X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=f101ab5692834e95f9559d7795f03cb67420271f;hb=4232f0a5699af84c5361e6cea446a97e7bcc788e;hp=692c2fde137e81d89d6e25a2cbda80a00d0d7e4f;hpb=58d59957854fee335ca28d804297e0e0890bfa8a;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 692c2fd..f101ab5 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -19,7 +19,6 @@ package jalview.appletgui; -import jalview.jbappletgui.GAlignFrame; import jalview.schemes.*; import jalview.datamodel.*; import jalview.analysis.*; @@ -31,8 +30,8 @@ import java.io.InputStreamReader; import java.io.BufferedReader; import java.net.URL; -public class AlignFrame - extends GAlignFrame + +public class AlignFrame extends Frame { final AlignmentPanel alignPanel; public final AlignViewport viewport; @@ -43,6 +42,12 @@ public class AlignFrame public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title) { + try{ + jbInit(); + }catch(Exception ex) + { + ex.printStackTrace(); + } this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); @@ -1467,4 +1472,603 @@ public class AlignFrame } } + + ////////////////////////////////////////////////////////////////////////////////// + //JBuilder Graphics here + + 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 dbref = 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(); + protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + + private void jbInit() throws Exception { + + setMenuBar(alignFrameMenuBar); + + MenuItem item; + + // dynamically fill save as menu with available formats + for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) + { + + item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats. + elementAt( + i)); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + + + 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); + } + }); + dbref.setLabel("ShowSequence DB Refs"); + dbref.setActionCommand(""); + dbref.setState(true); + dbref.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + dbref_actionPerformed(e); + } + }); + 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); + } + }); + seqLimits.setState(true); + seqLimits.setLabel("Show Sequence Limits"); + seqLimits.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + seqLimits_itemStateChanged(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(dbref); + viewMenu.add(seqLimits); + viewMenu.addSeparator(); + viewMenu.add(wrapMenuItem); + viewMenu.add(scaleAbove); + viewMenu.add(scaleLeft); + viewMenu.add(scaleRight); + viewMenu.addSeparator(); + 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); + } } +