/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.jbgui;\r
\r
-import jalview.gui.Preferences;\r
-\r
-import jalview.schemes.ColourSchemeProperty;\r
-\r
import java.awt.*;\r
import java.awt.event.*;\r
-\r
import javax.swing.*;\r
-import javax.swing.event.AncestorEvent;\r
-import javax.swing.event.AncestorListener;\r
-\r
-\r
-public class GAlignFrame extends JInternalFrame {\r
- protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
- protected JMenu fileMenu = new JMenu();\r
- protected JMenuItem closeMenuItem = new JMenuItem();\r
- protected JMenu editMenu = new JMenu();\r
- protected JMenu viewMenu = new JMenu();\r
- protected JMenu colourMenu = new JMenu();\r
- protected JMenu calculateMenu = new JMenu();\r
- protected JMenu webService = new JMenu();\r
- protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
- protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
- protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
- protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
- protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
- protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
- protected JMenuItem sortIDMenuItem = new JMenuItem();\r
- protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
- protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
- protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
- protected JMenuItem PCAMenuItem = new JMenuItem();\r
- protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
- protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
- protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public JLabel statusBar = new JLabel();\r
- protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
- protected JMenu outputTextboxMenu = new JMenu();\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
- JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem htmlMenuItem = new JMenuItem();\r
- JMenuItem overviewMenuItem = new JMenuItem();\r
- protected JMenuItem undoMenuItem = new JMenuItem();\r
- protected JMenuItem redoMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
- public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem printMenuItem = new JMenuItem();\r
- public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
- JMenuItem findMenuItem = new JMenuItem();\r
- JMenu searchMenu = new JMenu();\r
- public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
- JMenuItem deleteGroups = new JMenuItem();\r
- JMenuItem delete = new JMenuItem();\r
- JMenuItem copy = new JMenuItem();\r
- JMenuItem cut = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
- JMenuItem pasteNew = new JMenuItem();\r
- JMenuItem pasteThis = new JMenuItem();\r
- public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
- JMenuItem createPNG = new JMenuItem();\r
- protected JMenuItem font = new JMenuItem();\r
- public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
- JMenuItem epsFile = new JMenuItem();\r
- JMenuItem LoadtreeMenuItem = new JMenuItem();\r
- JMenuItem jnet = new JMenuItem();\r
- public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
- public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
- JMenuItem modifyPID = new JMenuItem();\r
- JMenuItem modifyConservation = new JMenuItem();\r
- protected JMenu sortByTreeMenu = new JMenu();\r
- protected JMenu sort = new JMenu();\r
- JMenu calculate = new JMenu();\r
- JMenuItem msaAlignMenuItem = new JMenuItem();\r
- JMenu jMenu2 = new JMenu();\r
- JMenuItem padGapsMenuitem = new JMenuItem();\r
- JMenuItem ClustalRealign = new JMenuItem();\r
-\r
- public GAlignFrame() {\r
- ButtonGroup colours = new ButtonGroup();\r
- colours.add(noColourmenuItem);\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- colours.add(strandColour);\r
- colours.add(turnColour);\r
- colours.add(buriedColour);\r
- colours.add(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
- colours.add(nucleotideColour);\r
-\r
- noColourmenuItem.setSelected(true);\r
-\r
- String defaultColour = Preferences.defaultColour;\r
-\r
- if (defaultColour != null) {\r
- int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
-\r
- switch (index) {\r
- case ColourSchemeProperty.CLUSTAL:\r
- clustalColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.BLOSUM:\r
- BLOSUM62Colour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.PID:\r
- PIDColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.ZAPPO:\r
- zappoColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.HYDROPHOBIC:\r
- hydrophobicityColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.HELIX:\r
- helixColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.STRAND:\r
- strandColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.TURN:\r
- turnColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.BURIED:\r
- buriedColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.NUCLEOTIDE:\r
- nucleotideColour.setSelected(true);\r
-\r
- break;\r
-\r
- case ColourSchemeProperty.USER_DEFINED:\r
- userDefinedColour.setSelected(true);\r
-\r
- break;\r
- }\r
- }\r
-\r
- try {\r
- jbInit();\r
- setJMenuBar(alignFrameMenuBar);\r
-\r
- JMenuItem item;\r
-\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
- item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
- i));\r
- item.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add(item);\r
- }\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
-\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- fileMenu.setMnemonic('F');\r
- fileMenu.setText("File");\r
- saveAlignmentMenu.setMnemonic('L');\r
- saveAlignmentMenu.setText("Save As");\r
- saveAlignmentMenu.addActionListener(new ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- saveAlignmentMenu_actionPerformed(e);\r
- }\r
- });\r
- closeMenuItem.setMnemonic('C');\r
- closeMenuItem.setText("Close");\r
- closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- closeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- editMenu.setText("Edit");\r
- viewMenu.setText("View");\r
- colourMenu.setText("Colour");\r
- calculateMenu.setText("Calculate");\r
- webService.setText("Web Service");\r
- selectAllSequenceMenuItem.setText("Select all");\r
- selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_A,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- deselectAllSequenceMenuItem.setText("Deselect All");\r
- deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- invertSequenceMenuItem.setText("Invert Selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- invertSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2LeftMenuItem.setText("Remove Left");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- remove2LeftMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2RightMenuItem.setText("Remove Right");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- remove2RightMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeAllGapsMenuItem.setText("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeAllGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewBoxesMenuItem.setText("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- viewBoxesMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewTextMenuItem.setText("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- viewTextMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortPairwiseMenuItem.setText("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortPairwiseMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortIDMenuItem.setText("by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortIDMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortGroupMenuItem.setText("by Group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeRedundancyMenuItem.setText("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeRedundancyMenuItem_actionPerformed(e);\r
- }\r
- });\r
- pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
- }\r
- });\r
- PCAMenuItem.setText("Principal Component Analysis...");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- PCAMenuItem_actionPerformed(e);\r
- }\r
- });\r
- averageDistanceTreeMenuItem.setText(\r
- "Average Distance Using % Identity...");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- neighbourTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- clustalAlignMenuItem.setText("Clustal Alignment...");\r
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- clustalAlignMenuItem_actionPerformed(e);\r
- }\r
- });\r
- this.getContentPane().setLayout(borderLayout1);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- alignFrameMenuBar.addAncestorListener(new AncestorListener() {\r
- public void ancestorAdded(AncestorEvent event) {\r
- alignFrameMenuBar_ancestorAdded(event);\r
- }\r
-\r
- public void ancestorRemoved(AncestorEvent event) {\r
- }\r
-\r
- public void ancestorMoved(AncestorEvent event) {\r
- }\r
- });\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setMnemonic('T');\r
- outputTextboxMenu.setText("Output to Textbox");\r
- clustalColour.setText("Clustalx");\r
-\r
- clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setText("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setText("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setText("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setText("Helix Propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setText("Strand Propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setText("Turn Propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setText("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.setText("User Defined...");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setText("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setText("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- avDistanceTreeBlosumMenuItem.setText(\r
- "Average Distance Using BLOSUM62...");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- njTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- annotationPanelMenuItem.setActionCommand("");\r
- annotationPanelMenuItem.setText("Show Annotations");\r
- annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
- annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- annotationPanelMenuItem_actionPerformed(e);\r
- }\r
- });\r
- colourTextMenuItem.setText("Colour Text");\r
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- colourTextMenuItem_actionPerformed(e);\r
- }\r
- });\r
- htmlMenuItem.setText("HTML");\r
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- htmlMenuItem_actionPerformed(e);\r
- }\r
- });\r
- overviewMenuItem.setText("Overview Window...");\r
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- overviewMenuItem_actionPerformed(e);\r
- }\r
- });\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setMnemonic('Z');\r
- undoMenuItem.setText("Undo");\r
- undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_Z,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- undoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setMnemonic('0');\r
- redoMenuItem.setText("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- redoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setText("By Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
- wrapMenuItem.setText("Wrap");\r
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- wrapMenuItem_actionPerformed(e);\r
- }\r
- });\r
- printMenuItem.setText("Print");\r
- printMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- printMenuItem_actionPerformed(e);\r
- }\r
- });\r
- renderGapsMenuItem.setText("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- renderGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- findMenuItem.setText("Find...");\r
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_F,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- findMenuItem_actionPerformed(e);\r
- }\r
- });\r
- searchMenu.setText("Search");\r
-\r
- abovePIDThreshold.setText("Above Identity Threshold");\r
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- abovePIDThreshold_actionPerformed(e);\r
- }\r
- });\r
- sequenceFeatures.setText("Sequence Features");\r
- sequenceFeatures.addActionListener(new ActionListener() {\r
- public void actionPerformed(ActionEvent actionEvent) {\r
- sequenceFeatures_actionPerformed(actionEvent);\r
- }\r
- });\r
- nucleotideColour.setText("Nucleotide");\r
- nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- nucleotideColour_actionPerformed(e);\r
- }\r
- });\r
- deleteGroups.setText("Undefine groups");\r
- deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- deleteGroups_actionPerformed(e);\r
- }\r
- });\r
- copy.setText("Copy");\r
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_C,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- copy.setMnemonic(KeyEvent.VK_C);\r
-\r
- copy.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- copy_actionPerformed(e);\r
- }\r
- });\r
- cut.setText("Cut");\r
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_X,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- cut.setMnemonic(KeyEvent.VK_X);\r
- cut.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- cut_actionPerformed(e);\r
- }\r
- });\r
- delete.setText("Delete");\r
- delete.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- delete_actionPerformed(e);\r
- }\r
- });\r
- jMenu1.setMnemonic('V');\r
- jMenu1.setText("Paste");\r
- pasteNew.setText("To New Alignment");\r
- pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
- java.awt.event.KeyEvent.VK_V,\r
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
- pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pasteNew_actionPerformed(e);\r
- }\r
- });\r
- pasteThis.setText("Add To This Alignment");\r
- pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pasteThis_actionPerformed(e);\r
- }\r
- });\r
- applyToAllGroups.setText("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- applyToAllGroups_actionPerformed(e);\r
- }\r
- });\r
- createPNG.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- createPNG_actionPerformed(e);\r
- }\r
- });\r
- createPNG.setActionCommand("Save As PNG Image");\r
- createPNG.setText("PNG");\r
- font.setText("Font...");\r
- font.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- font_actionPerformed(e);\r
- }\r
- });\r
- fullSeqId.setText("Show Full Sequence ID");\r
- fullSeqId.setState(true);\r
- fullSeqId.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- fullSeqId_actionPerformed(e);\r
- }\r
- });\r
- epsFile.setText("EPS");\r
- epsFile.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- epsFile_actionPerformed(e);\r
- }\r
- });\r
- LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
- LoadtreeMenuItem.setText("Load Assocated Tree");\r
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- LoadtreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- jnet.setText("JNet...");\r
- jnet.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- jpred_actionPerformed(e);\r
- }\r
- });\r
- scaleAbove.setVisible(false);\r
- scaleAbove.setText("Scale Above");\r
- scaleAbove.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- scaleAbove_actionPerformed(e);\r
- }\r
- });\r
- scaleLeft.setVisible(false);\r
- scaleLeft.setSelected(true);\r
- scaleLeft.setText("Scale Left");\r
- scaleLeft.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- scaleLeft_actionPerformed(e);\r
- }\r
- });\r
- scaleRight.setVisible(false);\r
- scaleRight.setSelected(true);\r
- scaleRight.setText("Scale Right");\r
- scaleRight.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- scaleRight_actionPerformed(e);\r
- }\r
- });\r
- modifyPID.setText("Modify Identity Threshold...");\r
- modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- modifyPID_actionPerformed(e);\r
- }\r
- });\r
- modifyConservation.setText("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- modifyConservation_actionPerformed(e);\r
- }\r
- });\r
- sortByTreeMenu.setText("By Tree Order");\r
- sort.setText("Sort");\r
- calculate.setText("Calculate Tree");\r
- msaAlignMenuItem.setText("Muscle Alignment...");\r
- msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- msaAlignMenuItem_actionPerformed(e);\r
- }\r
- });\r
- jMenu2.setText("Export");\r
- padGapsMenuitem.setText("Pad Gaps");\r
- padGapsMenuitem.addActionListener(new ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- padGapsMenuitem_actionPerformed(e);\r
- }\r
- });\r
- ClustalRealign.setText("Clustal Realign...");\r
- ClustalRealign.addActionListener(new ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- ClustalRealign_actionPerformed(e);\r
- }\r
- });\r
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
- alignFrameMenuBar.add(calculateMenu);\r
- fileMenu.add(saveAlignmentMenu);\r
- fileMenu.add(jMenu2);\r
- fileMenu.add(outputTextboxMenu);\r
- fileMenu.add(printMenuItem);\r
- fileMenu.addSeparator();\r
- fileMenu.add(LoadtreeMenuItem);\r
- fileMenu.addSeparator();\r
- fileMenu.add(closeMenuItem);\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.add(cut);\r
- editMenu.add(copy);\r
- editMenu.add(jMenu1);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\r
- editMenu.addSeparator();\r
- editMenu.add(padGapsMenuitem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(fullSeqId);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.add(sequenceFeatures);\r
- viewMenu.addSeparator();\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(applyToAllGroups);\r
- colourMenu.addSeparator();\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
- calculateMenu.add(sort);\r
- calculateMenu.add(calculate);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(webService);\r
- webService.add(clustalAlignMenuItem);\r
- webService.add(msaAlignMenuItem);\r
- webService.add(jnet);\r
- webService.add(ClustalRealign);\r
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
- jMenu1.add(pasteNew);\r
- jMenu1.add(pasteThis);\r
- sort.add(sortIDMenuItem);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- jMenu2.add(htmlMenuItem);\r
- jMenu2.add(epsFile);\r
- jMenu2.add(createPNG);\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+import javax.swing.event.*;\r
+\r
+import jalview.gui.*;\r
+import jalview.schemes.*;\r
+\r
+public class GAlignFrame\r
+ extends JInternalFrame\r
+{\r
+ protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
+ protected JMenu fileMenu = new JMenu();\r
+ protected JMenuItem closeMenuItem = new JMenuItem();\r
+ protected JMenu editMenu = new JMenu();\r
+ protected JMenu viewMenu = new JMenu();\r
+ protected JMenu colourMenu = new JMenu();\r
+ protected JMenu calculateMenu = new JMenu();\r
+ protected JMenu webService = new JMenu();\r
+ protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
+ protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
+ protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
+ protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
+ protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
+ protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
+ protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
+ public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
+ protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
+ protected JMenuItem sortIDMenuItem = new JMenuItem();\r
+ protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
+ protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
+ protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
+ protected JMenuItem PCAMenuItem = new JMenuItem();\r
+ protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
+ protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
+ protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public JLabel statusBar = new JLabel();\r
+ protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
+ protected JMenu outputTextboxMenu = new JMenu();\r
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem hydrophobicityColour = new\r
+ JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
+ JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
+ JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
+ public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
+ JMenuItem htmlMenuItem = new JMenuItem();\r
+ JMenuItem overviewMenuItem = new JMenuItem();\r
+ protected JMenuItem undoMenuItem = new JMenuItem();\r
+ protected JMenuItem redoMenuItem = new JMenuItem();\r
+ public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
+ public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
+ JMenuItem printMenuItem = new JMenuItem();\r
+ public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
+ JMenuItem findMenuItem = new JMenuItem();\r
+ JMenu searchMenu = new JMenu();\r
+ public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
+ JMenuItem deleteGroups = new JMenuItem();\r
+ JMenuItem delete = new JMenuItem();\r
+ JMenuItem copy = new JMenuItem();\r
+ JMenuItem cut = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
+ JMenuItem pasteNew = new JMenuItem();\r
+ JMenuItem pasteThis = new JMenuItem();\r
+ public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
+ JMenuItem createPNG = new JMenuItem();\r
+ protected JMenuItem font = new JMenuItem();\r
+ public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+ JMenuItem epsFile = new JMenuItem();\r
+ JMenuItem LoadtreeMenuItem = new JMenuItem();\r
+ JMenuItem jnet = new JMenuItem();\r
+ public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
+ JMenuItem modifyPID = new JMenuItem();\r
+ JMenuItem modifyConservation = new JMenuItem();\r
+ protected JMenu sortByTreeMenu = new JMenu();\r
+ protected JMenu sort = new JMenu();\r
+ JMenu calculate = new JMenu();\r
+ JMenuItem msaAlignMenuItem = new JMenuItem();\r
+ JMenu jMenu2 = new JMenu();\r
+ JMenuItem padGapsMenuitem = new JMenuItem();\r
+ JMenuItem ClustalRealign = new JMenuItem();\r
+\r
+ public GAlignFrame()\r
+ {\r
+ ButtonGroup colours = new ButtonGroup();\r
+ colours.add(noColourmenuItem);\r
+ colours.add(clustalColour);\r
+ colours.add(zappoColour);\r
+ colours.add(taylorColour);\r
+ colours.add(hydrophobicityColour);\r
+ colours.add(helixColour);\r
+ colours.add(strandColour);\r
+ colours.add(turnColour);\r
+ colours.add(buriedColour);\r
+ colours.add(userDefinedColour);\r
+ colours.add(PIDColour);\r
+ colours.add(BLOSUM62Colour);\r
+ colours.add(nucleotideColour);\r
+\r
+ noColourmenuItem.setSelected(true);\r
+\r
+ String defaultColour = Preferences.defaultColour;\r
+\r
+ if (defaultColour != null)\r
+ {\r
+ int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
+\r
+ switch (index)\r
+ {\r
+ case ColourSchemeProperty.CLUSTAL:\r
+ clustalColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BLOSUM:\r
+ BLOSUM62Colour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.PID:\r
+ PIDColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.ZAPPO:\r
+ zappoColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.HYDROPHOBIC:\r
+ hydrophobicityColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.HELIX:\r
+ helixColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.STRAND:\r
+ strandColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.TURN:\r
+ turnColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.BURIED:\r
+ buriedColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.NUCLEOTIDE:\r
+ nucleotideColour.setSelected(true);\r
+\r
+ break;\r
+\r
+ case ColourSchemeProperty.USER_DEFINED:\r
+ userDefinedColour.setSelected(true);\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ setJMenuBar(alignFrameMenuBar);\r
+\r
+ JMenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
+ {\r
+ item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
+ elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ fileMenu.setMnemonic('F');\r
+ fileMenu.setText("File");\r
+ saveAlignmentMenu.setMnemonic('L');\r
+ saveAlignmentMenu.setText("Save As");\r
+ saveAlignmentMenu.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ saveAlignmentMenu_actionPerformed(e);\r
+ }\r
+ });\r
+ closeMenuItem.setMnemonic('C');\r
+ closeMenuItem.setText("Close");\r
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ closeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ editMenu.setText("Edit");\r
+ viewMenu.setText("View");\r
+ colourMenu.setText("Colour");\r
+ calculateMenu.setText("Calculate");\r
+ webService.setText("Web Service");\r
+ selectAllSequenceMenuItem.setText("Select all");\r
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_A,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ deselectAllSequenceMenuItem.setText("Deselect All");\r
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
+ getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ deselectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ invertSequenceMenuItem.setText("Invert Selection");\r
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ invertSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2LeftMenuItem.setText("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ remove2LeftMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2RightMenuItem.setText("Remove Right");\r
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ remove2RightMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeAllGapsMenuItem.setText("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ removeAllGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewBoxesMenuItem.setText("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ viewBoxesMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewTextMenuItem.setText("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ viewTextMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortPairwiseMenuItem.setText("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortIDMenuItem.setText("by ID");\r
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sortIDMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortGroupMenuItem.setText("by Group");\r
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sortGroupMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeRedundancyMenuItem.setText("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ removeRedundancyMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pairwiseAlignmentMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ PCAMenuItem.setText("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ PCAMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ averageDistanceTreeMenuItem.setText(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ averageDistanceTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ neighbourTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ clustalAlignMenuItem.setText("Clustal Alignment");\r
+ clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ clustalAlignMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ this.getContentPane().setLayout(borderLayout1);\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
+ {\r
+ public void ancestorAdded(AncestorEvent event)\r
+ {\r
+ alignFrameMenuBar_ancestorAdded(event);\r
+ }\r
+\r
+ public void ancestorRemoved(AncestorEvent event)\r
+ {\r
+ }\r
+\r
+ public void ancestorMoved(AncestorEvent event)\r
+ {\r
+ }\r
+ });\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setMnemonic('T');\r
+ outputTextboxMenu.setText("Output to Textbox");\r
+ clustalColour.setText("Clustalx");\r
+\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ clustalColour_actionPerformed(e);\r
+ }\r
+ });\r
+ zappoColour.setText("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ zappoColour_actionPerformed(e);\r
+ }\r
+ });\r
+ taylorColour.setText("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ taylorColour_actionPerformed(e);\r
+ }\r
+ });\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hydrophobicityColour_actionPerformed(e);\r
+ }\r
+ });\r
+ helixColour.setText("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ helixColour_actionPerformed(e);\r
+ }\r
+ });\r
+ strandColour.setText("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ strandColour_actionPerformed(e);\r
+ }\r
+ });\r
+ turnColour.setText("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ turnColour_actionPerformed(e);\r
+ }\r
+ });\r
+ buriedColour.setText("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setText("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setText("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setText("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setText(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setText("Show Annotations");\r
+ annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
+ annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ annotationPanelMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ colourTextMenuItem.setText("Colour Text");\r
+ colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ colourTextMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ htmlMenuItem.setText("HTML");\r
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ htmlMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ overviewMenuItem.setText("Overview Window");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setMnemonic('Z');\r
+ undoMenuItem.setText("Undo");\r
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_Z,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ undoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setMnemonic('0');\r
+ redoMenuItem.setText("Redo");\r
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setText("By Conservation");\r
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ conservationMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ noColourmenuItem.setText("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setText("Wrap");\r
+ wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ wrapMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ printMenuItem.setText("Print");\r
+ printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ printMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setText("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ renderGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ findMenuItem.setText("Find...");\r
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_F,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ searchMenu.setText("Search");\r
+\r
+ abovePIDThreshold.setText("Above Identity Threshold");\r
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ abovePIDThreshold_actionPerformed(e);\r
+ }\r
+ });\r
+ sequenceFeatures.setText("Sequence Features");\r
+ sequenceFeatures.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ sequenceFeatures_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ nucleotideColour.setText("Nucleotide");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setText("Undefine groups");\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_C,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ copy.setMnemonic(KeyEvent.VK_C);\r
+\r
+ copy.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setText("Cut");\r
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_X,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ cut.setMnemonic(KeyEvent.VK_X);\r
+ cut.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setText("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu1.setMnemonic('V');\r
+ jMenu1.setText("Paste");\r
+ pasteNew.setText("To New Alignment");\r
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_V,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setText("Add To This Alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setText("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ applyToAllGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ createPNG.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ createPNG(null);\r
+ }\r
+ });\r
+ createPNG.setActionCommand("Save As PNG Image");\r
+ createPNG.setText("PNG");\r
+ font.setText("Font...");\r
+ font.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+ fullSeqId.setText("Show Full Sequence ID");\r
+ fullSeqId.setState(true);\r
+ fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ fullSeqId_actionPerformed(e);\r
+ }\r
+ });\r
+ epsFile.setText("EPS");\r
+ epsFile.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ createEPS(null);\r
+ }\r
+ });\r
+ LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
+ LoadtreeMenuItem.setText("Load Assocated Tree");\r
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ LoadtreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ jnet.setText("JNet");\r
+ jnet.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ jpred_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleAbove.setVisible(false);\r
+ scaleAbove.setText("Scale Above");\r
+ scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ scaleAbove_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleLeft.setVisible(false);\r
+ scaleLeft.setSelected(true);\r
+ scaleLeft.setText("Scale Left");\r
+ scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ scaleLeft_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleRight.setVisible(false);\r
+ scaleRight.setSelected(true);\r
+ scaleRight.setText("Scale Right");\r
+ scaleRight.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ scaleRight_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyPID.setText("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setText("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setText("By Tree Order");\r
+ sort.setText("Sort");\r
+ calculate.setText("Calculate Tree");\r
+ msaAlignMenuItem.setText("Muscle Alignment");\r
+ msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ msaAlignMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenu2.setText("Export");\r
+ padGapsMenuitem.setText("Pad Gaps");\r
+ padGapsMenuitem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ padGapsMenuitem_actionPerformed(e);\r
+ }\r
+ });\r
+ ClustalRealign.setText("Clustal Realign");\r
+ ClustalRealign.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ClustalRealign_actionPerformed(e);\r
+ }\r
+ });\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(searchMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ fileMenu.add(saveAlignmentMenu);\r
+ fileMenu.add(jMenu2);\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(printMenuItem);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(LoadtreeMenuItem);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(jMenu1);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(selectAllSequenceMenuItem);\r
+ editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(invertSequenceMenuItem);\r
+ editMenu.add(deleteGroups);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ editMenu.addSeparator();\r
+ editMenu.add(padGapsMenuitem);\r
+ searchMenu.add(findMenuItem);\r
+ viewMenu.add(font);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(wrapMenuItem);\r
+ viewMenu.add(fullSeqId);\r
+ viewMenu.add(scaleAbove);\r
+ viewMenu.add(scaleLeft);\r
+ viewMenu.add(scaleRight);\r
+ viewMenu.add(viewBoxesMenuItem);\r
+ viewMenu.add(viewTextMenuItem);\r
+ viewMenu.add(colourTextMenuItem);\r
+ viewMenu.add(renderGapsMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.add(sequenceFeatures);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(webService);\r
+ webService.add(clustalAlignMenuItem);\r
+ webService.add(msaAlignMenuItem);\r
+ webService.add(jnet);\r
+ webService.add(ClustalRealign);\r
+ this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ jMenu1.add(pasteNew);\r
+ jMenu1.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ jMenu2.add(htmlMenuItem);\r
+ jMenu2.add(epsFile);\r
+ jMenu2.add(createPNG);\r
+ }\r
+\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void closeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void clustalColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void zappoColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void taylorColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void clustalColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void zappoColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void helixColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void taylorColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void strandColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void turnColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void helixColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void buriedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void strandColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void turnColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void buriedColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void PIDColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void printMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void printMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void findMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void findMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
- }\r
+ public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ }\r
\r
- protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void copy_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void cut_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void delete_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void createPNG_actionPerformed(ActionEvent e) {\r
- }\r
+ public void createPNG(java.io.File f)\r
+ {\r
+ }\r
\r
- protected void font_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void font_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void epsFile_actionPerformed(ActionEvent e) {\r
- }\r
+ public void createEPS(java.io.File f)\r
+ {\r
+ }\r
\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void jpred_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void scaleAbove_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void scaleLeft_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void scaleRight_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void modifyPID_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void preferences_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void preferences_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) {\r
- }\r
+ protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+ {\r
+ }\r
\r
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void padGapsMenuitem_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
\r
- protected void ClustalRealign_actionPerformed(ActionEvent e) {\r
- }\r
+ protected void ClustalRealign_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff