/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview 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 3 of the License, or (at your option) any later version. * * Jalview 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 Jalview. If not, see . */ package jalview.jbgui; import java.awt.*; import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; import jalview.schemes.*; public class GAlignFrame extends JInternalFrame { protected JMenuBar alignFrameMenuBar = new JMenuBar(); protected JMenu fileMenu = new JMenu(); protected JMenuItem closeMenuItem = new JMenuItem(); protected JMenu editMenu = new JMenu(); protected JMenu viewMenu = new JMenu(); protected JMenu colourMenu = new JMenu(); protected JMenu calculateMenu = new JMenu(); protected JMenu webService = new JMenu(); protected JMenuItem webServiceNoServices; protected JMenuItem selectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem(); protected JMenuItem invertSequenceMenuItem = new JMenuItem(); protected JMenuItem remove2LeftMenuItem = new JMenuItem(); protected JMenuItem remove2RightMenuItem = new JMenuItem(); protected JMenuItem removeGappedColumnMenuItem = new JMenuItem(); protected JMenuItem removeAllGapsMenuItem = new JMenuItem(); public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); protected JMenuItem sortPairwiseMenuItem = new JMenuItem(); protected JMenuItem sortIDMenuItem = new JMenuItem(); protected JMenuItem sortLengthMenuItem = new JMenuItem(); protected JMenuItem sortGroupMenuItem = new JMenuItem(); protected JMenu sortByAnnotScore = new JMenu(); protected JMenuItem removeRedundancyMenuItem = new JMenuItem(); protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(); protected JMenuItem PCAMenuItem = new JMenuItem(); protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem(); protected JMenuItem neighbourTreeMenuItem = new JMenuItem(); BorderLayout borderLayout1 = new BorderLayout(); public JLabel statusBar = new JLabel(); protected JMenuItem saveAs = new JMenuItem(); protected JMenu outputTextboxMenu = new JMenu(); protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); // protected JRadioButtonMenuItem covariationColour = new // JRadioButtonMenuItem(); JMenuItem njTreeBlosumMenuItem = new JMenuItem(); JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); JMenuItem htmlMenuItem = new JMenuItem(); JMenuItem overviewMenuItem = new JMenuItem(); protected JMenuItem undoMenuItem = new JMenuItem(); protected JMenuItem redoMenuItem = new JMenuItem(); public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); JMenuItem printMenuItem = new JMenuItem(); public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); JMenuItem findMenuItem = new JMenuItem(); public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); JMenuItem deleteGroups = new JMenuItem(); JMenuItem delete = new JMenuItem(); JMenuItem copy = new JMenuItem(); JMenuItem cut = new JMenuItem(); JMenu pasteMenu = new JMenu(); JMenuItem pasteNew = new JMenuItem(); JMenuItem pasteThis = new JMenuItem(); public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem(); JMenuItem createPNG = new JMenuItem(); protected JMenuItem font = new JMenuItem(); public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); JMenuItem epsFile = new JMenuItem(); JMenuItem LoadtreeMenuItem = new JMenuItem(); public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); protected JMenuItem modifyPID = new JMenuItem(); protected JMenuItem modifyConservation = new JMenuItem(); protected JMenu sortByTreeMenu = new JMenu(); protected JMenu sort = new JMenu(); protected JMenu calculateTree = new JMenu(); JMenu jMenu2 = new JMenu(); protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); protected ButtonGroup colours = new ButtonGroup(); JMenuItem vamsasStore = new JMenuItem(); protected JMenuItem showTranslation = new JMenuItem(); protected JMenuItem extractScores = new JMenuItem(); protected JMenu showProducts = new JMenu(); public JMenuItem openFeatureSettings = new JMenuItem(); JMenuItem fetchSequence = new JMenuItem(); JMenuItem annotationColour = new JMenuItem(); protected JMenuItem rnahelicesColour = new JMenuItem(); JMenuItem associatedData = new JMenuItem(); protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem(); JMenu addSequenceMenu = new JMenu(); JMenuItem addFromFile = new JMenuItem(); JMenuItem addFromText = new JMenuItem(); JMenuItem addFromURL = new JMenuItem(); JMenuItem exportAnnotations = new JMenuItem(); JMenuItem exportFeatures = new JMenuItem(); protected JPanel statusPanel = new JPanel(); GridLayout gridLayout1 = new GridLayout(); JMenu jMenu3 = new JMenu(); JMenuItem showAllSeqs = new JMenuItem(); JMenuItem showAllColumns = new JMenuItem(); JMenu hideMenu = new JMenu(); JMenuItem hideSelSequences = new JMenuItem(); JMenuItem hideSelColumns = new JMenuItem(); JMenuItem hideAllButSelection = new JMenuItem(); JMenuItem hideAllSelection = new JMenuItem(); JMenuItem showAllhidden = new JMenuItem(); protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); JMenuItem invertColSel = new JMenuItem(); protected JTabbedPane tabbedPane = new JTabbedPane(); JMenuItem save = new JMenuItem(); protected JMenuItem reload = new JMenuItem(); JMenuItem newView = new JMenuItem(); JMenuItem textColour = new JMenuItem(); JMenu formatMenu = new JMenu(); JMenu selectMenu = new JMenu(); protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); protected JMenuItem gatherViews = new JMenuItem(); protected JMenuItem expandViews = new JMenuItem(); JMenuItem pageSetup = new JMenuItem(); JMenuItem alignmentProperties = new JMenuItem(); JMenu tooltipSettingsMenu = new JMenu(); private JMenuItem justifyLeftMenuItem = new JMenuItem(); private JMenuItem justifyRightMenuItem = new JMenuItem(); JMenu autoAnnMenu = new JMenu(); protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); private JMenuItem grpsFromSelection = new JMenuItem(); public GAlignFrame() { try { jbInit(); setJMenuBar(alignFrameMenuBar); // dynamically fill save as menu with available formats for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); } }); outputTextboxMenu.add(item); } } catch (Exception e) { } if (!new jalview.util.Platform().isAMac()) { closeMenuItem.setMnemonic('C'); outputTextboxMenu.setMnemonic('T'); undoMenuItem.setMnemonic('Z'); redoMenuItem.setMnemonic('0'); copy.setMnemonic('C'); cut.setMnemonic('U'); pasteMenu.setMnemonic('P'); reload.setMnemonic('R'); } if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { java.util.Enumeration userColours = jalview.gui.UserDefinedColours .getUserColourSchemes().keys(); while (userColours.hasMoreElements()) { final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( userColours.nextElement().toString()); radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent evt) { if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { radioItem.removeActionListener(radioItem.getActionListeners()[0]); int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, "Remove from default list?", "Remove user defined colour", JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { jalview.gui.UserDefinedColours .removeColourFromDefaults(radioItem.getText()); colourMenu.remove(radioItem); } else { radioItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); } }); } } } }); radioItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); } }); colourMenu.insert(radioItem, 15); colours.add(radioItem); } } colours.add(noColourmenuItem); colours.add(clustalColour); colours.add(zappoColour); colours.add(taylorColour); colours.add(hydrophobicityColour); colours.add(helixColour); colours.add(strandColour); colours.add(turnColour); colours.add(buriedColour); colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(nucleotideColour); colours.add(purinePyrimidineColour); // colours.add(covariationColour); setColourSelected(jalview.bin.Cache .getDefault("DEFAULT_COLOUR", "None")); } public void setColourSelected(String defaultColour) { if (defaultColour != null) { int index = ColourSchemeProperty .getColourIndexFromName(defaultColour); switch (index) { case ColourSchemeProperty.CLUSTAL: clustalColour.setSelected(true); break; case ColourSchemeProperty.BLOSUM: BLOSUM62Colour.setSelected(true); break; case ColourSchemeProperty.PID: PIDColour.setSelected(true); break; case ColourSchemeProperty.ZAPPO: zappoColour.setSelected(true); break; case ColourSchemeProperty.TAYLOR: taylorColour.setSelected(true); break; case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break; case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break; case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break; case ColourSchemeProperty.TURN: turnColour.setSelected(true); break; case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break; case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break; case ColourSchemeProperty.PURINEPYRIMIDINE: purinePyrimidineColour.setSelected(true); break; /* * case ColourSchemeProperty.COVARIATION: * covariationColour.setSelected(true); * * break; */ case ColourSchemeProperty.USER_DEFINED: userDefinedColour.setSelected(true); break; case ColourSchemeProperty.NONE: default: noColourmenuItem.setSelected(true); break; } } } private void jbInit() throws Exception { fileMenu.setText("File"); saveAs.setText("Save As..."); saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false)); saveAs.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { saveAs_actionPerformed(e); } }); closeMenuItem.setText("Close"); closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); closeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { closeMenuItem_actionPerformed(false); } }); editMenu.setText("Edit"); viewMenu.setText("View"); colourMenu.setText("Colour"); calculateMenu.setText("Calculate"); webService.setText("Web Service"); selectAllSequenceMenuItem.setText("Select All"); selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false)); selectAllSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { selectAllSequenceMenuItem_actionPerformed(e); } }); deselectAllSequenceMenuItem.setText("Deselect All"); deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false)); deselectAllSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { deselectAllSequenceMenuItem_actionPerformed(e); } }); invertSequenceMenuItem.setText("Invert Sequence Selection"); invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false)); invertSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { invertSequenceMenuItem_actionPerformed(e); } }); grpsFromSelection.setText("Make Groups for selection"); grpsFromSelection.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { makeGrpsFromSelection_actionPerformed(e); } }); remove2LeftMenuItem.setText("Remove Left"); remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); remove2LeftMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { remove2LeftMenuItem_actionPerformed(e); } }); remove2RightMenuItem.setText("Remove Right"); remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); remove2RightMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { remove2RightMenuItem_actionPerformed(e); } }); removeGappedColumnMenuItem.setText("Remove Empty Columns"); removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false)); removeGappedColumnMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { removeGappedColumnMenuItem_actionPerformed(e); } }); removeAllGapsMenuItem.setText("Remove All Gaps"); removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false)); removeAllGapsMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { removeAllGapsMenuItem_actionPerformed(e); } }); justifyLeftMenuItem.setText("Left Justify Alignment"); justifyLeftMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { justifyLeftMenuItem_actionPerformed(e); } }); justifyRightMenuItem.setText("Right Justify Alignment"); justifyRightMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { justifyRightMenuItem_actionPerformed(e); } }); viewBoxesMenuItem.setText("Boxes"); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { viewBoxesMenuItem_actionPerformed(e); } }); viewTextMenuItem.setText("Text"); viewTextMenuItem.setState(true); viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { viewTextMenuItem_actionPerformed(e); } }); showNonconservedMenuItem.setText("Show nonconserved"); showNonconservedMenuItem.setState(false); showNonconservedMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { showUnconservedMenuItem_actionPerformed(e); } }); sortPairwiseMenuItem.setText("by Pairwise Identity"); sortPairwiseMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { sortPairwiseMenuItem_actionPerformed(e); } }); sortIDMenuItem.setText("by ID"); sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { sortIDMenuItem_actionPerformed(e); } }); sortLengthMenuItem.setText("By Length"); sortLengthMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { sortLengthMenuItem_actionPerformed(e); } }); sortGroupMenuItem.setText("by Group"); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { sortGroupMenuItem_actionPerformed(e); } }); removeRedundancyMenuItem.setText("Remove Redundancy..."); removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit .getDefaultToolkit().getMenuShortcutKeyMask(), false)); removeRedundancyMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { removeRedundancyMenuItem_actionPerformed(e); } }); pairwiseAlignmentMenuItem.setText("Pairwise Alignments..."); pairwiseAlignmentMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { pairwiseAlignmentMenuItem_actionPerformed(e); } }); PCAMenuItem.setText("Principal Component Analysis"); PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { PCAMenuItem_actionPerformed(e); } }); averageDistanceTreeMenuItem .setText("Average Distance Using % Identity"); averageDistanceTreeMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { averageDistanceTreeMenuItem_actionPerformed(e); } }); neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity"); neighbourTreeMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { neighbourTreeMenuItem_actionPerformed(e); } }); this.getContentPane().setLayout(borderLayout1); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBackground(Color.white); statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); statusBar.setText("Status bar"); outputTextboxMenu.setText("Output to Textbox"); clustalColour.setText("Clustalx"); clustalColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { clustalColour_actionPerformed(e); } }); zappoColour.setText("Zappo"); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { zappoColour_actionPerformed(e); } }); taylorColour.setText("Taylor"); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { taylorColour_actionPerformed(e); } }); hydrophobicityColour.setText("Hydrophobicity"); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { hydrophobicityColour_actionPerformed(e); } }); helixColour.setText("Helix Propensity"); helixColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { helixColour_actionPerformed(e); } }); strandColour.setText("Strand Propensity"); strandColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { strandColour_actionPerformed(e); } }); turnColour.setText("Turn Propensity"); turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { turnColour_actionPerformed(e); } }); buriedColour.setText("Buried Index"); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { buriedColour_actionPerformed(e); } }); userDefinedColour.setText("User Defined..."); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { userDefinedColour_actionPerformed(e); } }); PIDColour.setText("Percentage Identity"); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { PIDColour_actionPerformed(e); } }); BLOSUM62Colour.setText("BLOSUM62 Score"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { BLOSUM62Colour_actionPerformed(e); } }); nucleotideColour.setText("Nucleotide"); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { nucleotideColour_actionPerformed(e); } }); purinePyrimidineColour.setText("Purine/Pyrimidine"); purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { purinePyrimidineColour_actionPerformed(e); } }); /* * covariationColour.setText("Covariation"); * covariationColour.addActionListener(new java.awt.event.ActionListener() { * public void actionPerformed(ActionEvent e) { * covariationColour_actionPerformed(e); } }); */ avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62"); avDistanceTreeBlosumMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { avTreeBlosumMenuItem_actionPerformed(e); } }); njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62"); njTreeBlosumMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { njTreeBlosumMenuItem_actionPerformed(e); } }); annotationPanelMenuItem.setActionCommand(""); annotationPanelMenuItem.setText("Show Annotations"); annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault( "SHOW_ANNOTATIONS", true)); annotationPanelMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { annotationPanelMenuItem_actionPerformed(e); } }); colourTextMenuItem.setText("Colour Text"); colourTextMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { colourTextMenuItem_actionPerformed(e); } }); htmlMenuItem.setText("HTML"); htmlMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { htmlMenuItem_actionPerformed(e); } }); overviewMenuItem.setText("Overview Window"); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { overviewMenuItem_actionPerformed(e); } }); undoMenuItem.setEnabled(false); undoMenuItem.setText("Undo"); undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); undoMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { undoMenuItem_actionPerformed(e); } }); redoMenuItem.setEnabled(false); redoMenuItem.setText("Redo"); redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); redoMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { redoMenuItem_actionPerformed(e); } }); conservationMenuItem.setText("By Conservation"); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(e); } }); noColourmenuItem.setText("None"); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { noColourmenuItem_actionPerformed(e); } }); wrapMenuItem.setText("Wrap"); wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { wrapMenuItem_actionPerformed(e); } }); printMenuItem.setText("Print ..."); printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); printMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { printMenuItem_actionPerformed(e); } }); renderGapsMenuItem.setText("Show Gaps"); renderGapsMenuItem.setState(true); renderGapsMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { renderGapsMenuItem_actionPerformed(e); } }); findMenuItem.setText("Find..."); findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); findMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { findMenuItem_actionPerformed(e); } }); abovePIDThreshold.setText("Above Identity Threshold"); abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { abovePIDThreshold_actionPerformed(e); } }); showSeqFeatures.setText("Show Sequence Features"); showSeqFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { showSeqFeatures_actionPerformed(actionEvent); } }); /* * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); * showSeqFeaturesHeight.addActionListener(new ActionListener() { public * void actionPerformed(ActionEvent actionEvent) { * showSeqFeaturesHeight_actionPerformed(actionEvent); } }); */ showDbRefsMenuitem.setText("Show Database Refs"); showDbRefsMenuitem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showDbRefs_actionPerformed(e); } }); showNpFeatsMenuitem.setText("Show Non-Positional Features"); showNpFeatsMenuitem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showNpFeats_actionPerformed(e); } }); showGroupConservation.setText("Group Conservation"); showGroupConservation.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showGroupConservation_actionPerformed(e); } }); showGroupConsensus.setText("Group Consensus"); showGroupConsensus.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showGroupConsensus_actionPerformed(e); } }); showConsensusHistogram.setText("Show Consensus Histogram"); showConsensusHistogram.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showConsensusHistogram_actionPerformed(e); } }); showSequenceLogo.setText("Show Consensus Logo"); showSequenceLogo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showSequenceLogo_actionPerformed(e); } }); normaliseSequenceLogo.setText("Normalise Consensus Logo"); normaliseSequenceLogo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { normaliseSequenceLogo_actionPerformed(e); } }); applyAutoAnnotationSettings.setText("Apply to all groups"); applyAutoAnnotationSettings.setState(false); applyAutoAnnotationSettings.setVisible(true); applyAutoAnnotationSettings.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { applyAutoAnnotationSettings_actionPerformed(e); } }); nucleotideColour.setText("Nucleotide"); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { nucleotideColour_actionPerformed(e); } }); deleteGroups.setText("Undefine groups"); deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); deleteGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { deleteGroups_actionPerformed(e); } }); copy.setText("Copy"); copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); copy.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { copy_actionPerformed(e); } }); cut.setText("Cut"); cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); cut.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { cut_actionPerformed(e); } }); delete.setText("Delete"); delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false)); delete.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { delete_actionPerformed(e); } }); pasteMenu.setText("Paste"); pasteNew.setText("To New Alignment"); pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false)); pasteNew.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { pasteNew_actionPerformed(e); } }); pasteThis.setText("Add To This Alignment"); pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); pasteThis.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { pasteThis_actionPerformed(e); } }); applyToAllGroups.setText("Apply Colour To All Groups"); applyToAllGroups.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { applyToAllGroups_actionPerformed(e); } }); createPNG.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { createPNG(null); } }); createPNG.setActionCommand("Save As PNG Image"); createPNG.setText("PNG"); font.setText("Font..."); font.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { font_actionPerformed(e); } }); seqLimits.setText("Show Sequence Limits"); seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { seqLimit_actionPerformed(e); } }); epsFile.setText("EPS"); epsFile.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { createEPS(null); } }); LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set"); LoadtreeMenuItem.setText("Load Associated Tree"); LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { LoadtreeMenuItem_actionPerformed(e); } }); scaleAbove.setVisible(false); scaleAbove.setText("Scale Above"); scaleAbove.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { scaleAbove_actionPerformed(e); } }); scaleLeft.setVisible(false); scaleLeft.setSelected(true); scaleLeft.setText("Scale Left"); scaleLeft.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { scaleLeft_actionPerformed(e); } }); scaleRight.setVisible(false); scaleRight.setSelected(true); scaleRight.setText("Scale Right"); scaleRight.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { scaleRight_actionPerformed(e); } }); centreColumnLabelsMenuItem.setVisible(true); centreColumnLabelsMenuItem.setState(false); centreColumnLabelsMenuItem.setText("Centre Column Labels"); centreColumnLabelsMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { centreColumnLabels_actionPerformed(e); } }); followHighlightMenuItem.setVisible(true); followHighlightMenuItem.setState(true); followHighlightMenuItem.setText("Automatic Scrolling"); followHighlightMenuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { followHighlight_actionPerformed(); } }); modifyPID.setText("Modify Identity Threshold..."); modifyPID.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { modifyPID_actionPerformed(e); } }); modifyConservation.setText("Modify Conservation Threshold..."); modifyConservation .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { modifyConservation_actionPerformed(e); } }); sortByTreeMenu.setText("By Tree Order"); sort.setText("Sort"); sort.addMenuListener(new MenuListener() { public void menuSelected(MenuEvent e) { buildTreeMenu(); } public void menuDeselected(MenuEvent e) { } public void menuCanceled(MenuEvent e) { } }); sortByAnnotScore.setText("by Score"); sort.add(sortByAnnotScore); sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener() { public void menuCanceled(MenuEvent e) { } public void menuDeselected(MenuEvent e) { } public void menuSelected(MenuEvent e) { buildSortByAnnotationScoresMenu(); } }); sortByAnnotScore.setVisible(false); calculateTree.setText("Calculate Tree"); jMenu2.setText("Export Image"); padGapsMenuitem.setText("Pad Gaps"); padGapsMenuitem.setState(jalview.bin.Cache .getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { padGapsMenuitem_actionPerformed(e); } }); vamsasStore.setVisible(false); vamsasStore.setText("VAMSAS store"); vamsasStore.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { vamsasStore_actionPerformed(e); } }); showTranslation.setText("Translate cDNA"); showTranslation.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showTranslation_actionPerformed(e); } }); extractScores.setText("Extract Scores..."); extractScores.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { extractScores_actionPerformed(e); } }); extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based // score extraction showProducts.setText("Get Cross References"); /* * showProducts.addActionListener(new ActionListener() { * * public void actionPerformed(ActionEvent e) { * showProducts_actionPerformed(e); } }); */ openFeatureSettings.setText("Feature Settings..."); openFeatureSettings.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { featureSettings_actionPerformed(e); } }); fetchSequence.setText("Fetch Sequence(s)..."); fetchSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { fetchSequence_actionPerformed(e); } }); annotationColour.setText("By Annotation..."); annotationColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { annotationColour_actionPerformed(e); } }); rnahelicesColour.setText("By RNA helices"); rnahelicesColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { rnahelicesColour_actionPerformed(e); } }); associatedData.setText("Load Features / Annotations"); associatedData.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { associatedData_actionPerformed(e); } }); autoCalculate.setText("Autocalculate Consensus"); autoCalculate.setState(jalview.bin.Cache.getDefault( "AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { autoCalculate_actionPerformed(e); } }); sortByTree.setText("Sort Alignment With New Tree"); sortByTree.setToolTipText("Enable this to automatically sort
the alignment when you open
a new tree."); sortByTree.setState(jalview.bin.Cache.getDefault( "SORT_BY_TREE", false)); sortByTree.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { sortByTreeOption_actionPerformed(e); } }); listenToViewSelections.setText("Listen for selections"); listenToViewSelections.setToolTipText("When selected, selections in this view will mirror
selections made on the same sequences in other views."); listenToViewSelections.setState(false); listenToViewSelections.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { listenToViewSelections_actionPerformed(e); } }); addSequenceMenu.setText("Add Sequences"); addFromFile.setText("From File"); addFromFile.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { addFromFile_actionPerformed(e); } }); addFromText.setText("From Textbox"); addFromText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { addFromText_actionPerformed(e); } }); addFromURL.setText("From URL"); addFromURL.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { addFromURL_actionPerformed(e); } }); exportFeatures.setText("Export Features..."); exportFeatures.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { exportFeatures_actionPerformed(e); } }); exportAnnotations.setText("Export Annotations..."); exportAnnotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { exportAnnotations_actionPerformed(e); } }); statusPanel.setLayout(gridLayout1); jMenu3.setText("Show"); showAllSeqs.setText("All Sequences"); showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity."); showAllSeqs.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showAllSeqs_actionPerformed(e); } }); showAllColumns.setText("All Columns"); showAllColumns.setToolTipText("Ctrl+H toggles column visiblity."); showAllColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showAllColumns_actionPerformed(e); } }); hideMenu.setText("Hide"); hideSelSequences.setText("Selected Sequences"); hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity."); hideSelSequences.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { hideSelSequences_actionPerformed(e); } }); hideSelColumns.setText("Selected Columns"); hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity."); hideSelColumns.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { hideSelColumns_actionPerformed(e); } }); hideAllSelection.setText("Selected Region"); hideAllSelection.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { hideAllSelection_actionPerformed(e); } }); // TODO: should be hidden if no selection exists. hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)"); hideAllButSelection.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { hideAllButSelection_actionPerformed(e); } }); showAllhidden.setText("All Sequences and Columns"); showAllhidden .setToolTipText("H toggles visibility of hidden or selected regions."); showAllhidden.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showAllhidden_actionPerformed(e); } }); hiddenMarkers.setText("Show Hidden Markers"); hiddenMarkers.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { hiddenMarkers_actionPerformed(e); } }); invertColSel.setText("Invert Column Selection"); invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.ALT_MASK, false)); invertColSel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { invertColSel_actionPerformed(e); } }); tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() { public void stateChanged(ChangeEvent evt) { JTabbedPane pane = (JTabbedPane) evt.getSource(); int sel = pane.getSelectedIndex(); tabSelectionChanged(sel); } }); tabbedPane.addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent e) { tabbedPane_mousePressed(e); } }); tabbedPane.addFocusListener(new FocusAdapter() { public void focusGained(FocusEvent e) { tabbedPane_focusGained(e); } }); save.setText("Save"); save.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); save.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { save_actionPerformed(e); } }); reload.setEnabled(false); reload.setText("Reload"); reload.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { reload_actionPerformed(e); } }); newView.setText("New View"); newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit() .getMenuShortcutKeyMask(), false)); newView.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { newView_actionPerformed(e); } }); tabbedPane.setToolTipText(" Right-click to rename tab" + "
Press X to eXpand tabs, G to reGroup."); textColour.setText("Colour Text ..."); textColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { textColour_actionPerformed(e); } }); formatMenu.setText("Format"); selectMenu.setText("Select"); idRightAlign.setText("Right Align Sequence Id"); idRightAlign.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { idRightAlign_actionPerformed(e); } }); gatherViews.setEnabled(false); gatherViews.setText("Gather Views"); gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_G, 0, false)); gatherViews.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { gatherViews_actionPerformed(e); } }); expandViews.setEnabled(false); expandViews.setText("Expand Views"); expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke( java.awt.event.KeyEvent.VK_X, 0, false)); expandViews.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { expandViews_actionPerformed(e); } }); pageSetup.setText("Page Setup ..."); pageSetup.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { pageSetup_actionPerformed(e); } }); alignmentProperties.setText("Alignment Properties..."); alignmentProperties.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { alignmentProperties(); } }); tooltipSettingsMenu.setText("Sequence ID Tooltip"); autoAnnMenu.setText("Autocalculated Annotation"); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(webService); fileMenu.add(fetchSequence); fileMenu.add(addSequenceMenu); fileMenu.add(reload); fileMenu.addSeparator(); fileMenu.add(vamsasStore); fileMenu.add(save); fileMenu.add(saveAs); fileMenu.add(outputTextboxMenu); fileMenu.add(pageSetup); fileMenu.add(printMenuItem); fileMenu.addSeparator(); fileMenu.add(jMenu2); fileMenu.add(exportFeatures); fileMenu.add(exportAnnotations); fileMenu.add(LoadtreeMenuItem); fileMenu.add(associatedData); fileMenu.addSeparator(); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); editMenu.add(cut); editMenu.add(copy); editMenu.add(pasteMenu); editMenu.add(delete); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); editMenu.add(removeGappedColumnMenuItem); editMenu.add(removeAllGapsMenuItem); editMenu.add(removeRedundancyMenuItem); editMenu.addSeparator(); // dont add these yet in the CVS build - they cannot be undone! // Excluded from Jalview 2.5 release - undo needs to be implemented. // editMenu.add(justifyLeftMenuItem); // editMenu.add(justifyRightMenuItem); // editMenu.addSeparator(); editMenu.add(padGapsMenuitem); viewMenu.add(newView); viewMenu.add(expandViews); viewMenu.add(gatherViews); viewMenu.addSeparator(); viewMenu.add(jMenu3); viewMenu.add(hideMenu); viewMenu.addSeparator(); viewMenu.add(followHighlightMenuItem); viewMenu.add(annotationPanelMenuItem); autoAnnMenu.add(applyAutoAnnotationSettings); autoAnnMenu.add(showConsensusHistogram); autoAnnMenu.add(showSequenceLogo); autoAnnMenu.add(normaliseSequenceLogo); autoAnnMenu.addSeparator(); autoAnnMenu.add(showGroupConservation); autoAnnMenu.add(showGroupConsensus); viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); // viewMenu.add(showSeqFeaturesHeight); viewMenu.add(openFeatureSettings); tooltipSettingsMenu.add(showDbRefsMenuitem); tooltipSettingsMenu.add(showNpFeatsMenuitem); viewMenu.add(tooltipSettingsMenu); viewMenu.addSeparator(); viewMenu.add(alignmentProperties); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); colourMenu.add(textColour); 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(purinePyrimidineColour); // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); colourMenu.add(rnahelicesColour); calculateMenu.add(sort); calculateMenu.add(calculateTree); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.addSeparator(); calculateMenu.add(showTranslation); calculateMenu.add(showProducts); calculateMenu.add(autoCalculate); calculateMenu.add(sortByTree); calculateMenu.addSeparator(); calculateMenu.add(extractScores); webServiceNoServices = new JMenuItem(""); webService.add(webServiceNoServices); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); sort.add(sortLengthMenuItem); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); sort.add(sortByTreeMenu); calculateTree.add(averageDistanceTreeMenuItem); calculateTree.add(neighbourTreeMenuItem); calculateTree.add(avDistanceTreeBlosumMenuItem); calculateTree.add(njTreeBlosumMenuItem); jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); addSequenceMenu.add(addFromFile); addSequenceMenu.add(addFromText); addSequenceMenu.add(addFromURL); this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); statusPanel.add(statusBar, null); this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); jMenu3.add(showAllColumns); jMenu3.add(showAllSeqs); jMenu3.add(showAllhidden); hideMenu.add(hideSelColumns); hideMenu.add(hideSelSequences); hideMenu.add(hideAllSelection); hideMenu.add(hideAllButSelection); formatMenu.add(font); formatMenu.addSeparator(); formatMenu.add(wrapMenuItem); formatMenu.add(scaleAbove); formatMenu.add(scaleLeft); formatMenu.add(scaleRight); formatMenu.add(seqLimits); formatMenu.add(idRightAlign); formatMenu.add(hiddenMarkers); formatMenu.add(viewBoxesMenuItem); formatMenu.add(viewTextMenuItem); formatMenu.add(colourTextMenuItem); formatMenu.add(renderGapsMenuItem); formatMenu.add(centreColumnLabelsMenuItem); formatMenu.add(showNonconservedMenuItem); selectMenu.add(findMenuItem); selectMenu.addSeparator(); selectMenu.add(selectAllSequenceMenuItem); selectMenu.add(deselectAllSequenceMenuItem); selectMenu.add(invertSequenceMenuItem); selectMenu.add(invertColSel); selectMenu.add(deleteGroups); selectMenu.add(grpsFromSelection); // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574 //selectMenu.addSeparator(); //selectMenu.add(listenToViewSelections); } protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void listenToViewSelections_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void showAllhidden_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void hideAllButSelection_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void hideAllSelection_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void showConsensusHistogram_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void showSequenceLogo_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void showGroupConsensus_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void showGroupConservation_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void showSeqFeaturesHeight_actionPerformed( ActionEvent actionEvent) { // TODO Auto-generated method stub } protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void followHighlight_actionPerformed() { // TODO Auto-generated method stub } protected void showNpFeats_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void showDbRefs_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub } protected void centreColumnLabels_actionPerformed(ActionEvent e) { } protected void showProducts_actionPerformed(ActionEvent e) { } protected void buildSortByAnnotationScoresMenu() { } protected void extractScores_actionPerformed(ActionEvent e) { } protected void outputText_actionPerformed(ActionEvent e) { } public void addFromFile_actionPerformed(ActionEvent e) { } public void addFromText_actionPerformed(ActionEvent e) { } public void addFromURL_actionPerformed(ActionEvent e) { } public void exportFeatures_actionPerformed(ActionEvent e) { } public void exportAnnotations_actionPerformed(ActionEvent e) { } protected void htmlMenuItem_actionPerformed(ActionEvent e) { } protected void closeMenuItem_actionPerformed(boolean b) { } 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 sortLengthMenuItem_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 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) { } protected void userDefinedColour_actionPerformed(ActionEvent e) { } protected void PIDColour_actionPerformed(ActionEvent e) { } protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { } protected void purinePyrimidineColour_actionPerformed(ActionEvent e) { } /* * protected void covariationColour_actionPerformed(ActionEvent e) { } */ protected void noColourmenuItem_actionPerformed(ActionEvent e) { } protected void conservationMenuItem_actionPerformed(ActionEvent e) { } protected void printMenuItem_actionPerformed(ActionEvent e) { } protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { } protected void findMenuItem_actionPerformed(ActionEvent e) { } protected void abovePIDThreshold_actionPerformed(ActionEvent e) { } public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) { } protected void nucleotideColour_actionPerformed(ActionEvent e) { } protected void deleteGroups_actionPerformed(ActionEvent e) { } protected void copy_actionPerformed(ActionEvent e) { } protected void cut_actionPerformed(ActionEvent e) { } protected void delete_actionPerformed(ActionEvent e) { } protected void pasteNew_actionPerformed(ActionEvent e) { } protected void pasteThis_actionPerformed(ActionEvent e) { } protected void applyToAllGroups_actionPerformed(ActionEvent e) { } public void createPNG(java.io.File f) { } protected void font_actionPerformed(ActionEvent e) { } protected void seqLimit_actionPerformed(ActionEvent e) { } public void seqDBRef_actionPerformed(ActionEvent e) { } public void createEPS(java.io.File f) { } protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { } protected void jpred_actionPerformed(ActionEvent e) { } protected void scaleAbove_actionPerformed(ActionEvent e) { } protected void scaleLeft_actionPerformed(ActionEvent e) { } protected void scaleRight_actionPerformed(ActionEvent e) { } protected void modifyPID_actionPerformed(ActionEvent e) { } protected void modifyConservation_actionPerformed(ActionEvent e) { } protected void saveAs_actionPerformed(ActionEvent e) { } protected void padGapsMenuitem_actionPerformed(ActionEvent e) { } public void vamsasStore_actionPerformed(ActionEvent e) { } public void vamsasLoad_actionPerformed(ActionEvent e) { } public void showTranslation_actionPerformed(ActionEvent e) { } public void featureSettings_actionPerformed(ActionEvent e) { } public void fetchSequence_actionPerformed(ActionEvent e) { } public void smoothFont_actionPerformed(ActionEvent e) { } public void annotationColour_actionPerformed(ActionEvent e) { } public void rnahelicesColour_actionPerformed(ActionEvent e) { } public void associatedData_actionPerformed(ActionEvent e) { } public void autoCalculate_actionPerformed(ActionEvent e) { } public void sortByTreeOption_actionPerformed(ActionEvent e) { } public void showAllSeqs_actionPerformed(ActionEvent e) { } public void showAllColumns_actionPerformed(ActionEvent e) { } public void hideSelSequences_actionPerformed(ActionEvent e) { } public void hideSelColumns_actionPerformed(ActionEvent e) { } public void hiddenMarkers_actionPerformed(ActionEvent e) { } public void findPdbId_actionPerformed(ActionEvent e) { } public void enterPdbId_actionPerformed(ActionEvent e) { } public void pdbFile_actionPerformed(ActionEvent e) { } public void invertColSel_actionPerformed(ActionEvent e) { } public void tabSelectionChanged(int sel) { } public void tabbedPane_mousePressed(MouseEvent e) { } public void tabbedPane_focusGained(FocusEvent e) { requestFocus(); } public void save_actionPerformed(ActionEvent e) { } public void reload_actionPerformed(ActionEvent e) { } public void newView_actionPerformed(ActionEvent e) { } public void textColour_actionPerformed(ActionEvent e) { } public void idRightAlign_actionPerformed(ActionEvent e) { } public void expandViews_actionPerformed(ActionEvent e) { } public void gatherViews_actionPerformed(ActionEvent e) { } public void buildTreeMenu() { } public void pageSetup_actionPerformed(ActionEvent e) { } public void alignmentProperties() { } }