/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.jbgui;
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
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 JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
- protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
-
- protected JMenuItem sortIDMenuItem = new JMenuItem();
-
- protected JMenuItem sortLengthMenuItem = new JMenuItem();
-
- protected JMenuItem sortGroupMenuItem = new JMenuItem();
-
protected JMenu sortByAnnotScore = new JMenu();
- protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
-
- protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
-
- protected JMenuItem PCAMenuItem = new JMenuItem();
-
- protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
-
- protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
public JLabel statusBar = new JLabel();
- protected JMenuItem saveAs = new JMenuItem();
-
protected JMenu outputTextboxMenu = new JMenu();
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem 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 JMenuItem undoMenuItem = new JMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
- JMenuItem printMenuItem = new JMenuItem();
-
public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
- JMenuItem findMenuItem = new JMenuItem();
-
public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
- JMenuItem deleteGroups = new JMenuItem();
-
- JMenuItem 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();
- JMenuItem createPNG = new JMenuItem();
-
- JMenuItem createSVG = new JMenuItem();
-
- protected JMenuItem font = new JMenuItem();
-
public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
- JMenuItem epsFile = new JMenuItem();
-
- JMenuItem LoadtreeMenuItem = new JMenuItem();
-
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- protected JMenuItem modifyPID = new JMenuItem();
-
protected JMenuItem modifyConservation = new JMenuItem();
protected JMenu sortByTreeMenu = new JMenu();
protected JMenu calculateTree = new JMenu();
- JMenu jMenu2 = new JMenu();
-
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
protected ButtonGroup colours = new ButtonGroup();
- JMenuItem vamsasStore = new JMenuItem();
-
protected JMenuItem showTranslation = new JMenuItem();
- protected JMenu cdna = new JMenu();
-
- protected JMenuItem extractScores = new JMenuItem();
-
- protected JMenuItem expandAlignment = new JMenuItem();
-
protected JMenu showProducts = new JMenu();
- public JMenuItem openFeatureSettings = new JMenuItem();
-
- JMenuItem fetchSequence = new JMenuItem();
-
- JMenuItem annotationColour = new JMenuItem();
-
protected JMenuItem rnahelicesColour = new JMenuItem();
- JMenuItem associatedData = new JMenuItem();
-
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
- JMenu addSequenceMenu = new JMenu();
-
- JMenuItem addFromFile = new JMenuItem();
-
- JMenuItem addFromText = new JMenuItem();
-
- JMenuItem addFromURL = new JMenuItem();
-
- JMenuItem exportAnnotations = new JMenuItem();
-
- JMenuItem exportFeatures = new JMenuItem();
-
protected JPanel statusPanel = new JPanel();
- GridLayout gridLayout1 = new GridLayout();
-
- JMenu jMenu3 = new JMenu();
-
- JMenuItem showAllSeqs = new JMenuItem();
-
- JMenuItem showAllColumns = new JMenuItem();
-
- JMenu hideMenu = new JMenu();
-
- JMenuItem hideSelSequences = new JMenuItem();
-
- JMenuItem hideSelColumns = new JMenuItem();
-
- JMenuItem hideAllButSelection = new JMenuItem();
-
- JMenuItem hideAllSelection = new JMenuItem();
-
- JMenuItem showAllhidden = new JMenuItem();
-
protected 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();
-
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
- private Map<KeyStroke, ActionListener> accelerators = new HashMap<KeyStroke, ActionListener>();
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+
+ private SplitContainerI splitFrame;
public GAlignFrame()
{
// colours.add(covariationColour);
colours.add(tcoffeeColour);
colours.add(RNAInteractionColour);
- setColourSelected(jalview.bin.Cache
- .getDefault("DEFAULT_COLOUR", "None"));
-
+ setColourSelected(jalview.bin.Cache.getDefault(
+ Preferences.DEFAULT_COLOUR, "None"));
}
public void setColourSelected(String defaultColour)
private void jbInit() throws Exception
{
- fileMenu.setText(MessageManager.getString("action.file"));
-
- saveAs.setText(MessageManager.getString("action.save_as") + "...");
+ JMenuItem saveAs = new JMenuItem(
+ MessageManager.getString("action.save_as") + "...");
ActionListener al = new ActionListener()
{
@Override
};
addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
- editMenu.setText(MessageManager.getString("action.edit"));
- viewMenu.setText(MessageManager.getString("action.view"));
- annotationsMenu.setText(MessageManager.getString("action.annotations"));
+ 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"));
- calculateMenu.setText(MessageManager.getString("action.calculate"));
+ JMenu calculateMenu = new JMenu(
+ MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
-
- selectAllSequenceMenuItem.setText(MessageManager
+ JMenuItem selectAllSequenceMenuItem = new JMenuItem(
+ MessageManager
.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
};
addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
- deselectAllSequenceMenuItem.setText(MessageManager
- .getString("action.deselect_all"));
+ JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
+ MessageManager.getString("action.deselect_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
al = new ActionListener()
{
};
addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
- invertSequenceMenuItem.setText(MessageManager
- .getString("action.invert_sequence_selection"));
+ JMenuItem invertSequenceMenuItem = new JMenuItem(
+ MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
- grpsFromSelection.setText(MessageManager
- .getString("action.make_groups_selection"));
+ JMenuItem grpsFromSelection = new JMenuItem(
+ MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new ActionListener()
{
@Override
makeGrpsFromSelection_actionPerformed(e);
}
});
- expandAlignment.setText(MessageManager
- .getString("action.view_flanking_regions"));
+ JMenuItem expandAlignment = new JMenuItem(
+ MessageManager.getString("action.view_flanking_regions"));
expandAlignment.setToolTipText(MessageManager
.getString("label.view_flanking_regions"));
expandAlignment.addActionListener(new ActionListener()
expand_newalign(e);
}
});
- remove2LeftMenuItem.setText(MessageManager
- .getString("action.remove_left"));
+ JMenuItem remove2LeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_left"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
- remove2RightMenuItem.setText(MessageManager
- .getString("action.remove_right"));
+ JMenuItem remove2RightMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
- removeGappedColumnMenuItem.setText(MessageManager
- .getString("action.remove_empty_columns"));
+ JMenuItem removeGappedColumnMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
- removeAllGapsMenuItem.setText(MessageManager
- .getString("action.remove_all_gaps"));
+ JMenuItem removeAllGapsMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.SHIFT_MASK, false);
};
addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
- justifyLeftMenuItem.setText(MessageManager
- .getString("action.left_justify_alignment"));
+ JMenuItem justifyLeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.left_justify_alignment"));
justifyLeftMenuItem.addActionListener(new ActionListener()
{
@Override
justifyLeftMenuItem_actionPerformed(e);
}
});
- justifyRightMenuItem.setText(MessageManager
- .getString("action.right_justify_alignment"));
+ JMenuItem justifyRightMenuItem = new JMenuItem(
+ MessageManager.getString("action.right_justify_alignment"));
justifyRightMenuItem.addActionListener(new ActionListener()
{
@Override
showUnconservedMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText(MessageManager
- .getString("action.by_pairwise_id"));
+ JMenuItem sortPairwiseMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_pairwise_id"));
sortPairwiseMenuItem.addActionListener(new ActionListener()
{
@Override
sortPairwiseMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
+ JMenuItem sortIDMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(new ActionListener()
{
@Override
sortIDMenuItem_actionPerformed(e);
}
});
- sortLengthMenuItem
- .setText(MessageManager.getString("action.by_length"));
+ JMenuItem sortLengthMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_length"));
sortLengthMenuItem.addActionListener(new ActionListener()
{
@Override
sortLengthMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
+ JMenuItem sortGroupMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(new ActionListener()
{
@Override
}
});
- removeRedundancyMenuItem.setText(MessageManager.getString(
- "action.remove_redundancy").concat("..."));
+ JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
+ .getString("action.remove_redundancy").concat("..."));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
- pairwiseAlignmentMenuItem.setText(MessageManager
- .getString("action.pairwise_alignment"));
+ JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
+ MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
{
@Override
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText(MessageManager
- .getString("label.principal_component_analysis"));
+ JMenuItem PCAMenuItem = new JMenuItem(
+ MessageManager.getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(new ActionListener()
{
@Override
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem.setText(MessageManager
- .getString("label.average_distance_identity"));
+ JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.average_distance_identity"));
averageDistanceTreeMenuItem.addActionListener(new ActionListener()
{
@Override
averageDistanceTreeMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText(MessageManager
- .getString("label.neighbour_joining_identity"));
+ JMenuItem neighbourTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(new ActionListener()
{
@Override
neighbourTreeMenuItem_actionPerformed(e);
}
});
- this.getContentPane().setLayout(borderLayout1);
+
+ 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));
outputTextboxMenu.setText(MessageManager
.getString("label.out_to_textbox"));
clustalColour.setText(MessageManager.getString("label.clustalx"));
-
clustalColour.addActionListener(new ActionListener()
{
@Override
* });
*/
- avDistanceTreeBlosumMenuItem.setText(MessageManager
- .getString("label.average_distance_bloslum62"));
+ JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
+ MessageManager.getString("label.average_distance_bloslum62"));
avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
{
@Override
avTreeBlosumMenuItem_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText(MessageManager
- .getString("label.neighbour_blosum62"));
+ JMenuItem njTreeBlosumMenuItem = new JMenuItem(
+ MessageManager.getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem.addActionListener(new ActionListener()
{
@Override
SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
.valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name()));
- sortAnnBySequence.setText(MessageManager
- .getString("label.sort_annotations_by_sequence"));
+ 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()
sortAnnotations_actionPerformed();
}
});
- sortAnnByLabel.setText(MessageManager
- .getString("label.sort_annotations_by_label"));
sortAnnByLabel
.setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
sortAnnByLabel.addActionListener(new ActionListener()
colourTextMenuItem_actionPerformed(e);
}
});
- htmlMenuItem.setText(MessageManager.getString("label.html"));
+
+ JMenuItem htmlMenuItem = new JMenuItem(
+ MessageManager.getString("label.html"));
htmlMenuItem.addActionListener(new ActionListener()
{
@Override
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText(MessageManager
- .getString("label.overview_window"));
+
+ JMenuItem createBioJS = new JMenuItem(
+ MessageManager.getString("label.biojs_html_export"));
+ createBioJS.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ bioJSMenuItem_actionPerformed(e);
+ }
+ });
+
+ JMenuItem overviewMenuItem = new JMenuItem(
+ MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(new ActionListener()
{
@Override
}
});
- printMenuItem.setText(MessageManager.getString("action.print") + "...");
+ JMenuItem printMenuItem = new JMenuItem(
+ MessageManager.getString("action.print") + "...");
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
}
});
- findMenuItem.setText(MessageManager.getString("action.find"));
+ JMenuItem findMenuItem = new JMenuItem(
+ MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
});
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));
showAutoFirst.addActionListener(new ActionListener()
sortAnnotations_actionPerformed();
}
});
- showAutoLast.setText(MessageManager.getString("label.show_last"));
showAutoLast.setSelected(!showAutoFirst.isSelected());
showAutoLast.addActionListener(new ActionListener()
{
}
});
- deleteGroups
- .setText(MessageManager.getString("action.undefine_groups"));
+ JMenuItem deleteGroups = new JMenuItem(
+ MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
- createGroup.setText(MessageManager.getString("action.create_groups"));
+ JMenuItem createGroup = new JMenuItem(
+ MessageManager.getString("action.create_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, createGroup, al);
- unGroup.setText(MessageManager.getString("action.remove_group"));
+ JMenuItem unGroup = new JMenuItem(
+ MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.SHIFT_MASK, false);
};
addMenuActionAndAccelerator(keyStroke, cut, al);
- delete.setText(MessageManager.getString("action.delete"));
+ JMenuItem delete = new JMenuItem(
+ MessageManager.getString("action.delete"));
delete.addActionListener(new ActionListener()
{
@Override
});
pasteMenu.setText(MessageManager.getString("action.paste"));
- pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
+ JMenuItem pasteNew = new JMenuItem(
+ MessageManager.getString("label.to_new_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.SHIFT_MASK, false);
};
addMenuActionAndAccelerator(keyStroke, pasteNew, al);
- pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
+ JMenuItem pasteThis = new JMenuItem(
+ MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
applyToAllGroups_actionPerformed(e);
}
});
+ JMenuItem createPNG = new JMenuItem("PNG");
createPNG.addActionListener(new ActionListener()
{
@Override
});
createPNG.setActionCommand(MessageManager
.getString("label.save_png_image"));
- createPNG.setText("PNG");
- font.setText(MessageManager.getString("action.font"));
+ JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
{
@Override
font_actionPerformed(e);
}
});
-
seqLimits.setText(MessageManager
.getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimit_actionPerformed(e);
}
});
- epsFile.setText("EPS");
+ JMenuItem epsFile = new JMenuItem("EPS");
epsFile.addActionListener(new ActionListener()
{
@Override
}
});
- createSVG.setText("SVG");
+ JMenuItem createSVG = new JMenuItem("SVG");
createSVG.addActionListener(new ActionListener()
{
@Override
}
});
- LoadtreeMenuItem.setActionCommand(MessageManager
+ JMenuItem loadTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.load_associated_tree"));
+ loadTreeMenuItem.setActionCommand(MessageManager
.getString("label.load_tree_for_sequence_set"));
- LoadtreeMenuItem.setText(MessageManager
- .getString("label.load_associated_tree"));
- LoadtreeMenuItem.addActionListener(new ActionListener()
+ loadTreeMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- LoadtreeMenuItem_actionPerformed(e);
+ loadTreeMenuItem_actionPerformed(e);
}
});
});
- modifyPID.setText(MessageManager
- .getString("label.modify_identity_thereshold"));
+ JMenuItem modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_thereshold"));
modifyPID.addActionListener(new ActionListener()
{
@Override
calculateTree
.setText(MessageManager.getString("action.calculate_tree"));
- jMenu2.setText(MessageManager.getString("label.export_image"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem.setState(jalview.bin.Cache
.getDefault("PAD_GAPS", false));
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
}
});
- /*
- * cDNA menu options
- */
- cdna.setText(MessageManager.getString("label.cdna"));
- // link to available cDNA
- JMenuItem linkCdna = new JMenuItem(
- MessageManager.getString("label.link_cdna"));
- linkCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.link_cdna_tip")));
- linkCdna.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- linkCdna_actionPerformed();
- }
- });
- cdna.add(linkCdna);
- // align linked cDNA
- JMenuItem alignCdna = new JMenuItem(
- MessageManager.getString("label.align_cdna"));
- alignCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.align_cdna_tip")));
- alignCdna.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- alignCdna_actionPerformed();
- }
- });
- cdna.add(alignCdna);
-
- // view alignment as cDNA (when known)
- JMenuItem viewAsCdna = new JMenuItem(
- MessageManager.getString("label.view_as_cdna"));
- viewAsCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.view_as_cdna_tip")));
- viewAsCdna.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- viewAsCdna_actionPerformed();
- }
- });
- cdna.add(viewAsCdna);
-
- extractScores.setText(MessageManager.getString("label.extract_scores")
- + "...");
+ JMenuItem extractScores = new JMenuItem(
+ MessageManager.getString("label.extract_scores") + "...");
extractScores.addActionListener(new ActionListener()
{
@Override
// for show products actions see AlignFrame.canShowProducts
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
- openFeatureSettings.setText(MessageManager
- .getString("label.feature_settings"));
+
+ JMenuItem openFeatureSettings = new JMenuItem(
+ MessageManager.getString("label.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
@Override
featureSettings_actionPerformed(e);
}
});
- fetchSequence
- .setText(MessageManager.getString("label.fetch_sequences"));
+ JMenuItem fetchSequence = new JMenuItem(
+ MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
@Override
}
});
- annotationColour.setText(MessageManager
- .getString("action.by_annotation"));
+ JMenuItem annotationColour = new JMenuItem(
+ MessageManager.getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
@Override
}
});
+ JMenuItem annotationColumn = new JMenuItem(
+ MessageManager.getString("action.select_by_annotation"));
+ annotationColumn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColumn_actionPerformed(e);
+ }
+ });
+
rnahelicesColour.setText(MessageManager
.getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
}
});
- associatedData.setText(MessageManager
- .getString("label.load_features_annotations"));
+ JMenuItem associatedData = new JMenuItem(
+ MessageManager.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
{
@Override
}
});
- 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"));
+ 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()
showAllSeqs_actionPerformed(e);
}
});
- showAllColumns.setText(MessageManager.getString("label.all_columns"));
+ JMenuItem showAllColumns = new JMenuItem(
+ MessageManager.getString("label.all_columns"));
showAllColumns.setToolTipText(MessageManager
.getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
showAllColumns_actionPerformed(e);
}
});
- hideMenu.setText(MessageManager.getString("action.hide"));
- hideSelSequences.setText(MessageManager
- .getString("label.selected_sequences"));
+ 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()
hideSelSequences_actionPerformed(e);
}
});
- hideSelColumns.setText(MessageManager
- .getString("label.selected_columns"));
+ JMenuItem hideSelColumns = new JMenuItem(
+ MessageManager.getString("label.selected_columns"));
hideSelColumns.setToolTipText(MessageManager
.getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
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()
}
});
- invertColSel.setText(MessageManager
- .getString("action.invert_column_selection"));
+ JMenuItem invertColSel = new JMenuItem(
+ MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.ALT_MASK, false);
};
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
}
});
- save.setText(MessageManager.getString("action.save"));
+ JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
}
});
- newView.setText(MessageManager.getString("action.new_view"));
+ JMenuItem newView = new JMenuItem(
+ MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
- textColour.setText(MessageManager.getString("label.colour_text")
- + "...");
+ JMenuItem textColour = new JMenuItem(
+ MessageManager.getString("label.colour_text") + "...");
textColour.addActionListener(new ActionListener()
{
@Override
}
});
formatMenu.setText(MessageManager.getString("action.format"));
- selectMenu.setText(MessageManager.getString("action.select"));
+ JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
idRightAlign.setText(MessageManager
.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, expandViews, al);
- pageSetup
- .setText(MessageManager.getString("action.page_setup") + "...");
+ 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"));
+ JMenu tooltipSettingsMenu = new JMenu(
+ MessageManager.getString("label.sequence_id_tooltip"));
+ JMenu autoAnnMenu = new JMenu(
+ MessageManager.getString("label.autocalculated_annotation"));
+
+ JMenu exportImageMenu = new JMenu(
+ MessageManager.getString("label.export_image"));
+ JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
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(loadTreeMenuItem);
fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+
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(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
- viewMenu.addSeparator();
- viewMenu.add(showSeqFeatures);
- // viewMenu.add(showSeqFeaturesHeight);
- viewMenu.add(openFeatureSettings);
- tooltipSettingsMenu.add(showDbRefsMenuitem);
- tooltipSettingsMenu.add(showNpFeatsMenuitem);
- viewMenu.add(tooltipSettingsMenu);
- viewMenu.addSeparator();
- viewMenu.add(alignmentProperties);
- viewMenu.addSeparator();
- viewMenu.add(overviewMenuItem);
colourMenu.add(applyToAllGroups);
colourMenu.add(textColour);
colourMenu.addSeparator();
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
- calculateMenu.add(cdna);
calculateMenu.add(showProducts);
calculateMenu.add(autoCalculate);
calculateMenu.add(sortByTree);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
sort.add(sortByTreeMenu);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
- jMenu2.add(createSVG);
+ exportImageMenu.add(htmlMenuItem);
+ exportImageMenu.add(epsFile);
+ exportImageMenu.add(createPNG);
+ exportImageMenu.add(createBioJS);
+ exportImageMenu.add(createSVG);
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
- jMenu3.add(showAllColumns);
- jMenu3.add(showAllSeqs);
- jMenu3.add(showAllhidden);
+ showMenu.add(showAllColumns);
+ showMenu.add(showAllSeqs);
+ showMenu.add(showAllhidden);
hideMenu.add(hideSelColumns);
hideMenu.add(hideSelSequences);
hideMenu.add(hideAllSelection);
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
calculateMenu.add(expandAlignment);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
JMenuItem menuItem, ActionListener actionListener)
{
menuItem.setAccelerator(keyStroke);
- accelerators.put(keyStroke, actionListener);
+ accelerators.put(keyStroke, menuItem);
menuItem.addActionListener(actionListener);
}
- protected void viewAsCdna_actionPerformed()
- {
- }
-
- protected void alignCdna_actionPerformed()
- {
- }
-
- protected void linkCdna_actionPerformed()
- {
- }
-
/**
* Action on clicking sort annotations by type.
*
{
}
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
protected void closeMenuItem_actionPerformed(boolean b)
{
}
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
}
}
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
this.annotationSortOrder = annotationSortOrder;
}
- public Map<KeyStroke, ActionListener> getAccelerators()
+ 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 state)
+ {
+ }
}
git://source.jalview.org / jalview.git / blobdiff