/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.jbgui;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
protected JMenu viewMenu = new JMenu();
+ protected JMenu annotationsMenu = new JMenu();
+
protected JMenu colourMenu = new JMenu();
protected JMenu calculateMenu = new JMenu();
JMenuItem createBioJS = new JMenuItem();
+ JMenuItem createSVG = new JMenuItem();
+
protected JMenuItem font = new JMenuItem();
public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
JMenuItem annotationColour = new JMenuItem();
+ JMenuItem annotationColumn = new JMenuItem();
+
protected JMenuItem rnahelicesColour = new JMenuItem();
JMenuItem associatedData = new JMenuItem();
JMenuItem showAllhidden = new JMenuItem();
- protected JMenuItem showAllAnnotations = new JMenuItem();
+ protected JMenuItem showAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem showAllAlAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllAlAnnotations = new JMenuItem();
- protected JMenuItem hideAllAnnotations = new JMenuItem();
+ protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+ protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
+
private JMenuItem grpsFromSelection = new JMenuItem();
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ private boolean showAutoCalculatedAbove = false;
+
public GAlignFrame()
{
try
});
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"));
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()
+ showAllAlAnnotations.setText(MessageManager
+ .getString("label.show_all_al_annotations"));
+ final boolean isAnnotationPanelShown = annotationPanelMenuItem
+ .getState();
+ showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ showAllAlAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllAnnotations_actionPerformed(false, true);
+ }
+ });
+ hideAllAlAnnotations.setText(MessageManager
+ .getString("label.hide_all_al_annotations"));
+ hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllAlAnnotations.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- showAllAnnotations_actionPerformed();
+ hideAllAnnotations_actionPerformed(false, true);
}
});
- hideAllAnnotations.setText(MessageManager
- .getString("label.hide_all_annotations"));
- hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllAnnotations.addActionListener(new ActionListener()
+ showAllSeqAnnotations.setText(MessageManager
+ .getString("label.show_all_seq_annotations"));
+ showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+ showAllSeqAnnotations.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- hideAllAnnotations_actionPerformed();
+ showAllAnnotations_actionPerformed(true, false);
+ }
+ });
+ hideAllSeqAnnotations.setText(MessageManager
+ .getString("label.hide_all_seq_annotations"));
+ hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllSeqAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllAnnotations_actionPerformed(true, false);
+ }
+ });
+ SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBySequence.setText(MessageManager
+ .getString("label.sort_annotations_by_sequence"));
+ sortAnnBySequence
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ sortAnnBySequence.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setSelected(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
+ }
+ });
+ sortAnnByLabel.setText(MessageManager
+ .getString("label.sort_annotations_by_label"));
+ sortAnnByLabel
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnByLabel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean newState = sortAnnByLabel.getState();
+ sortAnnBySequence.setSelected(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
}
});
colourTextMenuItem.setText(MessageManager
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
applyAutoAnnotationSettings_actionPerformed(e);
}
+ });
+ ButtonGroup buttonGroup = new ButtonGroup();
+ buttonGroup.add(showAutoFirst);
+ buttonGroup.add(showAutoLast);
+ showAutoFirst.setText(MessageManager.getString("label.show_first"));
+ showAutoFirst.setSelected(Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE,
+ false));
+ showAutoFirst.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(showAutoFirst.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+ showAutoLast.setText(MessageManager.getString("label.show_last"));
+ showAutoLast.setSelected(!showAutoFirst.isSelected());
+ showAutoLast.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(!showAutoLast.isSelected());
+ sortAnnotations_actionPerformed();
+ }
});
nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
createPNG.setActionCommand(MessageManager
.getString("label.save_png_image"));
createPNG.setText("PNG");
+
font.setText(MessageManager.getString("action.font"));
font.addActionListener(new java.awt.event.ActionListener()
{
createEPS(null);
}
});
+
+ createSVG.setText("SVG");
+ createSVG.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSVG(null);
+ }
+ });
+
LoadtreeMenuItem.setActionCommand(MessageManager
.getString("label.load_tree_for_sequence_set"));
LoadtreeMenuItem.setText(MessageManager
sortByAnnotScore.setText(MessageManager
.getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
- sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+ sort.addMenuListener(new javax.swing.event.MenuListener()
{
@Override
}
});
+ annotationColumn.setText(MessageManager
+ .getString("action.select_by_annotation"));
+ annotationColumn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColumn_actionPerformed(e);
+ }
+ });
+
rnahelicesColour.setText(MessageManager
.getString("action.by_rna_helixes"));
rnahelicesColour.addActionListener(new ActionListener()
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);
- viewMenu.add(showAllAnnotations);
- viewMenu.add(hideAllAnnotations);
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllAlAnnotations);
+ annotationsMenu.add(hideAllAlAnnotations);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllSeqAnnotations);
+ annotationsMenu.add(hideAllSeqAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
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);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
jMenu2.add(createBioJS);
+ jMenu2.add(createSVG);
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
calculateMenu.add(expandAlignment);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
}
/**
+ * Action on clicking sort annotations by type.
+ *
+ * @param sortOrder
+ */
+ protected void sortAnnotations_actionPerformed()
+ {
+ }
+
+ /**
* Action on clicking Show all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
- protected void showAllAnnotations_actionPerformed()
+ protected void showAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
{
- setAllAnnotationsVisibility(true);
+ setAnnotationsVisibility(true, forSequences, forAlignment);
}
/**
* Action on clicking Hide all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
- protected void hideAllAnnotations_actionPerformed()
+ protected void hideAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
{
- setAllAnnotationsVisibility(false);
+ setAnnotationsVisibility(false, forSequences, forAlignment);
}
/**
- * Set the visibility of all annotations to true or false.
+ * Set the visibility of annotations to true or false. Can act on
+ * sequence-related annotations, or alignment-related, or both.
*
* @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
- protected void setAllAnnotationsVisibility(boolean visible)
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
{
}
{
}
+ public void createSVG(java.io.File f)
+ {
+
+ }
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
}
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
+
+ protected boolean isShowAutoCalculatedAbove()
+ {
+ return showAutoCalculatedAbove;
+ }
+
+ protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
+ {
+ this.showAutoCalculatedAbove = showAutoCalculatedAbove;
+ }
+
+ protected SequenceAnnotationOrder getAnnotationSortOrder()
+ {
+ return annotationSortOrder;
+ }
+
+ protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+ {
+ this.annotationSortOrder = annotationSortOrder;
+ }
}
git://source.jalview.org / jalview.git / blobdiff