package jalview.jbgui;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
+import jalview.hmmer.HmmerCommand;
+import jalview.io.FileFormatException;
import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
-import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu webService = new JMenu();
+ public JMenu webService = new JMenu();// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
+ // JBP - followed suite for these other service related GUI elements.
+ // TODO: check we really need these to be public
+ public JMenu hmmerMenu = new JMenu();
- protected JMenu hmmerMenu = new JMenu();
-
- protected JMenuItem hmmAlign = new JMenuItem();
-
- protected JMenuItem hmmSearch = new JMenuItem();
-
- protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
-
- protected JMenuItem webServiceNoServices;
+ public JMenuItem webServiceNoServices;
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
- public JLabel statusBar = new JLabel();
+ public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+ // sufficient for
+ // AlignFrame.printWriter
protected JMenu outputTextboxMenu = new JMenu();
protected JMenuItem modifyPID;
- protected JMenuItem annotationColour;
+ protected JRadioButtonMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
- protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenu showTranslation = new JMenu();
protected JMenuItem showReverse = new JMenuItem();
protected JMenuItem runGroovy = new JMenuItem();
+ protected JMenuItem loadVcf;
+
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+ protected JMenuItem openFeatureSettings;
+
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
{
try
{
+
+ // for Web-page embedding using id=align-frame-div
+ setName("jalview-alignment");
+
jbInit();
setJMenuBar(alignFrameMenuBar);
@Override
public void actionPerformed(ActionEvent e)
{
- outputText_actionPerformed(e);
+ outputText_actionPerformed(e.getActionCommand());
}
});
System.err.println(e.toString());
}
- if (!Platform.isAMac())
+ if (Platform.allowMnemonics()) // was "not mac and not JS"
{
closeMenuItem.setMnemonic('C');
outputTextboxMenu.setMnemonic('T');
private void jbInit() throws Exception
{
initColourMenu();
- initHMMERMenu();
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
@Override
public void actionPerformed(ActionEvent e)
{
- saveAs_actionPerformed(e);
+ saveAs_actionPerformed();
}
};
// FIXME getDefaultToolkit throws an exception in Headless mode
- KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ 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, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenu calculateMenu = new JMenu(
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
- hmmerMenu.setText(MessageManager.getString("action.hmmer"));
- String status = Cache.getProperty("HMMER_FUNCTIONING");
- if ("false".equals(status) || status == null)
- {
- hmmerMenu.setEnabled(false);
- }
- else
- {
- hmmerMenu.setEnabled(true);
- }
- hmmerMenu.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hmmerMenu_actionPerformed(e);
- }
- });
+
+ initHMMERMenu();
+
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
});
JMenuItem expandAlignment = new JMenuItem(
MessageManager.getString("action.view_flanking_regions"));
- expandAlignment.setToolTipText(MessageManager
- .getString("label.view_flanking_regions"));
+ expandAlignment.setToolTipText(
+ MessageManager.getString("label.view_flanking_regions"));
expandAlignment.addActionListener(new ActionListener()
{
@Override
});
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ false);
al = new ActionListener()
{
@Override
viewTextMenuItem_actionPerformed(e);
}
});
- showNonconservedMenuItem.setText(MessageManager
- .getString("label.show_non_conserved"));
+ showNonconservedMenuItem
+ .setText(MessageManager.getString("label.show_non_conserved"));
showNonconservedMenuItem.setState(false);
showNonconservedMenuItem.addActionListener(new ActionListener()
{
sortGroupMenuItem_actionPerformed(e);
}
});
+ JMenuItem sortEValueMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_evalue"));
+ sortEValueMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortEValueMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem sortBitScoreMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_bit_score"));
+ sortBitScoreMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortBitScoreMenuItem_actionPerformed(e);
+ }
+ });
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
}
};
addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
+ JMenuItem filterByEValue = new JMenuItem(
+ MessageManager.getString("action.filter_by_evalue"));
+ filterByEValue.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterByEValue_actionPerformed();
+ }
+
+ });
+
+ JMenuItem filterByScore = new JMenuItem(
+ MessageManager.getString("action.filter_by_score"));
+ filterByScore.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterByScore_actionPerformed();
+ }
+
+ });
JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
MessageManager.getString("action.pairwise_alignment"));
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"));
-
+
+ outputTextboxMenu
+ .setText(MessageManager.getString("label.out_to_textbox"));
+
+
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText(MessageManager
- .getString("label.show_annotations"));
- annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
- true));
+ annotationPanelMenuItem
+ .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()
{
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.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
- .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 = new JCheckBoxMenuItem(
- MessageManager
- .getString("label.colour_text"));
+ MessageManager.getString("label.colour_text"));
colourTextMenuItem.addActionListener(new ActionListener()
{
@Override
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
}
};
addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
-
- showSeqFeatures.setText(MessageManager
- .getString("label.show_sequence_features"));
+
+ 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()
MessageManager.getString("label.show_last"));
buttonGroup.add(showAutoFirst);
buttonGroup.add(showAutoLast);
- final boolean autoFirst = 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()
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ false);
al = new ActionListener()
{
@Override
addMenuActionAndAccelerator(keyStroke, unGroup, al);
copy.setText(MessageManager.getString("action.copy"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
-
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+
al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- copy_actionPerformed(e);
+ copy_actionPerformed();
}
};
addMenuActionAndAccelerator(keyStroke, copy, al);
cut.setText(MessageManager.getString("action.cut"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- cut_actionPerformed(e);
+ cut_actionPerformed();
}
};
addMenuActionAndAccelerator(keyStroke, cut, al);
@Override
public void actionPerformed(ActionEvent e)
{
- delete_actionPerformed(e);
+ delete_actionPerformed();
}
});
pasteMenu.setText(MessageManager.getString("action.paste"));
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ false);
al = new ActionListener()
{
@Override
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
createPNG(null);
}
});
- createPNG.setActionCommand(MessageManager
- .getString("label.save_png_image"));
-
+ createPNG.setActionCommand(
+ MessageManager.getString("label.save_png_image"));
JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
{
font_actionPerformed(e);
}
});
- seqLimits.setText(MessageManager
- .getString("label.show_sequence_limits"));
+ seqLimits.setText(
+ MessageManager.getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new ActionListener()
{
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
- loadTreeMenuItem.setActionCommand(MessageManager
- .getString("label.load_tree_for_sequence_set"));
+ loadTreeMenuItem.setActionCommand(
+ MessageManager.getString("label.load_tree_for_sequence_set"));
loadTreeMenuItem.addActionListener(new ActionListener()
{
@Override
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText(MessageManager
- .getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.setText(
+ MessageManager.getString("label.centre_column_labels"));
centreColumnLabelsMenuItem.addActionListener(new ActionListener()
{
@Override
});
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
- followHighlightMenuItem.setText(MessageManager
- .getString("label.automatic_scrolling"));
+ followHighlightMenuItem
+ .setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
{
}
});
- 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_pca"));
-
+
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree_pca"));
+
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
- padGapsMenuitem.setState(jalview.bin.Cache
- .getDefault("PAD_GAPS", false));
+ padGapsMenuitem
+ .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText(MessageManager
- .getString("label.translate_cDNA"));
- showTranslation.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
+
+ /*
+ * Translate as cDNA with sub-menu of translation tables
+ */
+ showTranslation
+ .setText(MessageManager.getString("label.translate_cDNA"));
+ boolean first = true;
+ for (final GeneticCodeI table : GeneticCodes.getInstance()
+ .getCodeTables())
+ {
+ JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+ showTranslation.add(item);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(table);
+ }
+ });
+ if (first)
{
- showTranslation_actionPerformed(e);
+ showTranslation.addSeparator();
}
- });
+ first = false;
+ }
+
showReverse.setText(MessageManager.getString("label.reverse"));
showReverse.addActionListener(new ActionListener()
{
showReverse_actionPerformed(false);
}
});
- showReverseComplement.setText(MessageManager
- .getString("label.reverse_complement"));
+ showReverseComplement
+ .setText(MessageManager.getString("label.reverse_complement"));
showReverseComplement.addActionListener(new ActionListener()
{
@Override
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
runGroovy.setText(MessageManager.getString("label.run_groovy"));
- runGroovy.setToolTipText(MessageManager
- .getString("label.run_groovy_tip"));
+ runGroovy.setToolTipText(
+ MessageManager.getString("label.run_groovy_tip"));
runGroovy.addActionListener(new ActionListener()
{
@Override
runGroovy_actionPerformed();
}
});
-
- JMenuItem openFeatureSettings = new JMenuItem(
+
+ openFeatureSettings = new JMenuItem(
MessageManager.getString("action.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
featureSettings_actionPerformed(e);
}
});
+
+ /*
+ * 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)
{
- fetchSequence_actionPerformed(e);
+ fetchSequence_actionPerformed();
}
});
}
}
});
- autoCalculate.setText(MessageManager
- .getString("label.autocalculate_consensus"));
- autoCalculate.setState(jalview.bin.Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
+ loadVcf = new JMenuItem(
+ MessageManager.getString("label.load_vcf_file"));
+ loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
+ loadVcf.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadVcf_actionPerformed();
+ }
+ });
+ autoCalculate.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setState(
+ jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
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.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.addActionListener(new ActionListener()
sortByTreeOption_actionPerformed(e);
}
});
-
- 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()
{
statusPanel.setLayout(new GridLayout());
JMenuItem showAllSeqs = new JMenuItem(
MessageManager.getString("label.all_sequences"));
- showAllSeqs.setToolTipText(MessageManager
- .getString("label.toggle_sequence_visibility"));
+ showAllSeqs.setToolTipText(
+ MessageManager.getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
{
@Override
});
JMenuItem showAllColumns = new JMenuItem(
MessageManager.getString("label.all_columns"));
- showAllColumns.setToolTipText(MessageManager
- .getString("label.toggle_columns_visibility"));
+ showAllColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
{
@Override
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.setToolTipText(
+ MessageManager.getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
{
@Override
});
JMenuItem hideSelColumns = new JMenuItem(
MessageManager.getString("label.selected_columns"));
- hideSelColumns.setToolTipText(MessageManager
- .getString("label.toggle_columns_visibility"));
+ hideSelColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
@Override
showAllhidden_actionPerformed(e);
}
});
- hiddenMarkers.setText(MessageManager
- .getString("action.show_hidden_markers"));
+ hiddenMarkers.setText(
+ MessageManager.getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
@Override
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.ALT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
+ false);
al = new ActionListener()
{
@Override
});
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
-
- idRightAlign.setText(MessageManager
- .getString("label.right_align_sequence_id"));
+
+ idRightAlign.setText(
+ MessageManager.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
@Override
});
JMenuItem selectHighlighted = new JMenuItem(
MessageManager.getString("action.select_highlighted_columns"));
- selectHighlighted.setToolTipText(MessageManager
- .getString("tooltip.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(
+ MessageManager.getString("tooltip.select_highlighted_columns"));
al = new ActionListener()
{
@Override
selectHighlightedColumns_actionPerformed(actionEvent);
}
};
- hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
- hmmBuild.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- hmmBuild_actionPerformed(e);
- } catch (IOException e1)
- {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (InterruptedException e1)
- {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
- }
-
- });
- hmmAlign.setText(MessageManager.getString("label.hmmalign"));
- hmmAlign.addActionListener(new ActionListener()
+ JMenuItem Filter = new JMenuItem(
+ MessageManager.getString("action.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(
+ MessageManager.getString("tooltip.select_highlighted_columns"));
+ al = new ActionListener()
{
-
@Override
- public void actionPerformed(ActionEvent e)
+ public void actionPerformed(ActionEvent actionEvent)
{
- try
- {
- hmmAlign_actionPerformed(e);
- } catch (IOException e1)
- {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (InterruptedException e1)
- {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
+ selectHighlightedColumns_actionPerformed(actionEvent);
}
-
- });
+ };
selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(webService);
- alignFrameMenuBar.add(hmmerMenu);
+ if (!Platform.isJS())
+ {
+ alignFrameMenuBar.add(hmmerMenu);
+ }
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(exportAnnotations);
fileMenu.add(loadTreeMenuItem);
fileMenu.add(associatedData);
+ if (!Platform.isJS())
+ {
+ fileMenu.add(loadVcf);
+ }
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+ editMenu.addSeparator();
+ editMenu.add(filterByEValue);
+ editMenu.add(filterByScore);
showMenu.add(showAllColumns);
showMenu.add(showAllSeqs);
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
-
-
+
sort.add(sortIDMenuItem);
sort.add(sortLengthMenuItem);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
+ sort.add(sortEValueMenuItem);
+ sort.add(sortBitScoreMenuItem);
sort.add(sortByTreeMenu);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(expandAlignment);
calculateMenu.add(extractScores);
- calculateMenu.addSeparator();
- calculateMenu.add(runGroovy);
-
+ if (!Platform.isJS())
+ {
+ calculateMenu.addSeparator();
+ calculateMenu.add(runGroovy);
+ }
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
- exportImageMenu.add(htmlMenuItem);
+ if (!Platform.isJS())
+ {
+ exportImageMenu.add(htmlMenuItem);
+ }
exportImageMenu.add(epsFile);
exportImageMenu.add(createPNG);
- exportImageMenu.add(createBioJS);
- exportImageMenu.add(createSVG);
+ if (!Platform.isJS())
+ {
+ exportImageMenu.add(createBioJS);
+ exportImageMenu.add(createSVG);
+ }
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
// selectMenu.add(listenToViewSelections);
}
- public void hmmerMenu_actionPerformed(ActionEvent e)
+ /**
+ * Constructs the entries on the HMMER menu
+ */
+ protected void initHMMERMenu()
{
+ /*
+ * hmmbuild
+ */
+ JMenu hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+ JMenuItem hmmBuildSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmBuildSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(false);
+ }
+ });
+ JMenuItem hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmbuild"));
+ hmmBuildRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuild_actionPerformed(true);
+ }
+ });
+ hmmBuild.add(hmmBuildRun);
+ hmmBuild.add(hmmBuildSettings);
+
+ /*
+ * hmmalign
+ */
+ JMenu hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
+ JMenuItem hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmalign"));
+ hmmAlignRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(true);
+ }
+ });
+ JMenuItem hmmAlignSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmAlignSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(false);
+ }
+ });
+ hmmAlign.add(hmmAlignRun);
+ hmmAlign.add(hmmAlignSettings);
+
+ /*
+ * hmmsearch
+ */
+ JMenu hmmSearch = new JMenu(
+ MessageManager.getString("label.hmmsearch"));
+ JMenuItem hmmSearchSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmSearchSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_actionPerformed(false);
+ }
+ });
+ JMenuItem hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmsearch"));
+ hmmSearchRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearch_actionPerformed(true);
+ }
+ });
+ JMenuItem addDatabase = new JMenuItem(
+ MessageManager.getString("label.add_database"));
+ addDatabase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ addDatabase_actionPerformed();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ hmmSearch.add(hmmSearchRun);
+ hmmSearch.add(hmmSearchSettings);
+ // hmmSearch.add(addDatabase);
+
+ /*
+ * jackhmmer
+ */
+ JMenu jackhmmer = new JMenu(
+ MessageManager.getString("label.jackhmmer"));
+ JMenuItem jackhmmerSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ jackhmmerSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jackhmmer_actionPerformed(false);
+ }
+ });
+ JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "jackhmmer"));
+ jackhmmerRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jackhmmer_actionPerformed(true);
+ }
+
+ });
+ /*
+ JMenuItem addDatabase = new JMenuItem(
+ MessageManager.getString("label.add_database"));
+ addDatabase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ addDatabase_actionPerformed();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ */
+ jackhmmer.add(jackhmmerRun);
+ jackhmmer.add(jackhmmerSettings);
+ // hmmSearch.add(addDatabase);
+
+ /*
+ * top level menu
+ */
+ hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ hmmerMenu.add(hmmBuild);
+ hmmerMenu.add(hmmAlign);
+ hmmerMenu.add(hmmSearch);
+ hmmerMenu.add(jackhmmer);
}
+ protected void loadVcf_actionPerformed()
+ {
+ }
+
/**
* Constructs the entries on the Colour menu (but does not add them to the
* menu).
*/
- protected void initHMMERMenu()
- {
- hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
- hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
- hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
- }
protected void initColourMenu()
{
applyToAllGroups = new JCheckBoxMenuItem(
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed(conservationMenuItem
- .isSelected());
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
}
});
modifyPID_actionPerformed();
}
});
- modifyConservation = new JMenuItem(
- MessageManager
+ modifyConservation = new JMenuItem(MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
{
}
});
- annotationColour = new JMenuItem(
+ annotationColour = new JRadioButtonMenuItem(
MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
annotationColour.addActionListener(new ActionListener()
{
@Override
{
}
- protected void outputText_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String formatName)
{
}
{
}
+ protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
protected void removeRedundancyMenuItem_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 autoAlignSeqs_actionPerformed(boolean selected)
+ protected void hmmBuild_actionPerformed(boolean withDefaults)
{
}
- protected void hmmAlign_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ protected void hmmSearch_actionPerformed(boolean withDefaults)
{
}
- protected void changeHMMERLocation_actionPerformed(ActionEvent e)
+ protected void jackhmmer_actionPerformed(boolean b)
{
}
- protected void hmmBuild_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ protected void addDatabase_actionPerformed()
+ throws FileFormatException, IOException
{
}
- protected void hmmSearch_actionPerformed(ActionEvent e)
+ protected void hmmAlign_actionPerformed(boolean withDefaults)
{
}
{
}
+ protected void filterByEValue_actionPerformed()
+ {
+ }
+
+ protected void filterByScore_actionPerformed()
+ {
+ }
+
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
{
}
- 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()
{
}
protected void showComplement_actionPerformed(boolean complement)
{
}
-
- protected void showInformationHistogram_actionPerformed(ActionEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
- {
- // TODO Auto-generated method stub
-
- }
}
git://source.jalview.org / jalview.git / blobdiff