features)
{
JMenu linkMenu = buildLinkMenu(seq, features);
// only add link menu if it has entries
if (linkMenu.getItemCount() > 0)
{
if (sequence != null)
{
sequenceMenu.add(linkMenu);
}
else
{
add(linkMenu);
}
}
}
/**
* Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
* "All" is added first, followed by a separator. Then add any annotation
* types associated with the current selection. Separate menus are built for
* the selected sequence group (if any), and the selected sequence.
*
* Some annotation rows are always rendered together - these can be identified
* by a common graphGroup property > -1. Only one of each group will be marked
* as visible (to avoid duplication of the display). For such groups we add a
* composite type name, e.g.
*
* IUPredWS (Long), IUPredWS (Short)
*
* @param seq
*/
protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
List forSequences)
{
showMenu.removeAll();
hideMenu.removeAll();
final List all = Arrays
.asList(new String[]
{ MessageManager.getString("label.all") });
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
* the insertion order, which is the order of the annotations on the
* alignment.
*/
Map>> shownTypes = new LinkedHashMap<>();
Map>> hiddenTypes = new LinkedHashMap<>();
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);
for (String calcId : hiddenTypes.keySet())
{
for (List type : hiddenTypes.get(calcId))
{
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 type : shownTypes.get(calcId))
{
addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
false, false);
}
}
// grey out 'hide annotations' if none are shown
hideMenu.setEnabled(!shownTypes.isEmpty());
}
/**
* Returns a list of sequences - either the current selection group (if there
* is one), else the specified single sequence.
*
* @param seq
* @return
*/
protected List getSequenceScope(SequenceI seq)
{
List forSequences = null;
final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
if (selectionGroup != null && selectionGroup.getSize() > 0)
{
forSequences = selectionGroup.getSequences();
}
else
{
forSequences = seq == null ? Collections. emptyList()
: Arrays.asList(seq);
}
return forSequences;
}
/**
* Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
* menus.
*
* @param showOrHideMenu
* the menu to add to
* @param forSequences
* the sequences whose annotations may be shown or hidden
* @param calcId
* @param types
* the label to add
* @param allTypes
* if true this is a special label meaning 'All'
* @param actionIsShow
* if true, the select menu item action is to show the annotation
* type, else hide
*/
protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
final List forSequences, String calcId,
final List types, final boolean allTypes,
final boolean actionIsShow)
{
String label = types.toString(); // [a, b, c]
label = label.substring(1, label.length() - 1); // a, b, c
final JMenuItem item = new JMenuItem(label);
item.setToolTipText(calcId);
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
types, forSequences, allTypes, actionIsShow);
refresh();
}
});
showOrHideMenu.add(item);
}
/**
*
* @param sg
* @param groupLinks
* not implemented -- empty list
*/
private void buildGroupURLMenu(SequenceGroup sg, List groupLinks)
{
// TODO: usability: thread off the generation of group url content so root
// menu appears asap
// sequence only URLs
// ID/regex match URLs
groupLinksMenu = new JMenu(
MessageManager.getString("action.group_link"));
// three types of url that might be created.
JMenu[] linkMenus = new JMenu[] { null,
new JMenu(MessageManager.getString("action.ids")),
new JMenu(MessageManager.getString("action.sequences")),
new JMenu(MessageManager.getString("action.ids_sequences")) };
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable<>();
for (int sq = 0; sq < seqs.length; sq++)
{
int start = seqs[sq].findPosition(sg.getStartRes()),
end = seqs[sq].findPosition(sg.getEndRes());
// just collect ids from dataset sequence
// TODO: check if IDs collected from selecton group intersects with the
// current selection, too
SequenceI sqi = seqs[sq];
while (sqi.getDatasetSequence() != null)
{
sqi = sqi.getDatasetSequence();
}
List dbr = sqi.getDBRefs();
int nd;
if (dbr != null && (nd = dbr.size()) > 0)
{
for (int d = 0; d < nd; d++)
{
DBRefEntry e = dbr.get(d);
String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
Object[] sarray = commonDbrefs.get(src);
if (sarray == null)
{
sarray = new Object[2];
sarray[0] = new int[] { 0 };
sarray[1] = new String[seqs.length];
commonDbrefs.put(src, sarray);
}
if (((String[]) sarray[1])[sq] == null)
{
if (!e.hasMap() || (e.getMap()
.locateMappedRange(start, end) != null))
{
((String[]) sarray[1])[sq] = e.getAccessionId();
((int[]) sarray[0])[0]++;
}
}
}
}
}
if (groupLinks.size() == 0)
{
return;
}
// now create group links for all distinct ID/sequence sets.
boolean addMenu = false; // indicates if there are any group links to give
// to user
// not implmeented -- empty list
for (String link : groupLinks)
{
GroupUrlLink urlLink = null;
try
{
urlLink = new GroupUrlLink(link);
} catch (Exception foo)
{
Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
continue;
}
;
if (!urlLink.isValid())
{
Cache.log.error(urlLink.getInvalidMessage());
continue;
}
final String label = urlLink.getLabel();
boolean usingNames = false;
// Now see which parts of the group apply for this URL
String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
String[] seqstr, ids; // input to makeUrl
if (idset != null)
{
int numinput = ((int[]) idset[0])[0];
String[] allids = ((String[]) idset[1]);
seqstr = new String[numinput];
ids = new String[numinput];
for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
{
if (allids[sq] != null)
{
ids[idcount] = allids[sq];
seqstr[idcount++] = idandseqs[1][sq];
}
}
}
else
{
// just use the id/seq set
seqstr = idandseqs[1];
ids = idandseqs[0];
usingNames = true;
}
// and try and make the groupURL!
Object[] urlset = null;
try
{
urlset = urlLink.makeUrlStubs(ids, seqstr,
"FromJalview" + System.currentTimeMillis(), false);
// { int[], boolean[] } only here
} catch (UrlStringTooLongException e)
{
}
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
addshowLink(linkMenus[type],
label + (((type & 1) == 1)
? ("(" + (usingNames ? "Names" : ltarget) + ")")
: ""),
urlLink, urlset);
addMenu = true;
}
}
if (addMenu)
{
groupLinksMenu = new JMenu(
MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
&& linkMenus[m].getMenuComponentCount() > 0)
{
groupLinksMenu.add(linkMenus[m]);
}
}
groupMenu.add(groupLinksMenu);
}
}
/**
* DOCUMENT ME!
*
* @throws Exception
* DOCUMENT ME!
*/
private void jbInit() throws Exception
{
groupMenu.setText(MessageManager.getString("label.selection"));
groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
groupName_actionPerformed();
}
});
sequenceMenu.setText(MessageManager.getString("label.sequence"));
sequenceName.setText(
MessageManager.getString("label.edit_name_description"));
sequenceName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sequenceName_actionPerformed();
}
});
chooseAnnotations
.setText(MessageManager.getString("action.choose_annotations"));
chooseAnnotations.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
chooseAnnotations_actionPerformed(e);
}
});
sequenceDetails
.setText(MessageManager.getString("label.sequence_details"));
sequenceDetails.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sequenceDetails_actionPerformed();
}
});
sequenceSelDetails
.setText(MessageManager.getString("label.sequence_details"));
sequenceSelDetails.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sequenceSelectionDetails_actionPerformed();
}
});
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
unGroupMenuItem_actionPerformed();
}
});
createGroupMenuItem
.setText(MessageManager.getString("action.create_group"));
createGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
createGroupMenuItem_actionPerformed();
}
});
outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
outline_actionPerformed();
}
});
showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
showBoxes_actionPerformed();
}
});
showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
}
});
showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
}
});
displayNonconserved
.setText(MessageManager.getString("label.show_non_conserved"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
showNonconserved_actionPerformed();
}
});
editMenu.setText(MessageManager.getString("action.edit"));
cut.setText(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed();
}
});
upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
}
});
lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
outputMenu.setText(
MessageManager.getString("label.out_to_textbox") + "...");
seqShowAnnotationsMenu
.setText(MessageManager.getString("label.show_annotations"));
seqHideAnnotationsMenu
.setText(MessageManager.getString("label.hide_annotations"));
groupShowAnnotationsMenu
.setText(MessageManager.getString("label.show_annotations"));
groupHideAnnotationsMenu
.setText(MessageManager.getString("label.hide_annotations"));
sequenceFeature.setText(
MessageManager.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
}
});
jMenu1.setText(MessageManager.getString("label.group"));
pdbStructureDialog.setText(
MessageManager.getString("label.show_pdbstruct_dialog"));
pdbStructureDialog.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
SequenceI[] selectedSeqs = new SequenceI[] { sequence };
if (ap.av.getSelectionGroup() != null)
{
selectedSeqs = ap.av.getSequenceSelection();
}
new StructureChooser(selectedSeqs, sequence, ap);
}
});
rnaStructureMenu
.setText(MessageManager.getString("label.view_rna_structure"));
// colStructureMenu.setText("Colour By Structure");
editSequence.setText(
MessageManager.getString("label.edit_sequence") + "...");
editSequence.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
editSequence_actionPerformed();
}
});
makeReferenceSeq.setText(
MessageManager.getString("label.mark_as_representative"));
makeReferenceSeq.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
makeReferenceSeq_actionPerformed(actionEvent);
}
});
hideInsertions
.setText(MessageManager.getString("label.hide_insertions"));
hideInsertions.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
hideInsertions_actionPerformed(e);
}
});
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
add(rnaStructureMenu);
add(pdbStructureDialog);
if (sequence != null)
{
add(hideInsertions);
}
// annotations configuration panel suppressed for now
// groupMenu.add(chooseAnnotations);
/*
* Add show/hide annotations to the Sequence menu, and to the Selection menu
* (if a selection group is in force).
*/
sequenceMenu.add(seqShowAnnotationsMenu);
sequenceMenu.add(seqHideAnnotationsMenu);
sequenceMenu.add(seqAddReferenceAnnotations);
groupMenu.add(groupShowAnnotationsMenu);
groupMenu.add(groupHideAnnotationsMenu);
groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
groupMenu.add(createGroupMenuItem);
groupMenu.add(unGroupMenuItem);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
sequenceMenu.add(makeReferenceSeq);
initColourMenu();
buildColourMenu();
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
editMenu.add(upperCase);
editMenu.add(lowerCase);
editMenu.add(toggle);
// JBPNote: These shouldn't be added here - should appear in a generic
// 'apply web service to this sequence menu'
// pdbMenu.add(RNAFold);
// pdbMenu.add(ContraFold);
jMenu1.add(groupName);
jMenu1.add(colourMenu);
jMenu1.add(showBoxes);
jMenu1.add(showText);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
}
/**
* Constructs the entries for the colour menu
*/
protected void initColourMenu()
{
colourMenu.setText(MessageManager.getString("label.group_colour"));
textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed();
}
});
abovePIDColour.setText(
MessageManager.getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
abovePIDColour_actionPerformed(abovePIDColour.isSelected());
}
});
modifyPID.setText(
MessageManager.getString("label.modify_identity_threshold"));
modifyPID.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
modifyPID_actionPerformed();
}
});
conservationMenuItem
.setText(MessageManager.getString("action.by_conservation"));
conservationMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed(
conservationMenuItem.isSelected());
}
});
annotationColour = new JRadioButtonMenuItem(
MessageManager.getString("action.by_annotation"));
annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
annotationColour.setEnabled(false);
annotationColour.setToolTipText(
MessageManager.getString("label.by_annotation_tooltip"));
modifyConservation.setText(MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
modifyConservation_actionPerformed();
}
});
}
/**
* Builds the group colour sub-menu, including any user-defined colours which
* were loaded at startup or during the Jalview session
*/
protected void buildColourMenu()
{
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null)
{
/*
* popup menu with no sequence group scope
*/
return;
}
colourMenu.removeAll();
colourMenu.add(textColour);
colourMenu.addSeparator();
ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
false);
bg.add(annotationColour);
colourMenu.add(annotationColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDColour);
colourMenu.add(modifyPID);
}
protected void modifyConservation_actionPerformed()
{
SequenceGroup sg = getGroup();
if (sg.cs != null)
{
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
}
protected void modifyPID_actionPerformed()
{
SequenceGroup sg = getGroup();
if (sg.cs != null)
{
// int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
// .getName());
// sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
SliderPanel.showPIDSlider();
}
}
/**
* Check for any annotations on the underlying dataset sequences (for the
* current selection group) which are not 'on the alignment'.If any are found,
* enable the option to add them to the alignment. The criteria for 'on the
* alignment' is finding an alignment annotation on the alignment, matched on
* calcId, label and sequenceRef.
*
* A tooltip is also constructed that displays the source (calcId) and type
* (label) of the annotations that can be added.
*
* @param menuItem
* @param forSequences
*/
protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
List forSequences)
{
menuItem.setEnabled(false);
/*
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
SortedMap tipEntries = new TreeMap<>();
final Map> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
candidates, al);
if (!candidates.isEmpty())
{
StringBuilder tooltip = new StringBuilder(64);
tooltip.append(MessageManager.getString("label.add_annotations_for"));
/*
* Found annotations that could be added. Enable the menu item, and
* configure its tooltip and action.
*/
menuItem.setEnabled(true);
for (String calcId : tipEntries.keySet())
{
tooltip.append("
" + calcId + "/" + tipEntries.get(calcId));
}
String tooltipText = JvSwingUtils.wrapTooltip(true,
tooltip.toString());
menuItem.setToolTipText(tooltipText);
menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
addReferenceAnnotations_actionPerformed(candidates);
}
});
}
}
/**
* Add annotations to the sequences and to the alignment.
*
* @param candidates
* a map whose keys are sequences on the alignment, and values a list
* of annotations to add to each sequence
*/
protected void addReferenceAnnotations_actionPerformed(
Map> candidates)
{
final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
final AlignmentI alignment = this.ap.getAlignment();
AlignmentUtils.addReferenceAnnotations(candidates, alignment,
selectionGroup);
refresh();
}
protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
{
if (!ap.av.getAlignment().hasSeqrep())
{
// initialise the display flags so the user sees something happen
ap.av.setDisplayReferenceSeq(true);
ap.av.setColourByReferenceSeq(true);
ap.av.getAlignment().setSeqrep(sequence);
}
else
{
if (ap.av.getAlignment().getSeqrep() == sequence)
{
ap.av.getAlignment().setSeqrep(null);
}
else
{
ap.av.getAlignment().setSeqrep(sequence);
}
}
refresh();
}
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
BitSet inserts = new BitSet();
boolean markedPopup = false;
// mark inserts in current selection
if (ap.av.getSelectionGroup() != null)
{
// mark just the columns in the selection group to be hidden
inserts.set(ap.av.getSelectionGroup().getStartRes(),
ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
// now clear columns without gaps
for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
{
if (sq == sequence)
{
markedPopup = true;
}
inserts.and(sq.getInsertionsAsBits());
}
hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
ap.av.getSelectionGroup().getEndRes());
}
// now mark for sequence under popup if we haven't already done it
else if (!markedPopup && sequence != null)
{
inserts.or(sequence.getInsertionsAsBits());
// and set hidden columns accordingly
hidden.hideColumns(inserts);
}
refresh();
}
protected void sequenceSelectionDetails_actionPerformed()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
}
protected void sequenceDetails_actionPerformed()
{
createSequenceDetailsReport(new SequenceI[] { sequence });
}
public void createSequenceDetailsReport(SequenceI[] sequences)
{
StringBuilder contents = new StringBuilder(128);
contents.append("");
for (SequenceI seq : sequences)
{
contents.append("" + MessageManager.formatMessage(
"label.create_sequence_details_report_annotation_for",
new Object[]
{ seq.getDisplayId(true) }) + "
");
new SequenceAnnotationReport(null).createSequenceAnnotationReport(
contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
contents.append("
");
}
contents.append("");
String report = contents.toString();
JInternalFrame frame;
if (Platform.isJS())
{
JLabel textLabel = new JLabel();
textLabel.setText(report);
textLabel.setBackground(Color.WHITE);
JPanel pane = new JPanel(new BorderLayout());
pane.setOpaque(true);
pane.setBackground(Color.WHITE);
pane.add(textLabel, BorderLayout.NORTH);
frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(pane));
}
else
/**
* Java only
*
* @j2sIgnore
*/
{
CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
cap.setText(report);
frame = cap;
}
Desktop.addInternalFrame(frame,
MessageManager.formatMessage("label.sequence_details_for",
(sequences.length == 1 ? new Object[]
{ sequences[0].getDisplayId(true) }
: new Object[]
{ MessageManager
.getString("label.selection") })),
500, 400);
}
protected void showNonconserved_actionPerformed()
{
getGroup().setShowNonconserved(displayNonconserved.isSelected());
refresh();
}
/**
* call to refresh view after settings change
*/
void refresh()
{
ap.updateAnnotation();
// removed paintAlignment(true) here:
// updateAnnotation calls paintAlignment already, so don't need to call
// again
PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
}
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
*/
/**
* DOCUMENT ME!
*
* @param selected
*
* @param e
* DOCUMENT ME!
*/
public void abovePIDColour_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
{
return;
}
if (selected)
{
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
int threshold = SliderPanel.setPIDSliderSource(ap,
sg.getGroupColourScheme(), getGroup().getName());
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
else
// remove PIDColouring
{
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
SliderPanel.hidePIDSlider();
}
modifyPID.setEnabled(selected);
refresh();
}
/**
* Open a panel where the user can choose which types of sequence annotation
* to show or hide.
*
* @param e
*/
protected void chooseAnnotations_actionPerformed(ActionEvent e)
{
// todo correct way to guard against opening a duplicate panel?
new AnnotationChooser(ap);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void conservationMenuItem_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
{
return;
}
if (selected)
{
// JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, ap.av.getConsPercGaps());
sg.cs.setConservation(c);
SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
sg.getName());
SliderPanel.showConservationSlider();
}
else
// remove ConservationColouring
{
sg.cs.setConservation(null);
SliderPanel.hideConservationSlider();
}
modifyConservation.setEnabled(selected);
refresh();
}
/**
* Shows a dialog where group name and description may be edited
*/
protected void groupName_actionPerformed()
{
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
sg.getDescription(),
MessageManager.getString("label.group_name"),
MessageManager.getString("label.group_description"));
dialog.showDialog(ap.alignFrame,
MessageManager.getString("label.edit_group_name_description"),
new Runnable()
{
@Override
public void run()
{
sg.setName(dialog.getName());
sg.setDescription(dialog.getDescription());
refresh();
}
});
}
/**
* Get selection group - adding it to the alignment if necessary.
*
* @return sequence group to operate on
*/
SequenceGroup getGroup()
{
SequenceGroup sg = ap.av.getSelectionGroup();
// this method won't add a new group if it already exists
if (sg != null)
{
ap.av.getAlignment().addGroup(sg);
}
return sg;
}
/**
* Shows a dialog where sequence name and description may be edited
*/
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
sequence.getDescription(),
MessageManager.getString("label.sequence_name"),
MessageManager.getString("label.sequence_description"));
dialog.showDialog(ap.alignFrame,
MessageManager.getString(
"label.edit_sequence_name_description"),
new Runnable()
{
@Override
public void run()
{
if (dialog.getName() != null)
{
if (dialog.getName().indexOf(" ") > -1)
{
JvOptionPane.showMessageDialog(ap,
MessageManager.getString(
"label.spaces_converted_to_underscores"),
MessageManager.getString(
"label.no_spaces_allowed_sequence_name"),
JvOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
ap.paintAlignment(false, false);
}
sequence.setDescription(dialog.getDescription());
ap.av.firePropertyChange("alignment", null,
ap.av.getAlignment().getSequences());
}
});
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
void unGroupMenuItem_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
refresh();
}
void createGroupMenuItem_actionPerformed()
{
getGroup(); // implicitly creates group - note - should apply defaults / use
// standard alignment window logic for this
refresh();
}
/**
* Offers a colour chooser and sets the selected colour as the group outline
*/
protected void outline_actionPerformed()
{
String title = MessageManager
.getString("label.select_outline_colour");
ColourChooserListener listener = new ColourChooserListener()
{
@Override
public void colourSelected(Color c)
{
getGroup().setOutlineColour(c);
refresh();
};
};
JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
title, Color.BLUE, listener);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void showBoxes_actionPerformed()
{
getGroup().setDisplayBoxes(showBoxes.isSelected());
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void showText_actionPerformed()
{
getGroup().setDisplayText(showText.isSelected());
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void showColourText_actionPerformed()
{
getGroup().setColourText(showColourText.isSelected());
refresh();
}
void hideSequences(boolean representGroup)
{
ap.av.hideSequences(sequence, representGroup);
}
public void copy_actionPerformed()
{
ap.alignFrame.copy_actionPerformed();
}
public void cut_actionPerformed()
{
ap.alignFrame.cut_actionPerformed();
}
void changeCase(ActionEvent e)
{
Object source = e.getSource();
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg != null)
{
List startEnd = ap.av.getVisibleRegionBoundaries(
sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
if (source == toggle)
{
description = MessageManager.getString("label.toggle_case");
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
description = MessageManager.getString("label.to_upper_case");
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
description = MessageManager.getString("label.to_lower_case");
caseChange = ChangeCaseCommand.TO_LOWER;
}
ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
ap.av.firePropertyChange("alignment", null,
ap.av.getAlignment().getSequences());
}
}
public void outputText_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
Desktop.addInternalFrame(cap, MessageManager
.formatMessage("label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
// or we simply trust the user wants
// wysiwig behaviour
FileFormatI fileFormat = FileFormats.getInstance()
.forName(e.getActionCommand());
cap.setText(
new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
public void sequenceFeature_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null)
{
return;
}
List seqs = new ArrayList<>();
List features = new ArrayList<>();
/*
* assemble dataset sequences, and template new sequence features,
* for the amend features dialog
*/
int gSize = sg.getSize();
for (int i = 0; i < gSize; i++)
{
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
int end = sg.findEndRes(sg.getSequenceAt(i));
if (start <= end)
{
seqs.add(sg.getSequenceAt(i).getDatasetSequence());
features.add(new SequenceFeature(null, null, start, end, null));
}
}
/*
* an entirely gapped region will generate empty lists of sequence / features
*/
if (!seqs.isEmpty())
{
new FeatureEditor(ap, seqs, features, true).showDialog();
}
}
public void textColour_actionPerformed()
{
SequenceGroup sg = getGroup();
if (sg != null)
{
new TextColourChooser().chooseColour(ap, sg);
}
}
public void colourByStructure(String pdbid)
{
Annotation[] anots = ap.av.getStructureSelectionManager()
.colourSequenceFromStructure(sequence, pdbid);
AlignmentAnnotation an = new AlignmentAnnotation("Structure",
"Coloured by " + pdbid, anots);
ap.av.getAlignment().addAnnotation(an);
an.createSequenceMapping(sequence, 0, true);
// an.adjustForAlignment();
ap.av.getAlignment().setAnnotationIndex(an, 0);
ap.adjustAnnotationHeight();
sequence.addAlignmentAnnotation(an);
}
/**
* Shows a dialog where sequence characters may be edited. Any changes are
* applied, and added as an available 'Undo' item in the edit commands
* history.
*/
public void editSequence_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg != null)
{
if (sequence == null)
{
sequence = sg.getSequenceAt(0);
}
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
sg.getEndRes() + 1),
null, MessageManager.getString("label.edit_sequence"), null);
dialog.showDialog(ap.alignFrame,
MessageManager.getString("label.edit_sequence"),
new Runnable()
{
@Override
public void run()
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
Action.REPLACE,
dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(
ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1,
ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
ap.av.firePropertyChange("alignment", null,
ap.av.getAlignment().getSequences());
}
});
}
}
/**
* Action on user selecting an item from the colour menu (that does not have
* its bespoke action handler)
*
* @return
*/
@Override
public void changeColour_actionPerformed(String colourSchemeName)
{
SequenceGroup sg = getGroup();
/*
* switch to the chosen colour scheme (or null for None)
*/
ColourSchemeI colourScheme = ColourSchemes.getInstance()
.getColourScheme(colourSchemeName, ap.av, sg,
ap.av.getHiddenRepSequences());
sg.setColourScheme(colourScheme);
if (colourScheme instanceof Blosum62ColourScheme
|| colourScheme instanceof PIDColourScheme)
{
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
}
refresh();
}
}