X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=6253e36d4b4b434eec97d3ae53c8edb3e0f35e04;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=b7c903eb020eb97bb49be1da998e1fbe10d3cac2;hpb=10cc0aa63a3c0df54838258157485f14e30cd874;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index b7c903e..6253e36 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,1600 +1,2420 @@ -/* - * 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.jbgui; - -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; - -import jalview.schemes.*; -import java.awt.BorderLayout; - -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 sortGroupMenuItem = new JMenuItem(); - 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(); - protected JMenuItem clustalAlignMenuItem = new JMenuItem(); - BorderLayout borderLayout1 = new BorderLayout(); - public JLabel statusBar = new JLabel(); - protected JMenuItem saveAlignmentMenu = 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(); - JMenuItem njTreeBlosumMenuItem = new JMenuItem(); - JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(); - public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem colourTextMenuItem = 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(); - JMenu searchMenu = new JMenu(); - public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem(); - public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); - JMenuItem deleteGroups = new JMenuItem(); - JMenuItem delete = new JMenuItem(); - JMenuItem copy = new JMenuItem(); - JMenuItem cut = new JMenuItem(); - JMenu jMenu1 = 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(); - JMenu calculate = new JMenu(); - JMenu jMenu2 = new JMenu(); - protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); - protected ButtonGroup colours = new ButtonGroup(); - JMenuItem vamsasStore = new JMenuItem(); - protected JMenuItem showTranslation = new JMenuItem(); - public JMenuItem featureSettings = new JMenuItem(); - JMenuItem fetchSequence = new JMenuItem(); - protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem(); - JMenuItem annotationColour = new JMenuItem(); - JMenuItem associatedData = new JMenuItem(); - protected JCheckBoxMenuItem autoCalculate = 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 jMenu4 = new JMenu(); - JMenuItem hideSelSequences = new JMenuItem(); - JMenuItem hideSelColumns = new JMenuItem(); - protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); - JMenuItem invertColSel = new JMenuItem(); - - public GAlignFrame() - { - - - try - { - jbInit(); - setJMenuBar(alignFrameMenuBar); - - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++) - { - JMenuItem item = new JMenuItem( (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) - { - } - - - 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); - - 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.NONE: - noColourmenuItem.setSelected(true); - break; - 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.USER_DEFINED: - userDefinedColour.setSelected(true); - - break; - } - } - - } - - private void jbInit() - throws Exception - { - fileMenu.setMnemonic('F'); - fileMenu.setText("File"); - saveAlignmentMenu.setMnemonic('L'); - saveAlignmentMenu.setText("Save As"); - saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java. - awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false)); - saveAlignmentMenu.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - saveAlignmentMenu_actionPerformed(e); - } - }); - closeMenuItem.setMnemonic('C'); - closeMenuItem.setText("Close"); - closeMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - closeMenuItem_actionPerformed(e); - } - }); - 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.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - invertSequenceMenuItem_actionPerformed(e); - } - }); - remove2LeftMenuItem.setText("Remove Left"); - remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - remove2LeftMenuItem_actionPerformed(e); - } - }); - remove2RightMenuItem.setText("Remove Right"); - remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - remove2RightMenuItem_actionPerformed(e); - } - }); - removeGappedColumnMenuItem.setText("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(new java.awt.event. - ActionListener() - { - public void actionPerformed(ActionEvent e) - { - removeGappedColumnMenuItem_actionPerformed(e); - } - }); - removeAllGapsMenuItem.setText("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - removeAllGapsMenuItem_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); - } - }); - 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); - } - }); - sortGroupMenuItem.setText("by Group"); - sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sortGroupMenuItem_actionPerformed(e); - } - }); - removeRedundancyMenuItem.setText("Remove Redundancy..."); - 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.setMnemonic('T'); - 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); - } - }); - 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.setMnemonic('Z'); - 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.setMnemonic('0'); - redoMenuItem.setText("Redo"); - 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.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); - } - }); - searchMenu.setText("Search"); - - 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); - } - }); - nucleotideColour.setText("Nucleotide"); - nucleotideColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - nucleotideColour_actionPerformed(e); - } - }); - deleteGroups.setText("Undefine groups"); - 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.setMnemonic(KeyEvent.VK_C); - - 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.setMnemonic(KeyEvent.VK_X); - cut.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - cut_actionPerformed(e); - } - }); - delete.setText("Delete"); - delete.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - delete_actionPerformed(e); - } - }); - jMenu1.setMnemonic('V'); - jMenu1.setText("Paste"); - pasteNew.setText("To New Alignment"); - pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke( - java.awt.event.KeyEvent.VK_V, - Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false)); - pasteNew.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pasteNew_actionPerformed(e); - } - }); - pasteThis.setText("Add To This Alignment"); - pasteThis.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pasteThis_actionPerformed(e); - } - }); - applyToAllGroups.setText("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - 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); - } - }); - 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"); - calculate.setText("Calculate Tree"); - - jMenu2.setText("Export"); - 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); - } - }); - - /* tabbedPane.addChangeListener(new ChangeListener() - { - public void stateChanged(ChangeEvent ece) - { - - tabSelected(); - } - });*/ - featureSettings.setText("Feature Settings..."); - featureSettings.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); - } - }); - smoothFont.setText("Smooth Fonts"); - smoothFont.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - smoothFont_actionPerformed(e); - } - }); - smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false)); - annotationColour.setText("By Annotation..."); - annotationColour.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - annotationColour_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); - } - }); - 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.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showAllSeqs_actionPerformed(e); - } - }); - showAllColumns.setText("All Columns"); - showAllColumns.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showAllColumns_actionPerformed(e); - } - }); - jMenu4.setText("Hide"); - hideSelSequences.setText("Selected Sequences"); - hideSelSequences.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hideSelSequences_actionPerformed(e); - } - }); - hideSelColumns.setText("Selected Columns"); - hideSelColumns.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hideSelColumns_actionPerformed(e); - } - }); - hiddenMarkers.setText("Hidden Markers"); - hiddenMarkers.setState(true); - hiddenMarkers.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hiddenMarkers_actionPerformed(e); - } - }); - invertColSel.setText("Invert Column Selection"); - invertColSel.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - invertColSel_actionPerformed(e); - } - }); - - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(webService); - fileMenu.add(addSequenceMenu); - fileMenu.add(fetchSequence); - fileMenu.addSeparator(); - fileMenu.add(vamsasStore); - fileMenu.add(saveAlignmentMenu); - fileMenu.add(jMenu2); - fileMenu.add(outputTextboxMenu); - fileMenu.add(printMenuItem); - fileMenu.addSeparator(); - 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(jMenu1); - editMenu.add(delete); - editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(invertColSel); - editMenu.add(deleteGroups); - editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); - editMenu.addSeparator(); - editMenu.add(padGapsMenuitem); - searchMenu.add(findMenuItem); - viewMenu.add(font); - viewMenu.add(smoothFont); - viewMenu.addSeparator(); - viewMenu.add(jMenu3); - viewMenu.add(jMenu4); - viewMenu.add(hiddenMarkers); - viewMenu.addSeparator(); - viewMenu.add(wrapMenuItem); - viewMenu.add(seqLimits); - viewMenu.add(scaleAbove); - viewMenu.add(scaleLeft); - viewMenu.add(scaleRight); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(annotationPanelMenuItem); - viewMenu.addSeparator(); - viewMenu.add(showSeqFeatures); - viewMenu.add(featureSettings); - 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); - colourMenu.add(annotationColour); - calculateMenu.add(sort); - calculateMenu.add(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - calculateMenu.addSeparator(); - calculateMenu.add(showTranslation); - calculateMenu.add(autoCalculate); - webServiceNoServices=new JMenuItem(""); - webService.add(webServiceNoServices);jMenu1.add(pasteNew); - jMenu1.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.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); - jMenu3.add(showAllColumns); - jMenu3.add(showAllSeqs); - jMenu4.add(hideSelColumns); - jMenu4.add(hideSelSequences); - } - - 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(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 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 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 saveAlignmentMenu_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 associatedData_actionPerformed(ActionEvent e) - { - - } - - public void autoCalculate_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) - { - - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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(); + + 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(); + + protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + + 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 featureSettings = new JMenuItem(); + + JMenuItem fetchSequence = new JMenuItem(); + + JMenuItem annotationColour = 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 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); + + 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.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); + } + }); + 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); + } + + }); + 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); } }); + */ + featureSettings.setText("Feature Settings..."); + featureSettings.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); + } + }); + 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.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); + viewMenu.addSeparator(); + viewMenu.add(showSeqFeatures); + // viewMenu.add(showSeqFeaturesHeight); + + viewMenu.add(featureSettings); + 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(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + colourMenu.add(annotationColour); + 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 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 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 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() + { + + } +}