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.schemes.ColourSchemeProperty;
+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.Toolkit;
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.util.HashMap;
+import java.util.Map;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.JTabbedPane;
-import javax.swing.SwingUtilities;
+import javax.swing.KeyStroke;
import javax.swing.event.ChangeEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+@SuppressWarnings("serial")
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 annotationsMenu = 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 JMenu webService = new JMenu();// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
- public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+ public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
- public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
- protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
-
- protected JMenuItem sortIDMenuItem = new JMenuItem();
-
- protected JMenuItem sortLengthMenuItem = new JMenuItem();
-
- protected JMenuItem sortGroupMenuItem = new JMenuItem();
+ protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
- protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
-
- protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
-
- protected JMenuItem PCAMenuItem = new JMenuItem();
-
- protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
-
- protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- public JLabel statusBar = new JLabel();
-
- protected JMenuItem saveAs = new JMenuItem();
+ public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+ // sufficient for
+ // AlignFrame.printWriter
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 JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
-
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
-
- JMenuItem njTreeBlosumMenuItem = new JMenuItem();
-
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-
- public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
-
- JMenuItem htmlMenuItem = new JMenuItem();
-
- JMenuItem overviewMenuItem = new JMenuItem();
+ protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
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();
+ protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
-
- JMenuItem deleteGroups = new JMenuItem();
-
- JMenuItem createGroup = new JMenuItem();
-
- JMenuItem unGroup = 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();
+ protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
- JMenuItem createPNG = new JMenuItem();
+ protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
- JMenuItem createBioJS = new JMenuItem();
+ protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
- JMenuItem createSVG = new JMenuItem();
+ protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- protected JMenuItem font = new JMenuItem();
+ protected JCheckBoxMenuItem applyToAllGroups;
- public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
-
- JMenuItem epsFile = new JMenuItem();
+ protected JMenu colourMenu = new JMenu();
- JMenuItem LoadtreeMenuItem = new JMenuItem();
+ protected JMenuItem textColour;
- public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem conservationMenuItem;
- public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+ protected JMenuItem modifyConservation;
- public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem abovePIDThreshold;
- protected JMenuItem modifyPID = new JMenuItem();
+ protected JMenuItem modifyPID;
- protected JMenuItem modifyConservation = new JMenuItem();
+ protected JRadioButtonMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JMenu sort = new JMenu();
- protected JMenu calculateTree = new JMenu();
-
- JMenu jMenu2 = new JMenu();
+ protected JMenuItem calculateTree = new JMenuItem();
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
- protected ButtonGroup colours = new ButtonGroup();
-
- JMenuItem vamsasStore = new JMenuItem();
+ protected JMenu showTranslation = new JMenu();
- protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenuItem showReverse = new JMenuItem();
- protected JMenuItem extractScores = new JMenuItem();
-
- protected JMenuItem expandAlignment = new JMenuItem();
+ protected JMenuItem showReverseComplement = new JMenuItem();
protected JMenu showProducts = new JMenu();
- public JMenuItem openFeatureSettings = new JMenuItem();
-
- JMenuItem fetchSequence = new JMenuItem();
-
- JMenuItem annotationColour = new JMenuItem();
-
- JMenuItem annotationColumn = new JMenuItem();
+ protected JMenuItem runGroovy = new JMenuItem();
- protected JMenuItem rnahelicesColour = new JMenuItem();
-
- JMenuItem associatedData = new JMenuItem();
+ protected JMenuItem loadVcf;
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
- JMenu addSequenceMenu = new JMenu();
-
- JMenuItem addFromFile = new JMenuItem();
-
- JMenuItem addFromText = new JMenuItem();
-
- JMenuItem addFromURL = new JMenuItem();
-
- JMenuItem exportAnnotations = new JMenuItem();
-
- JMenuItem exportFeatures = new JMenuItem();
-
protected JPanel statusPanel = new JPanel();
- GridLayout gridLayout1 = new GridLayout();
-
- JMenu jMenu3 = new JMenu();
-
- JMenuItem showAllSeqs = new JMenuItem();
-
- JMenuItem showAllColumns = new JMenuItem();
-
- JMenu hideMenu = new JMenu();
-
- JMenuItem hideSelSequences = new JMenuItem();
-
- JMenuItem hideSelColumns = new JMenuItem();
-
- JMenuItem hideAllButSelection = new JMenuItem();
-
- JMenuItem hideAllSelection = new JMenuItem();
-
- JMenuItem showAllhidden = new JMenuItem();
-
protected JMenuItem showAllSeqAnnotations = new JMenuItem();
protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
protected JMenuItem hideAllAlAnnotations = new JMenuItem();
- protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
-
- protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
- JMenuItem invertColSel = new JMenuItem();
-
protected JTabbedPane tabbedPane = new JTabbedPane();
- JMenuItem save = new JMenuItem();
-
protected JMenuItem reload = new JMenuItem();
- JMenuItem newView = new JMenuItem();
-
- JMenuItem textColour = new JMenuItem();
-
- JMenu formatMenu = new JMenu();
-
- JMenu selectMenu = new JMenu();
+ protected JMenu formatMenu = new JMenu();
protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
protected JMenuItem expandViews = new JMenuItem();
- JMenuItem pageSetup = new JMenuItem();
-
- JMenuItem alignmentProperties = new JMenuItem();
-
- JMenu tooltipSettingsMenu = new JMenu();
-
- private JMenuItem justifyLeftMenuItem = new JMenuItem();
-
- private JMenuItem justifyRightMenuItem = new JMenuItem();
-
- JMenu autoAnnMenu = new JMenu();
-
protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
-
- private JMenuItem grpsFromSelection = new JMenuItem();
+ protected JMenuItem openFeatureSettings;
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
+
+ private SplitContainerI splitFrame;
+
public GAlignFrame()
{
try
{
+
+ // for Web-page embedding using id=align-frame-div
+ setName("jalview-alignment");
+
jbInit();
setJMenuBar(alignFrameMenuBar);
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
- JMenuItem item = new JMenuItem(
- jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+ JMenuItem item = new JMenuItem(ff);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- outputText_actionPerformed(e);
+ outputText_actionPerformed(e.getActionCommand());
}
});
System.err.println(e.toString());
}
- if (!new jalview.util.Platform().isAMac())
+ if (Platform.allowMnemonics()) // was "not mac and not JS"
{
closeMenuItem.setMnemonic('C');
outputTextboxMenu.setMnemonic('T');
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()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isControlDown()
- || SwingUtilities.isRightMouseButton(evt))
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop,
- MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.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()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
- colours.add(nucleotideColour);
- colours.add(purinePyrimidineColour);
- // colours.add(covariationColour);
- colours.add(tcoffeeColour);
- colours.add(RNAInteractionColour);
- setColourSelected(jalview.bin.Cache
- .getDefault("DEFAULT_COLOUR", "None"));
-
}
- public void setColourSelected(String defaultColour)
+ private void jbInit() throws Exception
{
+ initColourMenu();
- if (defaultColour != null)
+ JMenuItem saveAs = new JMenuItem(
+ MessageManager.getString("action.save_as"));
+ ActionListener al = new ActionListener()
{
- int index = ColourSchemeProperty
- .getColourIndexFromName(defaultColour);
-
- switch (index)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- 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.TCOFFEE:
- tcoffeeColour.setSelected(true);
- break;
-
- case ColourSchemeProperty.PURINEPYRIMIDINE:
- purinePyrimidineColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.RNAINTERACTION:
- RNAInteractionColour.setSelected(true);
-
- break;
- /*
- * case ColourSchemeProperty.COVARIATION:
- * covariationColour.setSelected(true);
- *
- * break;
- */
- case ColourSchemeProperty.USER_DEFINED:
- userDefinedColour.setSelected(true);
+ saveAs_actionPerformed();
+ }
+ };
- break;
- case ColourSchemeProperty.NONE:
- default:
- noColourmenuItem.setSelected(true);
- break;
+ // 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"));
+ 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);
- private void jbInit() throws Exception
- {
- fileMenu.setText(MessageManager.getString("action.file"));
- saveAs.setText(MessageManager.getString("action.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()
+ 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)
{
- saveAs_actionPerformed(e);
+ deselectAllSequenceMenuItem_actionPerformed(e);
}
- });
- closeMenuItem.setText(MessageManager.getString("action.close"));
- closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ 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)
{
- closeMenuItem_actionPerformed(false);
+ invertSequenceMenuItem_actionPerformed(e);
}
- });
- editMenu.setText(MessageManager.getString("action.edit"));
- viewMenu.setText(MessageManager.getString("action.view"));
- annotationsMenu.setText(MessageManager.getString("action.annotations"));
- colourMenu.setText(MessageManager.getString("action.colour"));
- calculateMenu.setText(MessageManager.getString("action.calculate"));
- webService.setText(MessageManager.getString("action.web_service"));
- selectAllSequenceMenuItem.setText(MessageManager
- .getString("action.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()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- selectAllSequenceMenuItem_actionPerformed(e);
- }
- });
- deselectAllSequenceMenuItem.setText(MessageManager
- .getString("action.deselect_all"));
- deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
- deselectAllSequenceMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- deselectAllSequenceMenuItem_actionPerformed(e);
- }
- });
- invertSequenceMenuItem.setText(MessageManager
- .getString("action.invert_sequence_selection"));
- invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- invertSequenceMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- invertSequenceMenuItem_actionPerformed(e);
- }
- });
- grpsFromSelection.setText(MessageManager
- .getString("action.make_groups_selection"));
- grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+ };
+ 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);
}
});
- expandAlignment.setText(MessageManager
- .getString("action.view_flanking_regions"));
- expandAlignment.setToolTipText(MessageManager
- .getString("label.view_flanking_regions"));
- expandAlignment.addActionListener(new java.awt.event.ActionListener()
+ 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);
}
});
- remove2LeftMenuItem.setText(MessageManager
- .getString("action.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()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- remove2LeftMenuItem_actionPerformed(e);
- }
- });
- remove2RightMenuItem.setText(MessageManager
- .getString("action.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()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- remove2RightMenuItem_actionPerformed(e);
- }
- });
- removeGappedColumnMenuItem.setText(MessageManager
- .getString("action.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()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeGappedColumnMenuItem_actionPerformed(e);
- }
- });
- removeAllGapsMenuItem.setText(MessageManager
- .getString("action.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()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeAllGapsMenuItem_actionPerformed(e);
- }
- });
- justifyLeftMenuItem.setText(MessageManager
- .getString("action.left_justify_alignment"));
- justifyLeftMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- justifyLeftMenuItem_actionPerformed(e);
- }
- });
- justifyRightMenuItem.setText(MessageManager
- .getString("action.right_justify_alignment"));
- justifyRightMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- justifyRightMenuItem_actionPerformed(e);
- }
- });
- viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- viewBoxesMenuItem_actionPerformed(e);
+ remove2LeftMenuItem_actionPerformed(e);
}
- });
- viewTextMenuItem.setText(MessageManager.getString("action.text"));
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ 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)
{
- viewTextMenuItem_actionPerformed(e);
+ remove2RightMenuItem_actionPerformed(e);
}
- });
- showNonconservedMenuItem.setText(MessageManager
- .getString("label.show_non_conversed"));
- showNonconservedMenuItem.setState(false);
- showNonconservedMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- showUnconservedMenuItem_actionPerformed(e);
- }
- });
- sortPairwiseMenuItem.setText(MessageManager
- .getString("action.by_pairwise_id"));
- sortPairwiseMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sortPairwiseMenuItem_actionPerformed(e);
- }
- });
- sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ 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)
{
- sortIDMenuItem_actionPerformed(e);
+ removeGappedColumnMenuItem_actionPerformed(e);
}
- });
- sortLengthMenuItem
- .setText(MessageManager.getString("action.by_length"));
- sortLengthMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sortLengthMenuItem_actionPerformed(e);
- }
- });
- sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ 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)
{
- sortGroupMenuItem_actionPerformed(e);
+ removeAllGapsMenuItem_actionPerformed(e);
}
- });
- removeRedundancyMenuItem.setText(MessageManager
- .getString("action.remove_redundancy").concat("..."));
- removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
- removeRedundancyMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- removeRedundancyMenuItem_actionPerformed(e);
- }
- });
- pairwiseAlignmentMenuItem.setText(MessageManager
- .getString("action.pairwise_alignment"));
- pairwiseAlignmentMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- pairwiseAlignmentMenuItem_actionPerformed(e);
- }
- });
- PCAMenuItem.setText(MessageManager
- .getString("label.principal_component_analysis"));
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PCAMenuItem_actionPerformed(e);
- }
- });
- averageDistanceTreeMenuItem.setText(MessageManager
- .getString("label.average_distance_identity"));
- averageDistanceTreeMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_actionPerformed(e);
- }
- });
- neighbourTreeMenuItem.setText(MessageManager
- .getString("label.neighbour_joining_identity"));
- neighbourTreeMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- 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(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setText(MessageManager
- .getString("label.out_to_textbox"));
- clustalColour.setText(MessageManager.getString("label.clustalx"));
+ };
+ addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
- clustalColour.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem justifyLeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.left_justify_alignment"));
+ justifyLeftMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- clustalColour_actionPerformed(e);
+ justifyLeftMenuItem_actionPerformed(e);
}
});
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem justifyRightMenuItem = new JMenuItem(
+ MessageManager.getString("action.right_justify_alignment"));
+ justifyRightMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- zappoColour_actionPerformed(e);
+ justifyRightMenuItem_actionPerformed(e);
}
});
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new java.awt.event.ActionListener()
+ viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- taylorColour_actionPerformed(e);
+ viewBoxesMenuItem_actionPerformed(e);
}
});
- hydrophobicityColour.setText(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new java.awt.event.ActionListener()
+ viewTextMenuItem.setText(MessageManager.getString("action.text"));
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- helixColour_actionPerformed(e);
+ viewTextMenuItem_actionPerformed(e);
}
});
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new java.awt.event.ActionListener()
+ showNonconservedMenuItem
+ .setText(MessageManager.getString("label.show_non_conserved"));
+ showNonconservedMenuItem.setState(false);
+ showNonconservedMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- strandColour_actionPerformed(e);
+ showUnconservedMenuItem_actionPerformed(e);
}
});
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sortPairwiseMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- turnColour_actionPerformed(e);
+ sortPairwiseMenuItem_actionPerformed(e);
}
});
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sortIDMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- buriedColour_actionPerformed(e);
+ sortIDMenuItem_actionPerformed(e);
}
});
- userDefinedColour.setText(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sortLengthMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_length"));
+ sortLengthMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- userDefinedColour_actionPerformed(e);
+ sortLengthMenuItem_actionPerformed(e);
}
});
- PIDColour
- .setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sortGroupMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- PIDColour_actionPerformed(e);
+ sortGroupMenuItem_actionPerformed(e);
}
});
- BLOSUM62Colour
- .setText(MessageManager.getString("label.blosum62_score"));
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+
+ 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)
{
- BLOSUM62Colour_actionPerformed(e);
+ removeRedundancyMenuItem_actionPerformed(e);
}
- });
- nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
+ JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
+ MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- nucleotideColour_actionPerformed(e);
+ pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed(e);
- }
- });
-
- RNAInteractionColour.setText("RNA Interaction type");
- RNAInteractionColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- RNAInteractionColour_actionPerformed(e);
- }
- });
- /*
- * covariationColour.setText("Covariation");
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_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"));
- avDistanceTreeBlosumMenuItem.setText(MessageManager
- .getString("label.average_distance_bloslum62"));
- avDistanceTreeBlosumMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
- njTreeBlosumMenuItem.setText(MessageManager
- .getString("label.neighbour_blosum62"));
- njTreeBlosumMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- njTreeBlosumMenuItem_actionPerformed(e);
- }
- });
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText(MessageManager
- .getString("label.show_annotations"));
- annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
- true));
+ annotationPanelMenuItem
+ .setText(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem
+ .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
annotationPanelMenuItem_actionPerformed(e);
}
});
- showAllAlAnnotations.setText(MessageManager
- .getString("label.show_all_al_annotations"));
+ showAllAlAnnotations.setText(
+ MessageManager.getString("label.show_all_al_annotations"));
final boolean isAnnotationPanelShown = annotationPanelMenuItem
.getState();
showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
showAllAnnotations_actionPerformed(false, true);
}
});
- hideAllAlAnnotations.setText(MessageManager
- .getString("label.hide_all_al_annotations"));
+ hideAllAlAnnotations.setText(
+ MessageManager.getString("label.hide_all_al_annotations"));
hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
hideAllAlAnnotations.addActionListener(new ActionListener()
{
hideAllAnnotations_actionPerformed(false, true);
}
});
- showAllSeqAnnotations.setText(MessageManager
- .getString("label.show_all_seq_annotations"));
+ showAllSeqAnnotations.setText(
+ MessageManager.getString("label.show_all_seq_annotations"));
showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
showAllSeqAnnotations.addActionListener(new ActionListener()
{
showAllAnnotations_actionPerformed(true, false);
}
});
- hideAllSeqAnnotations.setText(MessageManager
- .getString("label.hide_all_seq_annotations"));
+ hideAllSeqAnnotations.setText(
+ MessageManager.getString("label.hide_all_seq_annotations"));
hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
hideAllSeqAnnotations.addActionListener(new ActionListener()
{
SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
.valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name()));
- sortAnnBySequence.setText(MessageManager
- .getString("label.sort_annotations_by_sequence"));
- sortAnnBySequence
- .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ 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
{
boolean newState = sortAnnBySequence.getState();
sortAnnByLabel.setSelected(false);
- setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
- : SequenceAnnotationOrder.NONE);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
sortAnnotations_actionPerformed();
}
});
- sortAnnByLabel.setText(MessageManager
- .getString("label.sort_annotations_by_label"));
- sortAnnByLabel
- .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnByLabel.setSelected(
+ sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
sortAnnByLabel.addActionListener(new ActionListener()
{
@Override
{
boolean newState = sortAnnByLabel.getState();
sortAnnBySequence.setSelected(false);
- setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
- : SequenceAnnotationOrder.NONE);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
sortAnnotations_actionPerformed();
}
});
- colourTextMenuItem.setText(MessageManager
- .getString("label.colour_text"));
- colourTextMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- colourTextMenuItem_actionPerformed(e);
- }
- });
- htmlMenuItem.setText(MessageManager.getString("label.html"));
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ 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)
}
});
- // TODO uncomment when supported by MassageManager
- // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
- createBioJS.setText("BioJS");
+ JMenuItem createBioJS = new JMenuItem(
+ MessageManager.getString("label.biojs_html_export"));
createBioJS.addActionListener(new java.awt.event.ActionListener()
{
@Override
}
});
- overviewMenuItem.setText(MessageManager
- .getString("label.overview_window"));
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+ 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"));
- undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ 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"));
- redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
redoMenuItem_actionPerformed(e);
}
- });
- conservationMenuItem.setText(MessageManager
- .getString("action.by_conservation"));
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed(e);
- }
- });
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed(e);
- }
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+ wrapMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
wrapMenuItem_actionPerformed(e);
}
});
- printMenuItem.setText(MessageManager.getString("action.print") + "...");
- printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- printMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ 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 java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- renderGapsMenuItem_actionPerformed(e);
- }
- });
- findMenuItem.setText(MessageManager.getString("action.find"));
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.find_tip")));
- findMenuItem.addActionListener(new java.awt.event.ActionListener()
+ renderGapsMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- findMenuItem_actionPerformed(e);
+ renderGapsMenuItem_actionPerformed(e);
}
});
- abovePIDThreshold.setText(MessageManager
- .getString("label.above_identity_threshold"));
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+
+ 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)
{
- abovePIDThreshold_actionPerformed(e);
+ findMenuItem_actionPerformed(e);
}
- });
- showSeqFeatures.setText(MessageManager
- .getString("label.show_sequence_features"));
+ };
+ addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+
+ showSeqFeatures.setText(
+ MessageManager.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
@Override
* void actionPerformed(ActionEvent actionEvent) {
* showSeqFeaturesHeight_actionPerformed(actionEvent); } });
*/
- showDbRefsMenuitem.setText(MessageManager
- .getString("label.show_database_refs"));
+ showDbRefsMenuitem
+ .setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
}
});
- showNpFeatsMenuitem.setText(MessageManager
- .getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.setText(
+ MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
}
});
- showGroupConservation.setText(MessageManager
- .getString("label.group_conservation"));
+ showGroupConservation
+ .setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
});
- showGroupConsensus.setText(MessageManager
- .getString("label.group_consensus"));
+ showGroupConsensus
+ .setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
}
});
- showConsensusHistogram.setText(MessageManager
- .getString("label.show_consensus_histogram"));
+ showConsensusHistogram.setText(
+ MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
}
});
- showSequenceLogo.setText(MessageManager
- .getString("label.show_consensus_logo"));
+ showSequenceLogo
+ .setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
}
});
- normaliseSequenceLogo.setText(MessageManager
- .getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo
+ .setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
}
});
- applyAutoAnnotationSettings.setText(MessageManager
- .getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings
+ .setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
});
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);
- showAutoFirst.setText(MessageManager.getString("label.show_first"));
- showAutoFirst.setSelected(Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE,
- false));
+ final boolean autoFirst = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
+ showAutoFirst.setSelected(autoFirst);
+ setShowAutoCalculatedAbove(autoFirst);
showAutoFirst.addActionListener(new ActionListener()
{
@Override
sortAnnotations_actionPerformed();
}
});
- showAutoLast.setText(MessageManager.getString("label.show_last"));
showAutoLast.setSelected(!showAutoFirst.isSelected());
showAutoLast.addActionListener(new ActionListener()
{
}
});
- nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- nucleotideColour_actionPerformed(e);
+ annotationColumn_actionPerformed(e);
}
});
- tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
- tcoffeeColour.setEnabled(false);
- tcoffeeColour.addActionListener(new ActionListener()
+ 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)
{
- tcoffeeColorScheme_actionPerformed(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);
- deleteGroups
- .setText(MessageManager.getString("action.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()
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- deleteGroups_actionPerformed(e);
+ copy_actionPerformed();
}
- });
- createGroup.setText(MessageManager.getString("action.create_groups"));
- createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- createGroup.addActionListener(new java.awt.event.ActionListener()
+ };
+ 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)
{
- createGroup_actionPerformed(e);
+ cut_actionPerformed();
}
- });
- unGroup.setText(MessageManager.getString("action.remove_group"));
- unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.SHIFT_MASK, false));
- unGroup.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, cut, al);
+
+ JMenuItem delete = new JMenuItem(
+ MessageManager.getString("action.delete"));
+ delete.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- unGroup_actionPerformed(e);
+ delete_actionPerformed();
}
});
- copy.setText(MessageManager.getString("action.copy"));
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- copy.addActionListener(new java.awt.event.ActionListener()
+ 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)
{
- copy_actionPerformed(e);
+ pasteNew_actionPerformed(e);
}
- });
- cut.setText(MessageManager.getString("action.cut"));
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- cut.addActionListener(new java.awt.event.ActionListener()
+ };
+ 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)
{
- cut_actionPerformed(e);
+ pasteThis_actionPerformed(e);
}
- });
- delete.setText(MessageManager.getString("action.delete"));
- delete.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteThis, al);
+
+ JMenuItem createPNG = new JMenuItem("PNG");
+ createPNG.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- delete_actionPerformed(e);
+ createPNG(null);
}
});
- pasteMenu.setText(MessageManager.getString("action.paste"));
- pasteNew.setText(MessageManager.getString("label.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()
+ 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)
{
- pasteNew_actionPerformed(e);
+ font_actionPerformed(e);
}
});
- pasteThis.setText(MessageManager.getString("label.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()
+ seqLimits.setText(
+ MessageManager.getString("label.show_sequence_limits"));
+ seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- pasteThis_actionPerformed(e);
+ seqLimit_actionPerformed(e);
}
});
- applyToAllGroups.setText(MessageManager
- .getString("label.apply_colour_to_all_groups"));
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem epsFile = new JMenuItem("EPS");
+ epsFile.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- applyToAllGroups_actionPerformed(e);
+ createEPS(null);
}
});
- createPNG.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem createSVG = new JMenuItem("SVG");
+ createSVG.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- createPNG(null);
+ createSVG(null);
}
});
- createPNG.setActionCommand(MessageManager
- .getString("label.save_png_image"));
- createPNG.setText("PNG");
- font.setText(MessageManager.getString("action.font"));
- font.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem loadTreeFile = new JMenuItem(
+ MessageManager.getString("label.from_file"));
+
+ loadTreeFile.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- font_actionPerformed(e);
+ loadTreeMenuItem_actionPerformed(e);
}
});
- seqLimits.setText(MessageManager
- .getString("label.show_sequence_limits"));
- seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
- seqLimits.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem loadTreeUrl = new JMenuItem(
+ MessageManager.getString("label.from_url"));
+ loadTreeUrl.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- seqLimit_actionPerformed(e);
+ loadTreeUrlItem_actionPerformed(e);
}
});
- epsFile.setText("EPS");
- epsFile.addActionListener(new java.awt.event.ActionListener()
+
+
+
+ JMenuItem loadTreeBaseStudy = new JMenuItem(
+ MessageManager.getString("label.treebase_study"));
+ loadTreeBaseStudy.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
- createEPS(null);
+ loadTreeBaseStudy_actionPerformed(e);
+
+ } });
+
+
+
+ JMenuItem loadTreeBase = new JMenuItem(
+ MessageManager.getString("label.treebase"));
+ loadTreeBase.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreeBase_actionPerformed(e);
+
}
+
+
});
+ JMenuItem loadTreePfam = new JMenuItem(
+ MessageManager.getString("label.pfam"));
+ loadTreePfam.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreePfam_actionPerformed(e);
+
+ }
- createSVG.setText("SVG");
- createSVG.addActionListener(new java.awt.event.ActionListener()
+ });
+ JMenuItem loadTreeFam = new JMenuItem(
+ MessageManager.getString("label.treefam"));
+ loadTreeFam.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
- createSVG(null);
+ loadTreeFam_actionPerformed(e);
+
}
+
});
- LoadtreeMenuItem.setActionCommand(MessageManager
- .getString("label.load_tree_for_sequence_set"));
- LoadtreeMenuItem.setText(MessageManager
- .getString("label.load_associated_tree"));
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem loadTreeOfLife = new JMenuItem(
+ MessageManager.getString("label.tree_of_life"));
+ loadTreeOfLife.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
- LoadtreeMenuItem_actionPerformed(e);
+ loadTreeOfLife_actionPerformed(e);
+
}
+
+
});
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
- scaleAbove.addActionListener(new java.awt.event.ActionListener()
+ scaleAbove.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
scaleLeft.setVisible(false);
scaleLeft.setSelected(true);
scaleLeft.setText(MessageManager.getString("action.scale_left"));
- scaleLeft.addActionListener(new java.awt.event.ActionListener()
+ scaleLeft.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
scaleRight.setVisible(false);
scaleRight.setSelected(true);
scaleRight.setText(MessageManager.getString("action.scale_right"));
- scaleRight.addActionListener(new java.awt.event.ActionListener()
+ scaleRight.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText(MessageManager
- .getString("label.centre_column_labels"));
- centreColumnLabelsMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- centreColumnLabels_actionPerformed(e);
- }
- });
+ 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
+ .setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
});
- modifyPID.setText(MessageManager
- .getString("label.modify_identity_thereshold"));
- modifyPID.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- modifyPID_actionPerformed(e);
- }
- });
- modifyConservation.setText(MessageManager
- .getString("label.modify_conservation_thereshold"));
- modifyConservation
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- modifyConservation_actionPerformed(e);
- }
- });
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
@Override
public void menuSelected(MenuEvent e)
{
- buildTreeMenu();
+ buildTreeSortMenu();
}
@Override
{
}
});
- sortByAnnotScore.setText(MessageManager
- .getString("label.sort_by_score"));
+ sortByAnnotScore
+ .setText(MessageManager.getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
sort.addMenuListener(new javax.swing.event.MenuListener()
{
sortByAnnotScore.setVisible(false);
calculateTree
- .setText(MessageManager.getString("action.calculate_tree"));
+ .setText(MessageManager.getString("action.calculate_tree_pca"));
- jMenu2.setText(MessageManager.getString("label.export_image"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
- padGapsMenuitem.setState(jalview.bin.Cache
- .getDefault("PAD_GAPS", false));
+ padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
padGapsMenuitem_actionPerformed(e);
}
});
+ JMenuItem vamsasStore = new JMenuItem(
+ MessageManager.getString("label.vamsas_store"));
vamsasStore.setVisible(false);
- vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
vamsasStore.addActionListener(new ActionListener()
{
@Override
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText(MessageManager
- .getString("label.translate_cDNA"));
- showTranslation.addActionListener(new ActionListener()
+
+ /*
+ * 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)
{
- showTranslation_actionPerformed(e);
+ showReverse_actionPerformed(false);
}
});
- extractScores.setText(MessageManager.getString("label.extract_scores")
- + "...");
- extractScores.addActionListener(new ActionListener()
+ showReverseComplement
+ .setText(MessageManager.getString("label.reverse_complement"));
+ showReverseComplement.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- extractScores_actionPerformed(e);
+ showReverse_actionPerformed(true);
}
});
- extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
- // score extraction
- showProducts.setText(MessageManager.getString("label.get_cross_refs"));
- /*
- * showProducts.addActionListener(new ActionListener() {
- *
- * public void actionPerformed(ActionEvent e) {
- * showProducts_actionPerformed(e); } });
- */
- openFeatureSettings.setText(MessageManager
- .getString("label.feature_settings"));
- openFeatureSettings.addActionListener(new ActionListener()
+
+ JMenuItem extractScores = new JMenuItem(
+ MessageManager.getString("label.extract_scores"));
+ extractScores.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- featureSettings_actionPerformed(e);
+ extractScores_actionPerformed(e);
}
});
- fetchSequence
- .setText(MessageManager.getString("label.fetch_sequences"));
- fetchSequence.addActionListener(new ActionListener()
+ 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)
{
- fetchSequence_actionPerformed(e);
+ runGroovy_actionPerformed();
}
});
- annotationColour.setText(MessageManager
- .getString("action.by_annotation"));
- annotationColour.addActionListener(new ActionListener()
+ openFeatureSettings = new JMenuItem(
+ MessageManager.getString("action.feature_settings"));
+ openFeatureSettings.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- annotationColour_actionPerformed(e);
+ featureSettings_actionPerformed(e);
}
});
- annotationColumn.setText(MessageManager
- .getString("action.select_by_annotation"));
- annotationColumn.addActionListener(new ActionListener()
+ /*
+ * add sub-menu of database we can fetch from
+ */
+ JMenuItem fetchSequence = new JMenuItem(
+ MessageManager.getString("label.fetch_sequences"));
+ fetchSequence.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- annotationColumn_actionPerformed(e);
+ fetchSequence_actionPerformed();
}
});
- rnahelicesColour.setText(MessageManager
- .getString("action.by_rna_helixes"));
- rnahelicesColour.addActionListener(new ActionListener()
+ JMenuItem associatedData = new JMenuItem(
+ MessageManager.getString("label.load_features_annotations"));
+ associatedData.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- rnahelicesColour_actionPerformed(e);
+ associatedData_actionPerformed(e);
}
});
-
- associatedData.setText(MessageManager
- .getString("label.load_features_annotations"));
- associatedData.addActionListener(new ActionListener()
+ 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)
{
- associatedData_actionPerformed(e);
+ loadVcf_actionPerformed();
}
});
- autoCalculate.setText(MessageManager
- .getString("label.autocalculate_consensus"));
- autoCalculate.setState(jalview.bin.Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
+ autoCalculate.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
autoCalculate_actionPerformed(e);
}
});
- sortByTree.setText(MessageManager
- .getString("label.sort_alignment_new_tree"));
- sortByTree
- .setToolTipText("<html>"
- + MessageManager
- .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
- sortByTree
- .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ sortByTree.setText(
+ MessageManager.getString("label.sort_alignment_new_tree"));
+ sortByTree.setToolTipText("<html>" + MessageManager.getString(
+ "label.enable_automatically_sort_alignment_when_open_new_tree"));
+ sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
@Override
}
});
- listenToViewSelections.setText(MessageManager
- .getString("label.listen_for_selections"));
+ listenToViewSelections.setText(
+ MessageManager.getString("label.listen_for_selections"));
listenToViewSelections
- .setToolTipText("<html>"
- + MessageManager
- .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+ .setToolTipText("<html>" + MessageManager.getString(
+ "label.selections_mirror_selections_made_same_sequences_other_views"));
listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
}
});
- addSequenceMenu
- .setText(MessageManager.getString("label.add_sequences"));
- addFromFile.setText(MessageManager.getString("label.from_file"));
+ JMenu addSequenceMenu = new JMenu(
+ MessageManager.getString("label.add_sequences"));
+ JMenuItem addFromFile = new JMenuItem(
+ MessageManager.getString("label.from_file"));
addFromFile.addActionListener(new ActionListener()
{
@Override
addFromFile_actionPerformed(e);
}
});
- addFromText.setText(MessageManager.getString("label.from_textbox"));
+ JMenuItem addFromText = new JMenuItem(
+ MessageManager.getString("label.from_textbox"));
addFromText.addActionListener(new ActionListener()
{
@Override
addFromText_actionPerformed(e);
}
});
- addFromURL.setText(MessageManager.getString("label.from_url"));
+ JMenuItem addFromURL = new JMenuItem(
+ MessageManager.getString("label.from_url"));
addFromURL.addActionListener(new ActionListener()
{
@Override
addFromURL_actionPerformed(e);
}
});
- exportFeatures.setText(MessageManager
- .getString("label.export_features"));
+ JMenuItem exportFeatures = new JMenuItem(
+ MessageManager.getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
@Override
exportFeatures_actionPerformed(e);
}
});
- exportAnnotations.setText(MessageManager
- .getString("label.export_annotations"));
+ JMenuItem exportAnnotations = new JMenuItem(
+ MessageManager.getString("label.export_annotations"));
exportAnnotations.addActionListener(new ActionListener()
{
@Override
exportAnnotations_actionPerformed(e);
}
});
- statusPanel.setLayout(gridLayout1);
- jMenu3.setText(MessageManager.getString("action.show"));
- showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
- showAllSeqs.setToolTipText(MessageManager
- .getString("label.toggle_sequence_visibility"));
+ 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
showAllSeqs_actionPerformed(e);
}
});
- showAllColumns.setText(MessageManager.getString("label.all_columns"));
- showAllColumns.setToolTipText(MessageManager
- .getString("label.toggle_columns_visibility"));
+ JMenuItem showAllColumns = new JMenuItem(
+ MessageManager.getString("label.all_columns"));
+ showAllColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
{
@Override
showAllColumns_actionPerformed(e);
}
});
- hideMenu.setText(MessageManager.getString("action.hide"));
- hideSelSequences.setText(MessageManager
- .getString("label.selected_sequences"));
- hideSelSequences.setToolTipText(MessageManager
- .getString("label.toggle_sequence_visibility"));
+ 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
hideSelSequences_actionPerformed(e);
}
});
- hideSelColumns.setText(MessageManager
- .getString("label.selected_columns"));
- hideSelColumns.setToolTipText(MessageManager
- .getString("label.toggle_columns_visibility"));
+ JMenuItem hideSelColumns = new JMenuItem(
+ MessageManager.getString("label.selected_columns"));
+ hideSelColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
@Override
hideSelColumns_actionPerformed(e);
}
});
- hideAllSelection.setText(MessageManager
- .getString("label.selected_region"));
+ JMenuItem hideAllSelection = new JMenuItem(
+ MessageManager.getString("label.selected_region"));
hideAllSelection.addActionListener(new ActionListener()
{
@Override
}
});
// TODO: should be hidden if no selection exists.
- hideAllButSelection.setText(MessageManager
- .getString("label.all_but_selected_region"));
+ JMenuItem hideAllButSelection = new JMenuItem(
+ MessageManager.getString("label.all_but_selected_region"));
hideAllButSelection.addActionListener(new ActionListener()
{
@Override
hideAllButSelection_actionPerformed(e);
}
});
- showAllhidden.setText(MessageManager
- .getString("label.all_sequences_columns"));
+ JMenuItem showAllhidden = new JMenuItem(
+ MessageManager.getString("label.all_sequences_columns"));
showAllhidden.setToolTipText(MessageManager
.getString("label.toggles_visibility_hidden_selected_regions"));
showAllhidden.addActionListener(new ActionListener()
showAllhidden_actionPerformed(e);
}
});
- hiddenMarkers.setText(MessageManager
- .getString("action.show_hidden_markers"));
+ hiddenMarkers.setText(
+ MessageManager.getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
@Override
hiddenMarkers_actionPerformed(e);
}
});
- invertColSel.setText(MessageManager
- .getString("action.invert_column_selection"));
- invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.ALT_MASK, false));
- invertColSel.addActionListener(new ActionListener()
+
+ 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
@Override
public void mousePressed(MouseEvent e)
{
- tabbedPane_mousePressed(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()
tabbedPane_focusGained(e);
}
});
- save.setText(MessageManager.getString("action.save"));
- save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- save.addActionListener(new ActionListener()
+
+ 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()
reload_actionPerformed(e);
}
});
- newView.setText(MessageManager.getString("action.new_view"));
- newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
- newView.addActionListener(new ActionListener()
+
+ 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("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
- textColour.setText(MessageManager.getString("label.colour_text")
- + "...");
- textColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- textColour_actionPerformed(e);
- }
- });
+
formatMenu.setText(MessageManager.getString("action.format"));
- selectMenu.setText(MessageManager.getString("action.select"));
- idRightAlign.setText(MessageManager
- .getString("label.right_align_sequence_id"));
+ JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
+ idRightAlign.setText(
+ MessageManager.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
@Override
idRightAlign_actionPerformed(e);
}
});
+
gatherViews.setEnabled(false);
gatherViews.setText(MessageManager.getString("action.gather_views"));
- gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_G, 0, false));
- gatherViews.addActionListener(new ActionListener()
+ 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"));
- expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_X, 0, false));
- expandViews.addActionListener(new ActionListener()
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
+ al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
expandViews_actionPerformed(e);
}
- });
- pageSetup
- .setText(MessageManager.getString("action.page_setup") + "...");
+ };
+ addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
+ JMenuItem pageSetup = new JMenuItem(
+ MessageManager.getString("action.page_setup"));
pageSetup.addActionListener(new ActionListener()
{
@Override
pageSetup_actionPerformed(e);
}
});
- alignmentProperties.setText(MessageManager
- .getString("label.alignment_props") + "...");
+ JMenuItem alignmentProperties = new JMenuItem(
+ MessageManager.getString("label.alignment_props"));
alignmentProperties.addActionListener(new ActionListener()
{
@Override
alignmentProperties();
}
});
- tooltipSettingsMenu.setText(MessageManager
- .getString("label.sequence_id_tooltip"));
- autoAnnMenu.setText(MessageManager
- .getString("label.autocalculated_annotation"));
+ 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);
+ }
+ };
+ 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 loadTreeDb = new JMenu(
+ MessageManager.getString("label.from_database"));
+
+ JMenu loadTreeMenu = new JMenu(
+ MessageManager.getString("label.load_associated_tree"));
+ // loadTreeMenu.setToolTipText(
+ // MessageManager.getString("label.load_tree_for_sequence_set"));
+
+ JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
+
+ loadTreeDb.add(loadTreeBaseStudy);
+ loadTreeDb.add(loadTreeBase);
+ loadTreeDb.add(loadTreePfam);
+ loadTreeDb.add(loadTreeFam);
+ loadTreeDb.add(loadTreeOfLife);
+
+ loadTreeMenu.add(loadTreeFile);
+ loadTreeMenu.add(loadTreeUrl);
+ loadTreeMenu.add(loadTreeDb);
+
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(webService);
+ if (!Platform.isJS())
+ {
+ alignFrameMenuBar.add(webService);
+ }
+
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(reload);
fileMenu.add(pageSetup);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
- fileMenu.add(jMenu2);
+ fileMenu.add(exportImageMenu);
fileMenu.add(exportFeatures);
fileMenu.add(exportAnnotations);
- fileMenu.add(LoadtreeMenuItem);
+ fileMenu.add(loadTreeMenu);
fileMenu.add(associatedData);
+ if (!Platform.isJS())
+ {
+ 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(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+
+ 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(jMenu3);
+ 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);
autoAnnMenu.add(normaliseSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
- autoAnnMenu.add(showGroupConsensus);
- annotationsMenu.add(autoAnnMenu);
- viewMenu.addSeparator();
- viewMenu.add(showSeqFeatures);
- // viewMenu.add(showSeqFeaturesHeight);
+ autoAnnMenu.add(showGroupConsensus);
+ annotationsMenu.add(autoAnnMenu);
- viewMenu.add(openFeatureSettings);
- tooltipSettingsMenu.add(showDbRefsMenuitem);
- tooltipSettingsMenu.add(showNpFeatsMenuitem);
- viewMenu.add(tooltipSettingsMenu);
- viewMenu.addSeparator();
- viewMenu.add(alignmentProperties);
- viewMenu.addSeparator();
- viewMenu.add(overviewMenuItem);
- colourMenu.add(applyToAllGroups);
- colourMenu.add(textColour);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideColour);
- colourMenu.add(purinePyrimidineColour);
- colourMenu.add(RNAInteractionColour);
- // colourMenu.add(covariationColour);
- colourMenu.add(tcoffeeColour);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
+ sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortPairwiseMenuItem);
+ sort.add(sortByTreeMenu);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
- calculateMenu.add(PCAMenuItem);
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);
+ if (!Platform.isJS())
+ {
+ calculateMenu.addSeparator();
+ calculateMenu.add(runGroovy);
+ }
+
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortLengthMenuItem);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- sort.add(sortByTreeMenu);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
- jMenu2.add(createBioJS);
- jMenu2.add(createSVG);
+ if (!Platform.isJS())
+ {
+ exportImageMenu.add(htmlMenuItem);
+ }
+ exportImageMenu.add(epsFile);
+ exportImageMenu.add(createPNG);
+ if (!Platform.isJS())
+ {
+ 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);
- jMenu3.add(showAllColumns);
- jMenu3.add(showAllSeqs);
- jMenu3.add(showAllhidden);
- hideMenu.add(hideSelColumns);
- hideMenu.add(hideSelSequences);
- hideMenu.add(hideAllSelection);
- hideMenu.add(hideAllButSelection);
formatMenu.add(font);
formatMenu.addSeparator();
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
selectMenu.add(annotationColumn);
- calculateMenu.add(expandAlignment);
+ selectMenu.add(selectHighlighted);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
// selectMenu.addSeparator();
// selectMenu.add(listenToViewSelections);
+
+
+ }
+
+ protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeFam_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreePfam_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeBase_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ 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);
}
/**
}
- protected void showSeqFeaturesHeight_actionPerformed(
- ActionEvent actionEvent)
- {
- // TODO Auto-generated method stub
-
- }
-
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
{
}
- protected void showProducts_actionPerformed(ActionEvent e)
- {
- }
-
protected void buildSortByAnnotationScoresMenu()
{
}
{
}
- protected void outputText_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String formatName)
{
}
{
}
- protected void PCAMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void clustalColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void zappoColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void taylorColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void helixColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void strandColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void turnColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void buriedColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void PIDColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void RNAInteractionColour_actionPerformed(ActionEvent e)
- {
- }
-
- /*
- * protected void covariationColour_actionPerformed(ActionEvent e) { }
- */
-
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
{
}
- protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ protected void abovePIDThreshold_actionPerformed(boolean selected)
{
}
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
- {
- }
-
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
}
- protected void cut_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ protected void delete_actionPerformed()
{
}
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed(boolean selected)
{
}
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
}
- /**
- * Template method to handle the 'load T-Coffee scores' menu event.
- * <p>
- * Subclasses override this method to provide a custom action.
- *
- * @param event
- * The raised event
- */
- protected void loadScores_actionPerformed(ActionEvent event)
+ protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
{
}
+
+
/**
- * Template method to handle the 'Color T-Coffee scores' menu event.
+ * Template method to handle the 'load T-Coffee scores' menu event.
* <p>
* Subclasses override this method to provide a custom action.
*
* @param event
* The raised event
*/
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+ protected void loadScores_actionPerformed(ActionEvent event)
{
}
{
}
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
}
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed()
{
}
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
}
}
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
}
}
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
-
}
public void annotationColumn_actionPerformed(ActionEvent e)
{
-
- }
-
- public void rnahelicesColour_actionPerformed(ActionEvent e)
- {
-
}
public void associatedData_actionPerformed(ActionEvent e)
}
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
}
}
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
}
return annotationSortOrder;
}
- protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+ protected void setAnnotationSortOrder(
+ SequenceAnnotationOrder annotationSortOrder)
{
this.annotationSortOrder = annotationSortOrder;
}
+
+ public Map<KeyStroke, JMenuItem> 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)
+ {
+ }
}
git://source.jalview.org / jalview.git / blobdiff