEvent e) - { + protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) { + } - protected void delete_actionPerformed(ActionEvent e) - { + protected void clustalColour_actionPerformed(ActionEvent e) { + } - } + protected void zappoColour_actionPerformed(ActionEvent e) { + } - protected void pasteNew_actionPerformed(ActionEvent e) - { + protected void taylorColour_actionPerformed(ActionEvent e) { + } - } + protected void hydrophobicityColour_actionPerformed(ActionEvent e) { + } - protected void pasteThis_actionPerformed(ActionEvent e) - { + protected void helixColour_actionPerformed(ActionEvent e) { + } - } + protected void strandColour_actionPerformed(ActionEvent e) { + } - protected void applyToAllGroups_actionPerformed(ActionEvent e) - { + protected void turnColour_actionPerformed(ActionEvent e) { + } - } + protected void buriedColour_actionPerformed(ActionEvent e) { + } - protected void createPNG_actionPerformed(ActionEvent e) - { + protected void userDefinedColour_actionPerformed(ActionEvent e) { + } - } + protected void PIDColour_actionPerformed(ActionEvent e) { + } - protected void font_actionPerformed(ActionEvent e) - { + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { + } - } + protected void noColourmenuItem_actionPerformed(ActionEvent e) { + } - protected void fullSeqId_actionPerformed(ActionEvent e) - { + protected void conservationMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void printMenuItem_actionPerformed(ActionEvent e) { + } - protected void epsFile_actionPerformed(ActionEvent e) - { + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void findMenuItem_actionPerformed(ActionEvent e) { + } - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + protected void abovePIDThreshold_actionPerformed(ActionEvent e) { + } - } + public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) { + } - protected void jpred_actionPerformed(ActionEvent e) - { + protected void nucleotideColour_actionPerformed(ActionEvent e) { + } - } + protected void deleteGroups_actionPerformed(ActionEvent e) { + } - protected void scaleAbove_actionPerformed(ActionEvent e) - { + protected void copy_actionPerformed(ActionEvent e) { + } - } + protected void cut_actionPerformed(ActionEvent e) { + } - protected void scaleLeft_actionPerformed(ActionEvent e) - { + protected void delete_actionPerformed(ActionEvent e) { + } - } + protected void pasteNew_actionPerformed(ActionEvent e) { + } - protected void scaleRight_actionPerformed(ActionEvent e) - { + protected void pasteThis_actionPerformed(ActionEvent e) { + } - } + protected void applyToAllGroups_actionPerformed(ActionEvent e) { + } - protected void modifyPID_actionPerformed(ActionEvent e) - { + protected void createPNG_actionPerformed(ActionEvent e) { + } - } + protected void font_actionPerformed(ActionEvent e) { + } - protected void modifyConservation_actionPerformed(ActionEvent e) - { + protected void fullSeqId_actionPerformed(ActionEvent e) { + } - } + protected void epsFile_actionPerformed(ActionEvent e) { + } - protected void preferences_actionPerformed(ActionEvent e) - { + protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void jpred_actionPerformed(ActionEvent e) { + } - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) { + protected void scaleAbove_actionPerformed(ActionEvent e) { + } - } + protected void scaleLeft_actionPerformed(ActionEvent e) { + } - protected void inputText_actionPerformed(ActionEvent e) { + protected void scaleRight_actionPerformed(ActionEvent e) { + } - } + protected void modifyPID_actionPerformed(ActionEvent e) { + } - protected void documentation_actionPerformed(ActionEvent e) { + protected void modifyConservation_actionPerformed(ActionEvent e) { + } - } + protected void preferences_actionPerformed(ActionEvent e) { + } - protected void about_actionPerformed(ActionEvent e) { + protected void msaAlignMenuItem_actionPerformed(ActionEvent e) { + } - } + protected void inputText_actionPerformed(ActionEvent e) { + } + protected void documentation_actionPerformed(ActionEvent e) { + } + protected void about_actionPerformed(ActionEvent e) { + } } -