>();
for (String link : links)
{
UrlLink urlLink = null;
try
{
urlLink = new UrlLink(link);
} catch (Exception foo)
{
Cache.log.error("Exception for URLLink '" + link + "'", foo);
continue;
}
if (!urlLink.isValid())
{
Cache.log.error(urlLink.getInvalidMessage());
continue;
}
urlLink.createLinksFromSeq(seq, linkset);
}
addshowLinks(linkMenu, linkset.values());
// disable link menu if there are no valid entries
if (linkMenu.getItemCount() > 0)
{
linkMenu.setEnabled(true);
}
else
{
linkMenu.setEnabled(false);
}
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);
}
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();
}
DBRefEntry[] dbr = sqi.getDBRefs();
if (dbr != null && dbr.length > 0)
{
for (int d = 0; d < dbr.length; d++)
{
String src = dbr[d].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 (!dbr[d].hasMap()
|| (dbr[d].getMap().locateMappedRange(start, end) != null))
{
((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
((int[]) sarray[0])[0]++;
}
}
}
}
}
// now create group links for all distinct ID/sequence sets.
boolean addMenu = false; // indicates if there are any group links to give
// to user
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);
} 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);
}
}
private void addshowLinks(JMenu linkMenu, Collection> linkset)
{
for (List linkstrset : linkset)
{
// split linkstr into label and url
addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
}
}
/**
* add a show URL menu item to the given linkMenu
*
* @param linkMenu
* @param label
* - menu label string
* @param url
* - url to open
*/
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
"label.open_url_param", new Object[] { url }));
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
@Override
public void run()
{
showLink(url);
}
}).start();
}
});
linkMenu.add(item);
}
/**
* add a late bound groupURL item to the given linkMenu
*
* @param linkMenu
* @param label
* - menu label string
* @param urlgenerator
* GroupURLLink used to generate URL
* @param urlstub
* Object array returned from the makeUrlStubs function.
*/
private void addshowLink(JMenu linkMenu, String label,
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
"label.open_url_seqs_param",
new Object[] { urlgenerator.getUrl_prefix(),
urlgenerator.getNumberInvolved(urlstub) }));
// TODO: put in info about what is being sent.
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
@Override
public void run()
{
try
{
showLink(urlgenerator.constructFrom(urlstub));
} catch (UrlStringTooLongException e2)
{
}
}
}).start();
}
});
linkMenu.add(item);
}
/**
* 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(actionEvent);
}
});
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);
}
});
/*
* annotationMenuItem.setText("By Annotation");
* annotationMenuItem.addActionListener(new ActionListener() { public void
* actionPerformed(ActionEvent actionEvent) {
* annotationMenuItem_actionPerformed(actionEvent); } });
*/
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());
}
});
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();
ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
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)
{
if (sequence != null)
{
ColumnSelection cs = ap.av.getColumnSelection();
if (cs == null)
{
cs = new ColumnSelection();
}
cs.hideInsertionsFor(sequence);
ap.av.setColumnSelection(cs);
}
refresh();
}
protected void sequenceSelectionDetails_actionPerformed()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
}
protected void sequenceDetails_actionPerformed()
{
createSequenceDetailsReport(new SequenceI[] { sequence });
}
public void createSequenceDetailsReport(SequenceI[] sequences)
{
CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
StringBuilder contents = new StringBuilder(128);
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 != null) ? ap
.getSeqPanel().seqCanvas.fr.getMinMax()
: null);
contents.append("
");
}
cap.setText("" + contents.toString() + "");
Desktop.addInternalFrame(cap, 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();
ap.paintAlignment(true);
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();
}
public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
{
SequenceGroup sg = getGroup();
if (sg == null)
{
return;
}
AnnotationColourGradient acg = new AnnotationColourGradient(
sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
acg.setPredefinedColours(true);
sg.setColourScheme(acg);
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
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") + " ",
MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
if (!dialog.accept)
{
return;
}
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;
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
sequence.getDescription(),
" " + MessageManager.getString("label.sequence_name")
+ " ",
MessageManager.getString("label.sequence_description") + " ",
MessageManager
.getString("label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
{
return;
}
if (dialog.getName() != null)
{
if (dialog.getName().indexOf(" ") > -1)
{
JvOptionPane
.showMessageDialog(
ap,
MessageManager
.getString("label.spaces_converted_to_backslashes"),
MessageManager
.getString("label.no_spaces_allowed_sequence_name"),
JvOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
ap.paintAlignment(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();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_outline_colour"),
Color.BLUE);
if (col != null)
{
sg.setOutlineColour(col);
}
refresh();
}
/**
* 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();
}
public void showLink(String url)
{
try
{
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
void hideSequences(boolean representGroup)
{
ap.av.hideSequences(sequence, representGroup);
}
public void copy_actionPerformed()
{
ap.alignFrame.copy_actionPerformed(null);
}
public void cut_actionPerformed()
{
ap.alignFrame.cut_actionPerformed(null);
}
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;
}
int rsize = 0, gSize = sg.getSize();
SequenceI[] rseqs, seqs = new SequenceI[gSize];
SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
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[rsize] = sg.getSequenceAt(i).getDatasetSequence();
features[rsize] = new SequenceFeature(null, null, null, start, end,
"Jalview");
rsize++;
}
}
rseqs = new SequenceI[rsize];
tfeatures = new SequenceFeature[rsize];
System.arraycopy(seqs, 0, rseqs, 0, rsize);
System.arraycopy(features, 0, tfeatures, 0, rsize);
features = tfeatures;
seqs = rseqs;
if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
ap.highlightSearchResults(null);
}
}
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);
}
public void editSequence_actionPerformed(ActionEvent actionEvent)
{
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,
MessageManager.getString("label.edit_sequence"),
ap.alignFrame);
if (dialog.accept)
{
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();
if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
{
/*
* open a panel to load or configure a user-defined colour scheme
*/
new UserDefinedColours(ap, sg);
}
else
{
/*
* switch to the chosen colour scheme (or null for None)
*/
ColourSchemeI colourScheme = ColourSchemes.getInstance().getColourScheme(
colourSchemeName, 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();
}
}