/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
MessageManager.getString("label.edit_sequence"));
MenuItem sequenceDetails = new MenuItem(
- MessageManager.getString("label.sequence_details") + "...");
+ MessageManager.getString("label.sequence_details"));
MenuItem selSeqDetails = new MenuItem(
- MessageManager.getString("label.sequence_details") + "...");
+ MessageManager.getString("label.sequence_details"));
MenuItem makeReferenceSeq = new MenuItem();
-
+
SequenceI seq;
MenuItem revealAll = new MenuItem();
if (sg != null && sg.getSize() > 0)
{
editGroupName.setLabel(MessageManager.formatMessage(
- "label.name_param", new Object[]
- { sg.getName() }));
+ "label.name_param", new Object[] { sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
// collect matching db-refs
DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[]
- { target });
+ seq.getDBRef(), new String[] { target });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
.getString("action.set_as_reference")); // );
}
repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[]
- { seq.getName() }));
+ "label.represent_group_with", new Object[] { seq.getName() }));
}
else
{
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
Action.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
- ap.av.setShowSequenceFeatures(true);;
+ ap.av.setShowSequenceFeatures(true);
+ ;
ap.highlightSearchResults(null);
}
}
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.selection_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
+ "label.selection_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
protected void showSequenceDetails()
{
- createSequenceDetailsReport(new SequenceI[]
- { seq });
+ createSequenceDetailsReport(new SequenceI[] { seq });
}
public void createSequenceDetailsReport(SequenceI[] sequences)
for (SequenceI seq : sequences)
{
contents.append(MessageManager.formatMessage(
- "label.annotation_for_displayid", new Object[]
- { seq.getDisplayId(true) }));
- new SequenceAnnotationReport(null)
- .createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- false,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
- : null);
+ "label.annotation_for_displayid",
+ new Object[] { seq.getDisplayId(true) }));
+ new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
+ .getMinMax() : null);
contents.append("</p>");
}
Frame frame = new Frame();
+ (sequences.length == 1 ? sequences[0].getDisplayId(true)
: "Selection"), 600, 500);
cap.setText(MessageManager.formatMessage("label.html_content",
- new Object[]
- { contents.toString() }));
+ new Object[] { contents.toString() }));
}
void editName()
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new SequenceI[]
- { seq }, null, ap, AppletFormatAdapter.URL);
+ new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
+ null, ap, AppletFormatAdapter.URL);
}
else
{
- new MCview.AppletPDBViewer(entry, new SequenceI[]
- { seq }, null, ap, AppletFormatAdapter.URL);
+ new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+ ap, AppletFormatAdapter.URL);
}
}
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.paste_pdb_file_for_sequence", new Object[]
- { seq.getName() }), 400, 300);
+ "label.paste_pdb_file_for_sequence",
+ new Object[] { seq.getName() }), 400, 300);
}
}
pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[]
- { "" }));
+ "label.represent_group_with", new Object[] { "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
menu1.setLabel(MessageManager.getString("label.group") + ":");
noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
+ clustalColour.setLabel(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(this);
zappoColour.setLabel(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(this);
turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_percentage"));
- userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel("BLOSUM62");
BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
+ conservationMenuItem.setLabel(MessageManager
+ .getString("label.conservation"));
editMenu.add(copy);
copy.addActionListener(this);
getGroup().setDisplayText(showText.getState());
refresh();
}
+
public void makeReferenceSeq_actionPerformed()
{
if (!ap.av.getAlignment().hasSeqrep())
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null || sg.getSize() < 1)
{
- ap.av.hideSequence(new SequenceI[]
- { seq });
+ ap.av.hideSequence(new SequenceI[] { seq });
return;
}
{
showMenu.removeAll();
hideMenu.removeAll();
-
+
final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
showMenu.addSeparator();
hideMenu.addSeparator();
-
+
final AlignmentAnnotation[] annotations = ap.getAlignment()
.getAlignmentAnnotation();
-
+
/*
* Find shown/hidden annotations types, distinguished by source (calcId),
* and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
*/
Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
- AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
- hiddenTypes,
- AlignmentAnnotationUtils.asList(annotations),
- forSequences);
-
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations), forSequences);
+
for (String calcId : hiddenTypes.keySet())
{
for (List<String> type : hiddenTypes.get(calcId))
{
- addAnnotationTypeToShowHide(showMenu, forSequences,
- calcId, type, false, true);
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
}
}
// grey out 'show annotations' if none are hidden
showMenu.setEnabled(!hiddenTypes.isEmpty());
-
+
for (String calcId : shownTypes.keySet())
{
for (List<String> type : shownTypes.get(calcId))
{
- addAnnotationTypeToShowHide(hideMenu, forSequences,
- calcId, type, false, false);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+ false, false);
}
}
// grey out 'hide annotations' if none are shown
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
- forSequences, allTypes, actionIsShow);
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
refresh();
}
});