/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
protected JMenu viewMenu = new JMenu();
+ protected JMenu annotationsMenu = new JMenu();
+
protected JMenu colourMenu = new JMenu();
protected JMenu calculateMenu = new JMenu();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
JMenuItem deleteGroups = new JMenuItem();
-
+
JMenuItem createGroup = new JMenuItem();
+
JMenuItem unGroup = new JMenuItem();
JMenuItem delete = new JMenuItem();
protected JMenuItem extractScores = new JMenuItem();
+ protected JMenuItem expandAlignment = new JMenuItem();
+
protected JMenu showProducts = new JMenu();
public JMenuItem openFeatureSettings = new JMenuItem();
JMenuItem showAllhidden = new JMenuItem();
+ protected JMenuItem showAllAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllAnnotations = new JMenuItem();
+
+ protected JMenuItem sortAnnBySequence = new JMenuItem();
+
+ protected JMenuItem sortAnnByType = new JMenuItem();
+
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
JMenuItem invertColSel = new JMenuItem();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
}
} catch (Exception e)
{
+ System.err.println(e.toString());
}
if (!new jalview.util.Platform().isAMac())
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (evt.isControlDown()
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- MessageManager.getString("label.remove_from_default_list"),
- MessageManager.getString("label.remove_user_defined_colour"),
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
{
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);
colours.add(purinePyrimidineColour);
// colours.add(covariationColour);
colours.add(tcoffeeColour);
-
+ colours.add(RNAInteractionColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
purinePyrimidineColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.RNAINTERACTION:
+ RNAInteractionColour.setSelected(true);
+
+ break;
/*
* case ColourSchemeProperty.COVARIATION:
* covariationColour.setSelected(true);
| java.awt.event.KeyEvent.SHIFT_MASK, false));
saveAs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
saveAs_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
closeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
closeMenuItem_actionPerformed(false);
});
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.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.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.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.setText(MessageManager
+ .getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
makeGrpsFromSelection_actionPerformed(e);
}
});
-
- remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
+ expandAlignment.setText(MessageManager
+ .getString("action.view_flanking_regions"));
+ expandAlignment.setToolTipText(MessageManager
+ .getString("label.view_flanking_regions"));
+ expandAlignment.addActionListener(new java.awt.event.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.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.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.setText(MessageManager
+ .getString("action.remove_all_gaps"));
removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
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.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.setText(MessageManager
+ .getString("action.right_justify_alignment"));
justifyRightMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
justifyRightMenuItem_actionPerformed(e);
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
viewBoxesMenuItem_actionPerformed(e);
viewTextMenuItem.setState(true);
viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
viewTextMenuItem_actionPerformed(e);
}
});
- showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
+ 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.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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortIDMenuItem_actionPerformed(e);
}
});
- sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
+ 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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortGroupMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
+ 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.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.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.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.setText(MessageManager
+ .getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
neighbourTreeMenuItem_actionPerformed(e);
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"));
clustalColour.setText(MessageManager.getString("label.clustalx"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clustalColour_actionPerformed(e);
zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed(e);
taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+ 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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed(e);
}
});
- strandColour.setText(MessageManager.getString("label.strand_propensity"));
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed(e);
}
});
- turnColour.setText(MessageManager.getString("Turn Propensity"));
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed(e);
}
});
- buriedColour.setText(MessageManager.getString("Buried Index"));
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed(e);
}
});
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed(e);
}
});
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour
+ .setText(MessageManager.getString("label.blosum62_score"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed(e);
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideColour_actionPerformed(e);
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ 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() {
* covariationColour_actionPerformed(e); } });
*/
- avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
+ 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.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(jalview.bin.Cache.getDefault(
- "SHOW_ANNOTATIONS", true));
- annotationPanelMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotationPanelMenuItem_actionPerformed(e);
- }
- });
- colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
+ annotationPanelMenuItem.setText(MessageManager
+ .getString("label.show_annotations"));
+ annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
+ true));
+ annotationPanelMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationPanelMenuItem_actionPerformed(e);
+ }
+ });
+ /*
+ * Show/hide all annotations only enabled if annotation panel is shown
+ */
+ showAllAnnotations.setText(MessageManager
+ .getString("label.show_all_annotations"));
+ showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllAnnotations_actionPerformed();
+ }
+ });
+ hideAllAnnotations.setText(MessageManager
+ .getString("label.hide_all_annotations"));
+ hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllAnnotations_actionPerformed();
+ }
+ });
+ sortAnnBySequence.setText(MessageManager
+ .getString("label.sort_annotations_by_sequence"));
+ sortAnnBySequence.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortAnnotationsBySequence_actionPerformed();
+ }
+ });
+ sortAnnByType.setText(MessageManager
+ .getString("label.sort_annotations_by_type"));
+ sortAnnByType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortAnnotationsByType_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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
+ overviewMenuItem.setText(MessageManager
+ .getString("label.overview_window"));
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
overviewMenuItem_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
undoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
undoMenuItem_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
redoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
redoMenuItem_actionPerformed(e);
}
});
- conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
+ 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);
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
wrapMenuItem_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
printMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
printMenuItem_actionPerformed(e);
}
});
- renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
+ 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.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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
findMenuItem_actionPerformed(e);
}
});
- abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.setText(MessageManager
+ .getString("label.above_identity_threshold"));
abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
abovePIDThreshold_actionPerformed(e);
}
});
- showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
+ showSeqFeatures.setText(MessageManager
+ .getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
showSeqFeatures_actionPerformed(actionEvent);
* 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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showDbRefs_actionPerformed(e);
}
});
- showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.setText(MessageManager
+ .getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNpFeats_actionPerformed(e);
}
});
- showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
+ showGroupConservation.setText(MessageManager
+ .getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showGroupConservation_actionPerformed(e);
});
- showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
+ showGroupConsensus.setText(MessageManager
+ .getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showGroupConsensus_actionPerformed(e);
}
});
- showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
+ showConsensusHistogram.setText(MessageManager
+ .getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showConsensusHistogram_actionPerformed(e);
}
});
- showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
+ showSequenceLogo.setText(MessageManager
+ .getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showSequenceLogo_actionPerformed(e);
}
});
- normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo.setText(MessageManager
+ .getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
normaliseSequenceLogo_actionPerformed(e);
}
});
- applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings.setText(MessageManager
+ .getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
applyAutoAnnotationSettings_actionPerformed(e);
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideColour_actionPerformed(e);
}
});
- deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
+ 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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
deleteGroups_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
createGroup.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createGroup_actionPerformed(e);
});
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));
+ java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+ .getMenuShortcutKeyMask()
+ | java.awt.event.KeyEvent.SHIFT_MASK, false));
unGroup.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
unGroup_actionPerformed(e);
copy.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
cut.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed(e);
}
});
delete.setText(MessageManager.getString("action.delete"));
- delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
delete.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
delete_actionPerformed(e);
| java.awt.event.KeyEvent.SHIFT_MASK, false));
pasteNew.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pasteNew_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
pasteThis.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pasteThis_actionPerformed(e);
}
});
- applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setText(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
applyToAllGroups_actionPerformed(e);
});
createPNG.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createPNG(null);
}
});
- createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
+ createPNG.setActionCommand(MessageManager
+ .getString("label.save_png_image"));
createPNG.setText("PNG");
font.setText(MessageManager.getString("action.font"));
font.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
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 java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
seqLimit_actionPerformed(e);
epsFile.setText("EPS");
epsFile.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createEPS(null);
}
});
- LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
- LoadtreeMenuItem.setText(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 java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
LoadtreeMenuItem_actionPerformed(e);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
scaleAbove.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
scaleAbove_actionPerformed(e);
scaleLeft.setText(MessageManager.getString("action.scale_left"));
scaleLeft.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
scaleLeft_actionPerformed(e);
scaleRight.setText(MessageManager.getString("action.scale_right"));
scaleRight.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
scaleRight_actionPerformed(e);
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.setText(MessageManager
+ .getString("label.centre_column_labels"));
centreColumnLabelsMenuItem
.addActionListener(new java.awt.event.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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
followHighlight_actionPerformed();
});
- modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
+ 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.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"));
+ sortByTreeMenu
+ .setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
sort.addMenuListener(new MenuListener()
{
+ @Override
public void menuSelected(MenuEvent e)
{
buildTreeMenu();
}
+ @Override
public void menuDeselected(MenuEvent e)
{
}
+ @Override
public void menuCanceled(MenuEvent e)
{
}
});
- sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
+ sortByAnnotScore.setText(MessageManager
+ .getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
{
+ @Override
public void menuCanceled(MenuEvent e)
{
}
+ @Override
public void menuDeselected(MenuEvent e)
{
}
+ @Override
public void menuSelected(MenuEvent e)
{
buildSortByAnnotationScoresMenu();
});
sortByAnnotScore.setVisible(false);
- calculateTree.setText(MessageManager.getString("action.calculate_tree"));
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree"));
jMenu2.setText(MessageManager.getString("label.export_image"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
padGapsMenuitem_actionPerformed(e);
vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
vamsasStore.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
showTranslation.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showTranslation_actionPerformed(e);
}
});
- extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
+ extractScores.setText(MessageManager.getString("label.extract_scores")
+ + "...");
extractScores.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
extractScores_actionPerformed(e);
* public void actionPerformed(ActionEvent e) {
* showProducts_actionPerformed(e); } });
*/
- openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
+ openFeatureSettings.setText(MessageManager
+ .getString("label.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
featureSettings_actionPerformed(e);
}
});
- fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
+ fetchSequence
+ .setText(MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
fetchSequence_actionPerformed(e);
}
});
- annotationColour.setText(MessageManager.getString("action.by_annotation"));
+ annotationColour.setText(MessageManager
+ .getString("action.by_annotation"));
annotationColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
annotationColour_actionPerformed(e);
}
});
- rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
+ rnahelicesColour.setText(MessageManager
+ .getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
rnahelicesColour_actionPerformed(e);
}
});
- associatedData.setText(MessageManager.getString("label.load_features_annotations"));
+ associatedData.setText(MessageManager
+ .getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
associatedData_actionPerformed(e);
}
});
- autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setText(MessageManager
+ .getString("label.autocalculate_consensus"));
autoCalculate.setState(jalview.bin.Cache.getDefault(
"AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
autoCalculate_actionPerformed(e);
}
});
- sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
+ sortByTree.setText(MessageManager
+ .getString("label.sort_alignment_new_tree"));
sortByTree
- .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+ .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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
listenToViewSelections_actionPerformed(e);
}
});
- addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
+ addSequenceMenu
+ .setText(MessageManager.getString("label.add_sequences"));
addFromFile.setText(MessageManager.getString("label.from_file"));
addFromFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromFile_actionPerformed(e);
addFromText.setText(MessageManager.getString("label.from_textbox"));
addFromText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromText_actionPerformed(e);
addFromURL.setText(MessageManager.getString("label.from_url"));
addFromURL.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromURL_actionPerformed(e);
}
});
- exportFeatures.setText(MessageManager.getString("label.export_features"));
+ exportFeatures.setText(MessageManager
+ .getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
exportFeatures_actionPerformed(e);
}
});
- exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
+ exportAnnotations.setText(MessageManager
+ .getString("label.export_annotations"));
exportAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
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"));
+ showAllSeqs.setToolTipText(MessageManager
+ .getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showAllSeqs_actionPerformed(e);
}
});
showAllColumns.setText(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
public void actionPerformed(ActionEvent e)
{
showAllColumns_actionPerformed(e);
}
});
hideMenu.setText(MessageManager.getString("action.hide"));
- hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
- hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+ hideSelSequences.setText(MessageManager
+ .getString("label.selected_sequences"));
+ hideSelSequences.setToolTipText(MessageManager
+ .getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSelSequences_actionPerformed(e);
}
});
- hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
- hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+ hideSelColumns.setText(MessageManager
+ .getString("label.selected_columns"));
+ hideSelColumns.setToolTipText(MessageManager
+ .getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSelColumns_actionPerformed(e);
}
});
- hideAllSelection.setText(MessageManager.getString("label.selected_region"));
+ hideAllSelection.setText(MessageManager
+ .getString("label.selected_region"));
hideAllSelection.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideAllSelection_actionPerformed(e);
}
});
// TODO: should be hidden if no selection exists.
- hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
+ hideAllButSelection.setText(MessageManager
+ .getString("label.all_but_selected_region"));
hideAllButSelection.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideAllButSelection_actionPerformed(e);
}
});
- showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
- showAllhidden
- .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
+ showAllhidden.setText(MessageManager
+ .getString("label.all_sequences_columns"));
+ showAllhidden.setToolTipText(MessageManager
+ .getString("label.toggles_visibility_hidden_selected_regions"));
showAllhidden.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showAllhidden_actionPerformed(e);
}
});
-
- hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
+ hiddenMarkers.setText(MessageManager
+ .getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hiddenMarkers_actionPerformed(e);
}
});
- invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
+ 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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
invertColSel_actionPerformed(e);
});
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
JTabbedPane pane = (JTabbedPane) evt.getSource();
});
tabbedPane.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
tabbedPane_mousePressed(e);
});
tabbedPane.addFocusListener(new FocusAdapter()
{
+ @Override
public void focusGained(FocusEvent e)
{
tabbedPane_focusGained(e);
.getMenuShortcutKeyMask(), false));
save.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
save_actionPerformed(e);
reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
reload_actionPerformed(e);
.getMenuShortcutKeyMask(), false));
newView.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
newView_actionPerformed(e);
}
});
- tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
- textColour.setText(MessageManager.getString("label.colour_text") + "...");
+ 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"));
+ idRightAlign.setText(MessageManager
+ .getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
idRightAlign_actionPerformed(e);
java.awt.event.KeyEvent.VK_G, 0, false));
gatherViews.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
gatherViews_actionPerformed(e);
java.awt.event.KeyEvent.VK_X, 0, false));
expandViews.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
expandViews_actionPerformed(e);
}
});
- pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
+ pageSetup
+ .setText(MessageManager.getString("action.page_setup") + "...");
pageSetup.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pageSetup_actionPerformed(e);
}
});
- alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
+ alignmentProperties.setText(MessageManager
+ .getString("label.alignment_props") + "...");
alignmentProperties.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
alignmentProperties();
}
});
- tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
- autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
+ tooltipSettingsMenu.setText(MessageManager
+ .getString("label.sequence_id_tooltip"));
+ autoAnnMenu.setText(MessageManager
+ .getString("label.autocalculated_annotation"));
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(annotationsMenu);
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
viewMenu.add(hideMenu);
viewMenu.addSeparator();
viewMenu.add(followHighlightMenuItem);
- viewMenu.add(annotationPanelMenuItem);
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.add(showAllAnnotations);
+ annotationsMenu.add(hideAllAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByType);
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
- viewMenu.add(autoAnnMenu);
+ annotationsMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(showSeqFeatures);
// viewMenu.add(showSeqFeaturesHeight);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(RNAInteractionColour);
// colourMenu.add(covariationColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
calculateMenu.add(sortByTree);
calculateMenu.addSeparator();
calculateMenu.add(extractScores);
- webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
+ webServiceNoServices = new JMenuItem(
+ MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
sort.add(sortByTreeMenu);
- calculateTree.add(averageDistanceTreeMenuItem);
- calculateTree.add(neighbourTreeMenuItem);
- calculateTree.add(avDistanceTreeBlosumMenuItem);
- calculateTree.add(njTreeBlosumMenuItem);
jMenu2.add(htmlMenuItem);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+ calculateMenu.add(expandAlignment);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
// selectMenu.addSeparator();
// selectMenu.add(listenToViewSelections);
}
+ /**
+ * Action on clicking sort annotations by type.
+ */
+ protected void sortAnnotationsByType_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking sort annotations by sequence
+ */
+ protected void sortAnnotationsBySequence_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking Show all annotations.
+ */
+ protected void showAllAnnotations_actionPerformed()
+ {
+ setAllAnnotationsVisibility(true);
+ }
+
+ /**
+ * Action on clicking Hide all annotations.
+ */
+ protected void hideAllAnnotations_actionPerformed()
+ {
+ setAllAnnotationsVisibility(false);
+ }
+
+ /**
+ * Set the visibility of all annotations to true or false.
+ *
+ * @param visible
+ */
+ protected void setAllAnnotationsVisibility(boolean visible)
+ {
+
+ }
+
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
{
}
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
/*
* protected void covariationColour_actionPerformed(ActionEvent e) { }
*/
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
-
+
protected void createGroup_actionPerformed(ActionEvent e)
{
}
-
+
protected void unGroup_actionPerformed(ActionEvent e)
{
}
{
}
+
+ protected void expand_newalign(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff