X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=dba77dd2f09eb25c6ef8daf5b1d164721735cfee;hb=933e28e48b4f3bf98851cedd99ef345d45bf25a3;hp=17893bc38cf8f2954796db161dc2ab8f8c34c158;hpb=ddfa1a02dc5c2b1fd23ff0aa84ffe9d1d5167999;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 17893bc..579da08 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -1,1725 +1,2992 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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 javax.swing.event.*; - -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(); - 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(); - 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(); - 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(); - 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(); - 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 hideMenu = new JMenu(); - JMenuItem hideSelSequences = new JMenuItem(); - JMenuItem hideSelColumns = new JMenuItem(); - protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); - JMenuItem invertColSel = new JMenuItem(); - protected JTabbedPane tabbedPane = new JTabbedPane(); - JMenuItem save = new JMenuItem(); - JMenuItem jMenuItem1 = new JMenuItem(); - protected JMenuItem reload = new JMenuItem(); - JMenuItem newView = new JMenuItem(); - JMenuItem textColour = new JMenuItem(); - JMenu jMenu1 = new JMenu(); - JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem(); - 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 (!System.getProperty("os.name").startsWith("Mac")) - { - 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.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.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()|java.awt.event.KeyEvent.SHIFT_MASK, false)); - invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - invertSequenceMenuItem_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); - } - }); - 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.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); - } - }); - 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); - } - }); - 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 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); - } - }); - - - 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); - } - }); - 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); - } - }); - hideMenu.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("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(), 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("Text Colour"); - textColour.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - textColour_actionPerformed(e); - } - }); - jMenu1.setText("Format"); - jCheckBoxMenuItem1.setText("Right Align Ids"); - - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(jMenu1); - 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(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(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(invertColSel); - editMenu.add(deleteGroups); - editMenu.addSeparator(); - editMenu.add(findMenuItem); - editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); - editMenu.addSeparator(); - editMenu.add(padGapsMenuitem); - viewMenu.add(newView); - viewMenu.addSeparator(); - viewMenu.add(jMenu3); - viewMenu.add(hideMenu); - viewMenu.addSeparator(); - viewMenu.add(annotationPanelMenuItem); - viewMenu.addSeparator(); - viewMenu.add(showSeqFeatures); - viewMenu.add(featureSettings); - 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(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - calculateMenu.addSeparator(); - calculateMenu.add(showTranslation); - calculateMenu.add(autoCalculate); - webServiceNoServices=new JMenuItem(""); - webService.add(webServiceNoServices);pasteMenu.add(pasteNew); - pasteMenu.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); - this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); - jMenu3.add(showAllColumns); - jMenu3.add(showAllSeqs); - hideMenu.add(hideSelColumns); - hideMenu.add(hideSelSequences); - jMenu1.add(font); - jMenu1.addSeparator(); - jMenu1.add(seqLimits); - jMenu1.add(wrapMenuItem); - jMenu1.add(scaleAbove); - jMenu1.add(scaleLeft); - jMenu1.add(scaleRight); - jMenu1.add(hiddenMarkers); - jMenu1.add(viewBoxesMenuItem); - jMenu1.add(viewTextMenuItem); - jMenu1.add(colourTextMenuItem); - jMenu1.add(renderGapsMenuItem); - } - - 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 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 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) - { - - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.jbgui; + +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.analysis.GeneticCodeI; +import jalview.analysis.GeneticCodes; +import jalview.api.SplitContainerI; +import jalview.bin.Cache; +import jalview.gui.JvSwingUtils; +import jalview.gui.Preferences; +import jalview.hmmer.HmmerCommand; +import jalview.io.FileFormatException; +import jalview.io.FileFormats; +import jalview.schemes.ResidueColourScheme; +import jalview.util.MessageManager; +import jalview.util.Platform; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.GridLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + +import javax.swing.BorderFactory; +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JMenu; +import javax.swing.JMenuBar; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JTabbedPane; +import javax.swing.KeyStroke; +import javax.swing.event.ChangeEvent; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; + +public class GAlignFrame extends JInternalFrame +{ + protected JMenuBar alignFrameMenuBar = new JMenuBar(); + + protected JMenuItem closeMenuItem = new JMenuItem(); + + protected JMenu webService = new JMenu(); + + protected JMenu hmmerMenu = new JMenu(); + + protected JMenuItem webServiceNoServices; + + protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); + + protected JMenu sortByAnnotScore = new JMenu(); + + protected JLabel statusBar = new JLabel(); + + protected JMenu outputTextboxMenu = new JMenu(); + + protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); + + protected JMenuItem undoMenuItem = new JMenuItem(); + + protected JMenuItem redoMenuItem = new JMenuItem(); + + protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); + + public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); + + JMenuItem copy = new JMenuItem(); + + JMenuItem cut = new JMenuItem(); + + JMenu pasteMenu = new JMenu(); + + protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem applyToAllGroups; + + protected JMenu colourMenu = new JMenu(); + + protected JMenuItem textColour; + + protected JCheckBoxMenuItem conservationMenuItem; + + protected JMenuItem modifyConservation; + + protected JCheckBoxMenuItem abovePIDThreshold; + + protected JMenuItem modifyPID; + + protected JRadioButtonMenuItem annotationColour; + + protected JMenu sortByTreeMenu = new JMenu(); + + protected JMenu sort = new JMenu(); + + protected JMenuItem calculateTree = new JMenuItem(); + + protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); + + protected JMenu showTranslation = new JMenu(); + + protected JMenuItem showReverse = new JMenuItem(); + + protected JMenuItem showReverseComplement = new JMenuItem(); + + protected JMenu showProducts = new JMenu(); + + protected JMenuItem runGroovy = new JMenuItem(); + + protected JMenuItem loadVcf; + + protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem(); + + protected JPanel statusPanel = new JPanel(); + + protected JMenuItem showAllSeqAnnotations = new JMenuItem(); + + protected JMenuItem hideAllSeqAnnotations = new JMenuItem(); + + protected JMenuItem showAllAlAnnotations = new JMenuItem(); + + protected JMenuItem hideAllAlAnnotations = new JMenuItem(); + + protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); + + protected JTabbedPane tabbedPane = new JTabbedPane(); + + protected JMenuItem reload = new JMenuItem(); + + protected JMenu formatMenu = 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(); + + protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); + + private SequenceAnnotationOrder annotationSortOrder; + + private boolean showAutoCalculatedAbove = false; + + private Map accelerators = new HashMap<>(); + + private SplitContainerI splitFrame; + + public GAlignFrame() + { + try + { + jbInit(); + setJMenuBar(alignFrameMenuBar); + + // dynamically fill save as menu with available formats + for (String ff : FileFormats.getInstance().getWritableFormats(true)) + { + JMenuItem item = new JMenuItem(ff); + + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + } catch (Exception e) + { + System.err.println(e.toString()); + } + + if (!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'); + } + } + + private void jbInit() throws Exception + { + initColourMenu(); + + JMenuItem saveAs = new JMenuItem( + MessageManager.getString("action.save_as")); + ActionListener al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + saveAs_actionPerformed(e); + } + }; + + // FIXME getDefaultToolkit throws an exception in Headless mode + KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); + addMenuActionAndAccelerator(keyStroke, saveAs, al); + + closeMenuItem.setText(MessageManager.getString("action.close")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + closeMenuItem_actionPerformed(false); + } + }; + addMenuActionAndAccelerator(keyStroke, closeMenuItem, al); + + JMenu editMenu = new JMenu(MessageManager.getString("action.edit")); + JMenu viewMenu = new JMenu(MessageManager.getString("action.view")); + JMenu annotationsMenu = new JMenu( + MessageManager.getString("action.annotations")); + JMenu showMenu = new JMenu(MessageManager.getString("action.show")); + colourMenu.setText(MessageManager.getString("action.colour")); + JMenu calculateMenu = new JMenu( + MessageManager.getString("action.calculate")); + webService.setText(MessageManager.getString("action.web_service")); + + initHMMERMenu(); + + JMenuItem selectAllSequenceMenuItem = new JMenuItem( + MessageManager.getString("action.select_all")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + selectAllSequenceMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al); + + JMenuItem deselectAllSequenceMenuItem = new JMenuItem( + MessageManager.getString("action.deselect_all")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + deselectAllSequenceMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al); + + JMenuItem invertSequenceMenuItem = new JMenuItem( + MessageManager.getString("action.invert_sequence_selection")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + invertSequenceMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al); + + JMenuItem grpsFromSelection = new JMenuItem( + MessageManager.getString("action.make_groups_selection")); + grpsFromSelection.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + makeGrpsFromSelection_actionPerformed(e); + } + }); + JMenuItem expandAlignment = new JMenuItem( + MessageManager.getString("action.view_flanking_regions")); + expandAlignment.setToolTipText( + MessageManager.getString("label.view_flanking_regions")); + expandAlignment.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + expand_newalign(e); + } + }); + JMenuItem remove2LeftMenuItem = new JMenuItem( + MessageManager.getString("action.remove_left")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + remove2LeftMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al); + + JMenuItem remove2RightMenuItem = new JMenuItem( + MessageManager.getString("action.remove_right")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + remove2RightMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al); + + JMenuItem removeGappedColumnMenuItem = new JMenuItem( + MessageManager.getString("action.remove_empty_columns")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + removeGappedColumnMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al); + + JMenuItem removeAllGapsMenuItem = new JMenuItem( + MessageManager.getString("action.remove_all_gaps")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + removeAllGapsMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al); + + JMenuItem justifyLeftMenuItem = new JMenuItem( + MessageManager.getString("action.left_justify_alignment")); + justifyLeftMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + justifyLeftMenuItem_actionPerformed(e); + } + }); + JMenuItem justifyRightMenuItem = new JMenuItem( + MessageManager.getString("action.right_justify_alignment")); + justifyRightMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + justifyRightMenuItem_actionPerformed(e); + } + }); + viewBoxesMenuItem.setText(MessageManager.getString("action.boxes")); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + viewBoxesMenuItem_actionPerformed(e); + } + }); + viewTextMenuItem.setText(MessageManager.getString("action.text")); + viewTextMenuItem.setState(true); + viewTextMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + viewTextMenuItem_actionPerformed(e); + } + }); + showNonconservedMenuItem + .setText(MessageManager.getString("label.show_non_conserved")); + showNonconservedMenuItem.setState(false); + showNonconservedMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showUnconservedMenuItem_actionPerformed(e); + } + }); + JMenuItem sortPairwiseMenuItem = new JMenuItem( + MessageManager.getString("action.by_pairwise_id")); + sortPairwiseMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortPairwiseMenuItem_actionPerformed(e); + } + }); + JMenuItem sortIDMenuItem = new JMenuItem( + MessageManager.getString("action.by_id")); + sortIDMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortIDMenuItem_actionPerformed(e); + } + }); + JMenuItem sortLengthMenuItem = new JMenuItem( + MessageManager.getString("action.by_length")); + sortLengthMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortLengthMenuItem_actionPerformed(e); + } + }); + JMenuItem sortGroupMenuItem = new JMenuItem( + MessageManager.getString("action.by_group")); + sortGroupMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortGroupMenuItem_actionPerformed(e); + } + }); + JMenuItem sortEValueMenuItem = new JMenuItem( + MessageManager.getString("action.by_evalue")); + sortEValueMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortEValueMenuItem_actionPerformed(e); + } + }); + JMenuItem sortBitScoreMenuItem = new JMenuItem( + MessageManager.getString("action.by_bit_score")); + sortBitScoreMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortBitScoreMenuItem_actionPerformed(e); + } + }); + + JMenuItem removeRedundancyMenuItem = new JMenuItem( + MessageManager.getString("action.remove_redundancy")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + removeRedundancyMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); + + JMenuItem filterByEValue = new JMenuItem( + MessageManager.getString("action.filter_by_evalue")); + filterByEValue.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filterByEValue_actionPerformed(); + } + + }); + + JMenuItem filterByScore = new JMenuItem( + MessageManager.getString("action.filter_by_score")); + filterByScore.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filterByScore_actionPerformed(); + } + + }); + + JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( + MessageManager.getString("action.pairwise_alignment")); + pairwiseAlignmentMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + pairwiseAlignmentMenuItem_actionPerformed(e); + } + }); + + this.getContentPane().setLayout(new BorderLayout()); + 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(MessageManager.getString("label.status_bar")); + + outputTextboxMenu + .setText(MessageManager.getString("label.out_to_textbox")); + + + annotationPanelMenuItem.setActionCommand(""); + annotationPanelMenuItem + .setText(MessageManager.getString("label.show_annotations")); + annotationPanelMenuItem + .setState(Cache.getDefault("SHOW_ANNOTATIONS", true)); + annotationPanelMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + annotationPanelMenuItem_actionPerformed(e); + } + }); + showAllAlAnnotations.setText( + MessageManager.getString("label.show_all_al_annotations")); + final boolean isAnnotationPanelShown = annotationPanelMenuItem + .getState(); + showAllAlAnnotations.setEnabled(isAnnotationPanelShown); + showAllAlAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showAllAnnotations_actionPerformed(false, true); + } + }); + hideAllAlAnnotations.setText( + MessageManager.getString("label.hide_all_al_annotations")); + hideAllAlAnnotations.setEnabled(isAnnotationPanelShown); + hideAllAlAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideAllAnnotations_actionPerformed(false, true); + } + }); + showAllSeqAnnotations.setText( + MessageManager.getString("label.show_all_seq_annotations")); + showAllSeqAnnotations.setEnabled(isAnnotationPanelShown); + showAllSeqAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showAllAnnotations_actionPerformed(true, false); + } + }); + hideAllSeqAnnotations.setText( + MessageManager.getString("label.hide_all_seq_annotations")); + hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown); + hideAllSeqAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideAllAnnotations_actionPerformed(true, false); + } + }); + SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder + .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem( + MessageManager.getString("label.sort_annotations_by_sequence")); + final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem( + MessageManager.getString("label.sort_annotations_by_label")); + + + sortAnnBySequence.setSelected( + sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); + sortAnnBySequence.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + boolean newState = sortAnnBySequence.getState(); + sortAnnByLabel.setSelected(false); + setAnnotationSortOrder( + newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL + : SequenceAnnotationOrder.NONE); + sortAnnotations_actionPerformed(); + } + }); + sortAnnByLabel.setSelected( + sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + sortAnnByLabel.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + boolean newState = sortAnnByLabel.getState(); + sortAnnBySequence.setSelected(false); + setAnnotationSortOrder( + newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE + : SequenceAnnotationOrder.NONE); + sortAnnotations_actionPerformed(); + } + }); + colourTextMenuItem = new JCheckBoxMenuItem( + MessageManager.getString("label.colour_text")); + colourTextMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + colourTextMenuItem_actionPerformed(e); + } + }); + + JMenuItem htmlMenuItem = new JMenuItem( + MessageManager.getString("label.html")); + htmlMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + htmlMenuItem_actionPerformed(e); + } + }); + + JMenuItem createBioJS = new JMenuItem( + MessageManager.getString("label.biojs_html_export")); + createBioJS.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + bioJSMenuItem_actionPerformed(e); + } + }); + + JMenuItem overviewMenuItem = new JMenuItem( + MessageManager.getString("label.overview_window")); + overviewMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + overviewMenuItem_actionPerformed(e); + } + }); + + undoMenuItem.setEnabled(false); + undoMenuItem.setText(MessageManager.getString("action.undo")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + undoMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, undoMenuItem, al); + + redoMenuItem.setEnabled(false); + redoMenuItem.setText(MessageManager.getString("action.redo")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + redoMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); + + wrapMenuItem.setText(MessageManager.getString("label.wrap")); + wrapMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + wrapMenuItem_actionPerformed(e); + } + }); + + JMenuItem printMenuItem = new JMenuItem( + MessageManager.getString("action.print")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + printMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, printMenuItem, al); + + renderGapsMenuItem + .setText(MessageManager.getString("action.show_gaps")); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + renderGapsMenuItem_actionPerformed(e); + } + }); + + JMenuItem findMenuItem = new JMenuItem( + MessageManager.getString("action.find")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.find_tip"))); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + findMenuItem_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, findMenuItem, al); + + showSeqFeatures.setText( + MessageManager.getString("label.show_sequence_features")); + + showSeqFeatures.addActionListener(new ActionListener() + { + @Override + 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(MessageManager.getString("label.show_database_refs")); + showDbRefsMenuitem.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + showDbRefs_actionPerformed(e); + } + + }); + showNpFeatsMenuitem.setText( + MessageManager.getString("label.show_non_positional_features")); + showNpFeatsMenuitem.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + showNpFeats_actionPerformed(e); + } + + }); + showGroupConservation + .setText(MessageManager.getString("label.group_conservation")); + showGroupConservation.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + showGroupConservation_actionPerformed(e); + } + + }); + + showGroupConsensus + .setText(MessageManager.getString("label.group_consensus")); + showGroupConsensus.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + showGroupConsensus_actionPerformed(e); + } + + }); + showConsensusHistogram.setText( + MessageManager.getString("label.show_consensus_histogram")); + showConsensusHistogram.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + showConsensusHistogram_actionPerformed(e); + } + + }); + showSequenceLogo + .setText(MessageManager.getString("label.show_consensus_logo")); + showSequenceLogo.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + showSequenceLogo_actionPerformed(e); + } + + }); + normaliseSequenceLogo + .setText(MessageManager.getString("label.norm_consensus_logo")); + normaliseSequenceLogo.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + normaliseSequenceLogo_actionPerformed(e); + } + + }); + applyAutoAnnotationSettings + .setText(MessageManager.getString("label.apply_all_groups")); + applyAutoAnnotationSettings.setState(false); + applyAutoAnnotationSettings.setVisible(true); + applyAutoAnnotationSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + applyAutoAnnotationSettings_actionPerformed(e); + } + }); + + ButtonGroup buttonGroup = new ButtonGroup(); + final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem( + MessageManager.getString("label.show_first")); + final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem( + MessageManager.getString("label.show_last")); + buttonGroup.add(showAutoFirst); + buttonGroup.add(showAutoLast); + final boolean autoFirst = Cache + .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); + showAutoFirst.setSelected(autoFirst); + setShowAutoCalculatedAbove(autoFirst); + showAutoFirst.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + setShowAutoCalculatedAbove(showAutoFirst.isSelected()); + sortAnnotations_actionPerformed(); + } + }); + showAutoLast.setSelected(!showAutoFirst.isSelected()); + showAutoLast.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + setShowAutoCalculatedAbove(!showAutoLast.isSelected()); + sortAnnotations_actionPerformed(); + } + }); + + JMenuItem deleteGroups = new JMenuItem( + MessageManager.getString("action.undefine_groups")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + deleteGroups_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, deleteGroups, al); + + JMenuItem annotationColumn = new JMenuItem( + MessageManager.getString("action.select_by_annotation")); + annotationColumn.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + annotationColumn_actionPerformed(e); + } + }); + + JMenuItem createGroup = new JMenuItem( + MessageManager.getString("action.create_group")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createGroup_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, createGroup, al); + + JMenuItem unGroup = new JMenuItem( + MessageManager.getString("action.remove_group")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + unGroup_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, unGroup, al); + + copy.setText(MessageManager.getString("action.copy")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, copy, al); + + cut.setText(MessageManager.getString("action.cut")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + cut_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, cut, al); + + JMenuItem delete = new JMenuItem( + MessageManager.getString("action.delete")); + delete.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + delete_actionPerformed(e); + } + }); + + pasteMenu.setText(MessageManager.getString("action.paste")); + JMenuItem pasteNew = new JMenuItem( + MessageManager.getString("label.to_new_alignment")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, + false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + pasteNew_actionPerformed(e); + } catch (IOException | InterruptedException e1) + { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + } + }; + addMenuActionAndAccelerator(keyStroke, pasteNew, al); + + JMenuItem pasteThis = new JMenuItem( + MessageManager.getString("label.to_this_alignment")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + pasteThis_actionPerformed(e); + } catch (IOException | InterruptedException e1) + { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + } + }; + addMenuActionAndAccelerator(keyStroke, pasteThis, al); + + JMenuItem createPNG = new JMenuItem("PNG"); + createPNG.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createPNG(null); + } + }); + createPNG.setActionCommand( + MessageManager.getString("label.save_png_image")); + JMenuItem font = new JMenuItem(MessageManager.getString("action.font")); + font.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + font_actionPerformed(e); + } + }); + seqLimits.setText( + MessageManager.getString("label.show_sequence_limits")); + seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); + seqLimits.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + seqLimit_actionPerformed(e); + } + }); + JMenuItem epsFile = new JMenuItem("EPS"); + epsFile.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createEPS(null); + } + }); + + JMenuItem createSVG = new JMenuItem("SVG"); + createSVG.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createSVG(null); + } + }); + + JMenuItem loadTreeMenuItem = new JMenuItem( + MessageManager.getString("label.load_associated_tree")); + loadTreeMenuItem.setActionCommand( + MessageManager.getString("label.load_tree_for_sequence_set")); + loadTreeMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + loadTreeMenuItem_actionPerformed(e); + } + }); + + scaleAbove.setVisible(false); + scaleAbove.setText(MessageManager.getString("action.scale_above")); + scaleAbove.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + scaleAbove_actionPerformed(e); + } + }); + scaleLeft.setVisible(false); + scaleLeft.setSelected(true); + scaleLeft.setText(MessageManager.getString("action.scale_left")); + scaleLeft.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + scaleLeft_actionPerformed(e); + } + }); + scaleRight.setVisible(false); + scaleRight.setSelected(true); + scaleRight.setText(MessageManager.getString("action.scale_right")); + scaleRight.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + scaleRight_actionPerformed(e); + } + }); + centreColumnLabelsMenuItem.setVisible(true); + centreColumnLabelsMenuItem.setState(false); + centreColumnLabelsMenuItem.setText( + MessageManager.getString("label.centre_column_labels")); + centreColumnLabelsMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + centreColumnLabels_actionPerformed(e); + } + }); + followHighlightMenuItem.setVisible(true); + followHighlightMenuItem.setState(true); + followHighlightMenuItem + .setText(MessageManager.getString("label.automatic_scrolling")); + followHighlightMenuItem.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + followHighlight_actionPerformed(); + } + + }); + + sortByTreeMenu + .setText(MessageManager.getString("action.by_tree_order")); + sort.setText(MessageManager.getString("action.sort")); + sort.addMenuListener(new MenuListener() + { + @Override + public void menuSelected(MenuEvent e) + { + buildTreeSortMenu(); + } + + @Override + public void menuDeselected(MenuEvent e) + { + } + + @Override + public void menuCanceled(MenuEvent e) + { + } + }); + sortByAnnotScore + .setText(MessageManager.getString("label.sort_by_score")); + sort.add(sortByAnnotScore); + sort.addMenuListener(new javax.swing.event.MenuListener() + { + + @Override + public void menuCanceled(MenuEvent e) + { + } + + @Override + public void menuDeselected(MenuEvent e) + { + } + + @Override + public void menuSelected(MenuEvent e) + { + buildSortByAnnotationScoresMenu(); + } + }); + sortByAnnotScore.setVisible(false); + + calculateTree + .setText(MessageManager.getString("action.calculate_tree_pca")); + + padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); + padGapsMenuitem + .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false)); + padGapsMenuitem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + padGapsMenuitem_actionPerformed(e); + } + }); + JMenuItem vamsasStore = new JMenuItem( + MessageManager.getString("label.vamsas_store")); + vamsasStore.setVisible(false); + vamsasStore.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + vamsasStore_actionPerformed(e); + } + }); + + /* + * Translate as cDNA with sub-menu of translation tables + */ + showTranslation.setText(MessageManager + .getString("label.translate_cDNA")); + boolean first = true; + for (final GeneticCodeI table : GeneticCodes.getInstance() + .getCodeTables()) + { + JMenuItem item = new JMenuItem(table.getId() + " " + table.getName()); + showTranslation.add(item); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showTranslation_actionPerformed(table); + } + }); + if (first) + { + showTranslation.addSeparator(); + } + first = false; + } + + showReverse.setText(MessageManager.getString("label.reverse")); + showReverse.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showReverse_actionPerformed(false); + } + }); + showReverseComplement + .setText(MessageManager.getString("label.reverse_complement")); + showReverseComplement.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showReverse_actionPerformed(true); + } + }); + + JMenuItem extractScores = new JMenuItem( + MessageManager.getString("label.extract_scores")); + extractScores.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + extractScores_actionPerformed(e); + } + }); + extractScores.setVisible(true); + // JBPNote: TODO: make gui for regex based score extraction + + // for show products actions see AlignFrame.canShowProducts + showProducts.setText(MessageManager.getString("label.get_cross_refs")); + + runGroovy.setText(MessageManager.getString("label.run_groovy")); + runGroovy.setToolTipText( + MessageManager.getString("label.run_groovy_tip")); + runGroovy.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + runGroovy_actionPerformed(); + } + }); + + JMenuItem openFeatureSettings = new JMenuItem( + MessageManager.getString("action.feature_settings")); + openFeatureSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + featureSettings_actionPerformed(e); + } + }); + JMenuItem fetchSequence = new JMenuItem( + MessageManager.getString("label.fetch_sequences")); + fetchSequence.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + fetchSequence_actionPerformed(e); + } + }); + + JMenuItem associatedData = new JMenuItem( + MessageManager.getString("label.load_features_annotations")); + associatedData.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + associatedData_actionPerformed(e); + } catch (IOException | InterruptedException e1) + { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + } + }); + loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file")); + loadVcf.setToolTipText(MessageManager.getString("label.load_vcf")); + loadVcf.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + loadVcf_actionPerformed(); + } + }); + autoCalculate.setText( + MessageManager.getString("label.autocalculate_consensus")); + autoCalculate.setState( + jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); + autoCalculate.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + autoCalculate_actionPerformed(e); + } + }); + sortByTree.setText( + MessageManager.getString("label.sort_alignment_new_tree")); + sortByTree.setToolTipText("" + MessageManager.getString( + "label.enable_automatically_sort_alignment_when_open_new_tree")); + sortByTree + .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false)); + sortByTree.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sortByTreeOption_actionPerformed(e); + } + }); + + listenToViewSelections.setText( + MessageManager.getString("label.listen_for_selections")); + listenToViewSelections + .setToolTipText("" + MessageManager.getString( + "label.selections_mirror_selections_made_same_sequences_other_views")); + listenToViewSelections.setState(false); + listenToViewSelections.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + listenToViewSelections_actionPerformed(e); + } + }); + + JMenu addSequenceMenu = new JMenu( + MessageManager.getString("label.add_sequences")); + JMenuItem addFromFile = new JMenuItem( + MessageManager.getString("label.from_file")); + addFromFile.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + addFromFile_actionPerformed(e); + } + }); + JMenuItem addFromText = new JMenuItem( + MessageManager.getString("label.from_textbox")); + addFromText.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + addFromText_actionPerformed(e); + } + }); + JMenuItem addFromURL = new JMenuItem( + MessageManager.getString("label.from_url")); + addFromURL.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + addFromURL_actionPerformed(e); + } + }); + JMenuItem exportFeatures = new JMenuItem( + MessageManager.getString("label.export_features")); + exportFeatures.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + exportFeatures_actionPerformed(e); + } + }); + JMenuItem exportAnnotations = new JMenuItem( + MessageManager.getString("label.export_annotations")); + exportAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + exportAnnotations_actionPerformed(e); + } + }); + statusPanel.setLayout(new GridLayout()); + JMenuItem showAllSeqs = new JMenuItem( + MessageManager.getString("label.all_sequences")); + showAllSeqs.setToolTipText( + MessageManager.getString("label.toggle_sequence_visibility")); + showAllSeqs.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showAllSeqs_actionPerformed(e); + } + }); + JMenuItem showAllColumns = new JMenuItem( + MessageManager.getString("label.all_columns")); + showAllColumns.setToolTipText( + MessageManager.getString("label.toggle_columns_visibility")); + showAllColumns.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showAllColumns_actionPerformed(e); + } + }); + JMenu hideMenu = new JMenu(MessageManager.getString("action.hide")); + JMenuItem hideSelSequences = new JMenuItem( + MessageManager.getString("label.selected_sequences")); + hideSelSequences.setToolTipText( + MessageManager.getString("label.toggle_sequence_visibility")); + hideSelSequences.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideSelSequences_actionPerformed(e); + } + }); + JMenuItem hideSelColumns = new JMenuItem( + MessageManager.getString("label.selected_columns")); + hideSelColumns.setToolTipText( + MessageManager.getString("label.toggle_columns_visibility")); + hideSelColumns.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideSelColumns_actionPerformed(e); + } + }); + JMenuItem hideAllSelection = new JMenuItem( + MessageManager.getString("label.selected_region")); + hideAllSelection.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideAllSelection_actionPerformed(e); + } + }); + // TODO: should be hidden if no selection exists. + JMenuItem hideAllButSelection = new JMenuItem( + MessageManager.getString("label.all_but_selected_region")); + hideAllButSelection.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideAllButSelection_actionPerformed(e); + } + }); + JMenuItem showAllhidden = new JMenuItem( + MessageManager.getString("label.all_sequences_columns")); + showAllhidden.setToolTipText(MessageManager + .getString("label.toggles_visibility_hidden_selected_regions")); + showAllhidden.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showAllhidden_actionPerformed(e); + } + }); + hiddenMarkers.setText( + MessageManager.getString("action.show_hidden_markers")); + hiddenMarkers.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hiddenMarkers_actionPerformed(e); + } + }); + + JMenuItem invertColSel = new JMenuItem( + MessageManager.getString("action.invert_column_selection")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() + | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK, + false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + invertColSel_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, invertColSel, al); + + showComplementMenuItem.setVisible(false); + showComplementMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showComplement_actionPerformed(showComplementMenuItem.getState()); + } + }); + + tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() + { + @Override + public void stateChanged(ChangeEvent evt) + { + JTabbedPane pane = (JTabbedPane) evt.getSource(); + int sel = pane.getSelectedIndex(); + tabSelectionChanged(sel); + } + }); + tabbedPane.addMouseListener(new MouseAdapter() + { + @Override + public void mousePressed(MouseEvent e) + { + if (e.isPopupTrigger()) // Mac + { + tabbedPane_mousePressed(e); + } + } + + @Override + public void mouseReleased(MouseEvent e) + { + if (e.isPopupTrigger()) // Windows + { + tabbedPane_mousePressed(e); + } + } + }); + tabbedPane.addFocusListener(new FocusAdapter() + { + @Override + public void focusGained(FocusEvent e) + { + tabbedPane_focusGained(e); + } + }); + + JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + save_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, save, al); + + reload.setEnabled(false); + reload.setText(MessageManager.getString("action.reload")); + reload.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + reload_actionPerformed(e); + } + }); + + JMenuItem newView = new JMenuItem( + MessageManager.getString("action.new_view")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, + jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + newView_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, newView, al); + + tabbedPane.setToolTipText("" + + MessageManager.getString("label.rename_tab_eXpand_reGroup") + + ""); + + formatMenu.setText(MessageManager.getString("action.format")); + JMenu selectMenu = new JMenu(MessageManager.getString("action.select")); + + idRightAlign.setText( + MessageManager.getString("label.right_align_sequence_id")); + idRightAlign.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + idRightAlign_actionPerformed(e); + } + }); + + gatherViews.setEnabled(false); + gatherViews.setText(MessageManager.getString("action.gather_views")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + gatherViews_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, gatherViews, al); + + expandViews.setEnabled(false); + expandViews.setText(MessageManager.getString("action.expand_views")); + keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + expandViews_actionPerformed(e); + } + }; + addMenuActionAndAccelerator(keyStroke, expandViews, al); + + JMenuItem pageSetup = new JMenuItem( + MessageManager.getString("action.page_setup")); + pageSetup.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + pageSetup_actionPerformed(e); + } + }); + JMenuItem alignmentProperties = new JMenuItem( + MessageManager.getString("label.alignment_props")); + alignmentProperties.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + alignmentProperties(); + } + }); + JMenuItem selectHighlighted = new JMenuItem( + MessageManager.getString("action.select_highlighted_columns")); + selectHighlighted.setToolTipText( + MessageManager.getString("tooltip.select_highlighted_columns")); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + selectHighlightedColumns_actionPerformed(actionEvent); + } + }; + JMenuItem Filter = new JMenuItem( + MessageManager.getString("action.select_highlighted_columns")); + selectHighlighted.setToolTipText( + MessageManager.getString("tooltip.select_highlighted_columns")); + al = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + selectHighlightedColumns_actionPerformed(actionEvent); + } + }; + selectHighlighted.addActionListener(al); + JMenu tooltipSettingsMenu = new JMenu( + MessageManager.getString("label.sequence_id_tooltip")); + JMenu autoAnnMenu = new JMenu( + MessageManager.getString("label.autocalculated_annotation")); + + JMenu exportImageMenu = new JMenu( + MessageManager.getString("label.export_image")); + JMenu fileMenu = new JMenu(MessageManager.getString("action.file")); + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(selectMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(annotationsMenu); + alignFrameMenuBar.add(formatMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(webService); + alignFrameMenuBar.add(hmmerMenu); + + 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(exportImageMenu); + fileMenu.add(exportFeatures); + fileMenu.add(exportAnnotations); + fileMenu.add(loadTreeMenuItem); + fileMenu.add(associatedData); + fileMenu.add(loadVcf); + fileMenu.addSeparator(); + fileMenu.add(closeMenuItem); + + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + 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); + editMenu.addSeparator(); + editMenu.add(filterByEValue); + editMenu.add(filterByScore); + + showMenu.add(showAllColumns); + showMenu.add(showAllSeqs); + showMenu.add(showAllhidden); + hideMenu.add(hideSelColumns); + hideMenu.add(hideSelSequences); + hideMenu.add(hideAllSelection); + hideMenu.add(hideAllButSelection); + viewMenu.add(newView); + viewMenu.add(expandViews); + viewMenu.add(gatherViews); + viewMenu.addSeparator(); + viewMenu.add(showMenu); + viewMenu.add(hideMenu); + viewMenu.add(showComplementMenuItem); + viewMenu.addSeparator(); + viewMenu.add(followHighlightMenuItem); + viewMenu.addSeparator(); + viewMenu.add(showSeqFeatures); + // viewMenu.add(showSeqFeaturesHeight); + viewMenu.add(openFeatureSettings); + tooltipSettingsMenu.add(showDbRefsMenuitem); + tooltipSettingsMenu.add(showNpFeatsMenuitem); + viewMenu.add(tooltipSettingsMenu); + viewMenu.addSeparator(); + viewMenu.add(alignmentProperties); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + + annotationsMenu.add(annotationPanelMenuItem); + annotationsMenu.addSeparator(); + annotationsMenu.add(showAllAlAnnotations); + annotationsMenu.add(hideAllAlAnnotations); + annotationsMenu.addSeparator(); + annotationsMenu.add(showAllSeqAnnotations); + annotationsMenu.add(hideAllSeqAnnotations); + annotationsMenu.add(sortAnnBySequence); + annotationsMenu.add(sortAnnByLabel); + annotationsMenu.addSeparator(); + autoAnnMenu.add(showAutoFirst); + autoAnnMenu.add(showAutoLast); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.add(normaliseSequenceLogo); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + annotationsMenu.add(autoAnnMenu); + + sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + sort.add(sortEValueMenuItem); + sort.add(sortBitScoreMenuItem); + sort.add(sortByTreeMenu); + calculateMenu.add(sort); + calculateMenu.add(calculateTree); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.addSeparator(); + calculateMenu.add(showTranslation); + calculateMenu.add(showReverse); + calculateMenu.add(showReverseComplement); + calculateMenu.add(showProducts); + calculateMenu.add(autoCalculate); + calculateMenu.add(sortByTree); + calculateMenu.addSeparator(); + calculateMenu.add(expandAlignment); + calculateMenu.add(extractScores); + calculateMenu.addSeparator(); + calculateMenu.add(runGroovy); + + webServiceNoServices = new JMenuItem( + MessageManager.getString("label.no_services")); + webService.add(webServiceNoServices); + exportImageMenu.add(htmlMenuItem); + exportImageMenu.add(epsFile); + exportImageMenu.add(createPNG); + exportImageMenu.add(createBioJS); + exportImageMenu.add(createSVG); + 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); + + 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(createGroup); + selectMenu.add(unGroup); + selectMenu.add(grpsFromSelection); + selectMenu.add(deleteGroups); + selectMenu.add(annotationColumn); + selectMenu.add(selectHighlighted); + // TODO - determine if the listenToViewSelections button is needed : see bug + // JAL-574 + // selectMenu.addSeparator(); + // selectMenu.add(listenToViewSelections); + } + + /** + * Constructs the entries on the HMMER menu + */ + protected void initHMMERMenu() + { + /* + * hmmbuild + */ + JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild")); + JMenuItem hmmBuildSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + hmmBuildSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmBuild_actionPerformed(false); + } + }); + JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmbuild")); + hmmBuildRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmBuild_actionPerformed(true); + } + }); + hmmBuild.add(hmmBuildRun); + hmmBuild.add(hmmBuildSettings); + + /* + * hmmalign + */ + JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign")); + JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmalign")); + hmmAlignRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmAlign_actionPerformed(true); + } + }); + JMenuItem hmmAlignSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + hmmAlignSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmAlign_actionPerformed(false); + } + }); + hmmAlign.add(hmmAlignRun); + hmmAlign.add(hmmAlignSettings); + + /* + * hmmsearch + */ + JMenu hmmSearch = new JMenu( + MessageManager.getString("label.hmmsearch")); + JMenuItem hmmSearchSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + hmmSearchSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmSearch_actionPerformed(false); + } + }); + JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "hmmsearch")); + hmmSearchRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hmmSearch_actionPerformed(true); + } + }); + JMenuItem addDatabase = new JMenuItem( + MessageManager.getString("label.add_database")); + addDatabase.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + addDatabase_actionPerformed(); + } catch (IOException e1) + { + e1.printStackTrace(); + } + } + }); + hmmSearch.add(hmmSearchRun); + hmmSearch.add(hmmSearchSettings); + // hmmSearch.add(addDatabase); + + /* + * jackhmmer + */ + JMenu jackhmmer = new JMenu( + MessageManager.getString("label.jackhmmer")); + JMenuItem jackhmmerSettings = new JMenuItem( + MessageManager.getString("label.edit_settings_and_run")); + jackhmmerSettings.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + jackhmmer_actionPerformed(false); + } + }); + JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage( + "label.action_with_default_settings", "jackhmmer")); + jackhmmerRun.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + jackhmmer_actionPerformed(true); + } + + }); + /* + JMenuItem addDatabase = new JMenuItem( + MessageManager.getString("label.add_database")); + addDatabase.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + addDatabase_actionPerformed(); + } catch (IOException e1) + { + e1.printStackTrace(); + } + } + }); + */ + jackhmmer.add(jackhmmerRun); + jackhmmer.add(jackhmmerSettings); + // hmmSearch.add(addDatabase); + + /* + * top level menu + */ + hmmerMenu.setText(MessageManager.getString("action.hmmer")); + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + hmmerMenu.add(hmmBuild); + hmmerMenu.add(hmmAlign); + hmmerMenu.add(hmmSearch); + hmmerMenu.add(jackhmmer); + + } + + protected void loadVcf_actionPerformed() + { + } + + /** + * Constructs the entries on the Colour menu (but does not add them to the + * menu). + */ + protected void initColourMenu() + { + applyToAllGroups = new JCheckBoxMenuItem( + MessageManager.getString("label.apply_colour_to_all_groups")); + applyToAllGroups.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); + } + }); + + textColour = new JMenuItem( + MessageManager.getString("label.text_colour")); + textColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(); + } + }); + + conservationMenuItem = new JCheckBoxMenuItem( + MessageManager.getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed( + conservationMenuItem.isSelected()); + } + }); + + abovePIDThreshold = new JCheckBoxMenuItem( + MessageManager.getString("label.above_identity_threshold")); + abovePIDThreshold.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); + } + }); + modifyPID = new JMenuItem( + MessageManager.getString("label.modify_identity_threshold")); + modifyPID.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + modifyPID_actionPerformed(); + } + }); + modifyConservation = new JMenuItem(MessageManager + .getString("label.modify_conservation_threshold")); + modifyConservation.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + modifyConservation_actionPerformed(); + } + }); + + annotationColour = new JRadioButtonMenuItem( + MessageManager.getString("action.by_annotation")); + annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); + annotationColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + annotationColour_actionPerformed(); + } + }); + } + + protected void selectHighlightedColumns_actionPerformed( + ActionEvent actionEvent) + { + // TODO Auto-generated method stub + + } + + /** + * Generate the reverse sequence (or reverse complement if the flag is true) + * and add it to the alignment + * + * @param complement + */ + protected void showReverse_actionPerformed(boolean complement) + { + } + + /** + * Try to run script in a Groovy console, having first ensured that this + * alignframe is set as currentAlignFrame in Desktop + */ + protected void runGroovy_actionPerformed() + { + + } + + /** + * Adds the given action listener and key accelerator to the given menu item. + * Also saves in a lookup table to support lookup of action by key stroke. + * + * @param keyStroke + * @param menuItem + * @param actionListener + */ + protected void addMenuActionAndAccelerator(KeyStroke keyStroke, + JMenuItem menuItem, ActionListener actionListener) + { + menuItem.setAccelerator(keyStroke); + accelerators.put(keyStroke, menuItem); + menuItem.addActionListener(actionListener); + } + + /** + * Action on clicking sort annotations by type. + * + * @param sortOrder + */ + protected void sortAnnotations_actionPerformed() + { + } + + /** + * Action on clicking Show all annotations. + * + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + protected void showAllAnnotations_actionPerformed(boolean forSequences, + boolean forAlignment) + { + setAnnotationsVisibility(true, forSequences, forAlignment); + } + + /** + * Action on clicking Hide all annotations. + * + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + protected void hideAllAnnotations_actionPerformed(boolean forSequences, + boolean forAlignment) + { + setAnnotationsVisibility(false, forSequences, forAlignment); + } + + /** + * Set the visibility of annotations to true or false. Can act on + * sequence-related annotations, or alignment-related, or both. + * + * @param visible + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + protected void setAnnotationsVisibility(boolean visible, + boolean forSequences, boolean forAlignment) + { + + } + + protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void listenToViewSelections_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showAllhidden_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void hideAllButSelection_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void hideAllSelection_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showGroupConsensus_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showGroupConservation_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void 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 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 bioJSMenuItem_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 sortEValueMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void conservationMenuItem_actionPerformed(boolean selected) + { + } + + protected void printMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void findMenuItem_actionPerformed(ActionEvent e) + { + } + + protected void abovePIDThreshold_actionPerformed(boolean selected) + { + } + + public void showSeqFeatures_actionPerformed(ActionEvent actionEvent) + { + } + + protected void deleteGroups_actionPerformed(ActionEvent e) + { + } + + protected void createGroup_actionPerformed(ActionEvent e) + { + } + + protected void unGroup_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) + throws IOException, InterruptedException + { + } + + protected void pasteThis_actionPerformed(ActionEvent e) + throws IOException, InterruptedException + { + } + + protected void applyToAllGroups_actionPerformed(boolean selected) + { + } + + protected void hmmBuild_actionPerformed(boolean withDefaults) + { + } + + protected void hmmSearch_actionPerformed(boolean withDefaults) + { + } + + protected void jackhmmer_actionPerformed(boolean b) + { + } + + protected void addDatabase_actionPerformed() + throws FileFormatException, IOException + { + } + + protected void hmmAlign_actionPerformed(boolean withDefaults) + { + } + + 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) + { + } + + public void createSVG(java.io.File f) + { + + } + + protected void loadTreeMenuItem_actionPerformed(ActionEvent e) + { + + } + + /** + * Template method to handle the 'load T-Coffee scores' menu event. + *

+ * Subclasses override this method to provide a custom action. + * + * @param event + * The raised event + */ + protected void loadScores_actionPerformed(ActionEvent event) + { + + } + + protected void jpred_actionPerformed(ActionEvent e) + { + } + + protected void scaleAbove_actionPerformed(ActionEvent e) + { + } + + protected void scaleLeft_actionPerformed(ActionEvent e) + { + } + + protected void filterByEValue_actionPerformed() + { + } + + protected void filterByScore_actionPerformed() + { + } + + protected void scaleRight_actionPerformed(ActionEvent e) + { + } + + protected void modifyPID_actionPerformed() + { + } + + protected void modifyConservation_actionPerformed() + { + } + + 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(GeneticCodeI codeTable) + { + + } + + public void featureSettings_actionPerformed(ActionEvent e) + { + + } + + public void fetchSequence_actionPerformed(ActionEvent e) + { + + } + + public void smoothFont_actionPerformed(ActionEvent e) + { + + } + + public void annotationColour_actionPerformed() + { + } + + public void annotationColumn_actionPerformed(ActionEvent e) + { + } + + public void associatedData_actionPerformed(ActionEvent e) + throws IOException, InterruptedException + { + + } + + 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() + { + + } + + public void idRightAlign_actionPerformed(ActionEvent e) + { + + } + + public void expandViews_actionPerformed(ActionEvent e) + { + + } + + public void gatherViews_actionPerformed(ActionEvent e) + { + + } + + public void buildTreeSortMenu() + { + + } + + public void pageSetup_actionPerformed(ActionEvent e) + { + + } + + public void alignmentProperties() + { + + } + + protected void expand_newalign(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected boolean isShowAutoCalculatedAbove() + { + return showAutoCalculatedAbove; + } + + protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove) + { + this.showAutoCalculatedAbove = showAutoCalculatedAbove; + } + + protected SequenceAnnotationOrder getAnnotationSortOrder() + { + return annotationSortOrder; + } + + protected void setAnnotationSortOrder( + SequenceAnnotationOrder annotationSortOrder) + { + this.annotationSortOrder = annotationSortOrder; + } + + public Map getAccelerators() + { + return this.accelerators; + } + + /** + * Returns the selected index of the tabbed pane, or -1 if none selected + * (including the case where the tabbed pane has not been made visible). + * + * @return + */ + public int getTabIndex() + { + return tabbedPane.getSelectedIndex(); + } + + public JPanel getStatusPanel() + { + return statusPanel; + } + + /** + * Sets a reference to the containing split frame. Also makes the 'toggle + * split view' menu item visible and checked. + * + * @param sf + */ + public void setSplitFrame(SplitContainerI sf) + { + this.splitFrame = sf; + if (sf != null) + { + this.showComplementMenuItem.setVisible(true); + this.showComplementMenuItem.setState(true); + } + } + + public SplitContainerI getSplitViewContainer() + { + return this.splitFrame; + } + + protected void showComplement_actionPerformed(boolean complement) + { + } +}