pes = sq.getDatasetSequence().getPDBId();
if (pes != null && pes.size() > 0)
{
reppdb.put(pes.get(0).getId(), pes.get(0));
for (PDBEntry pe : pes)
{
pdbe.put(pe.getId(), pe);
if (sqass == null)
{
sqass = sq;
}
}
}
}
if (pdbe.size() > 0)
{
final PDBEntry[] pe = pdbe.values().toArray(
new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
new PDBEntry[reppdb.size()]);
final JMenuItem gpdbview, rpdbview;
if (pdbe.size() == 1)
{
structureMenu.add(gpdbview = new JMenuItem(MessageManager
.formatMessage("label.view_structure_for", new String[]
{ sqass.getDisplayId(false) })));
}
else
{
structureMenu.add(gpdbview = new JMenuItem(MessageManager
.formatMessage("label.view_all_structures", new String[]
{ new Integer(pdbe.size()).toString() })));
}
gpdbview.setToolTipText(MessageManager
.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
gpdbview.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new StructureViewer(ap.getStructureSelectionManager())
.viewStructures(ap, pe, ap.av.collateForPDB(pe));
}
});
if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
{
structureMenu.add(rpdbview = new JMenuItem(MessageManager
.formatMessage(
"label.view_all_representative_structures",
new String[]
{ new Integer(reppdb.size()).toString() })));
rpdbview.setToolTipText(MessageManager
.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
rpdbview.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new StructureViewer(ap.getStructureSelectionManager())
.viewStructures(ap, pr, ap.av.collateForPDB(pr));
}
});
}
}
}
else
{
groupMenu.setVisible(false);
editMenu.setVisible(false);
}
if (!isDefinedGroup)
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
jMenu1.setText(MessageManager.getString("action.edit_new_group"));
}
else
{
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
jMenu1.setText(MessageManager.getString("action.edit_group"));
}
if (seq == null)
{
sequenceMenu.setVisible(false);
structureMenu.setVisible(false);
}
if (links != null && links.size() > 0)
{
JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
String link = links.elementAt(i).toString();
UrlLink urlLink = null;
try
{
urlLink = new UrlLink(link);
} catch (Exception foo)
{
jalview.bin.Cache.log.error("Exception for URLLink '" + link
+ "'", foo);
continue;
}
;
if (!urlLink.isValid())
{
jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
continue;
}
final String label = urlLink.getLabel();
if (seq != null && urlLink.isDynamic())
{
// collect matching db-refs
DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
seq.getDBRef(), new String[]
{ urlLink.getTarget() });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
if (descr != null && descr.length() < 1)
{
descr = null;
}
if (dbr != null)
{
for (int r = 0; r < dbr.length; r++)
{
if (id != null && dbr[r].getAccessionId().equals(id))
{
// suppress duplicate link creation for the bare sequence ID
// string with this link
id = null;
}
// create Bare ID link for this RUL
String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
true);
if (urls != null)
{
for (int u = 0; u < urls.length; u += 2)
{
if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
linkset.addElement(urls[u] + "|" + urls[u + 1]);
addshowLink(linkMenu, label + "|" + urls[u],
urls[u + 1]);
}
}
}
}
}
if (id != null)
{
// create Bare ID link for this RUL
String[] urls = urlLink.makeUrls(id, true);
if (urls != null)
{
for (int u = 0; u < urls.length; u += 2)
{
if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
linkset.addElement(urls[u] + "|" + urls[u + 1]);
addshowLink(linkMenu, label, urls[u + 1]);
}
}
}
}
// Create urls from description but only for URL links which are regex
// links
if (descr != null && urlLink.getRegexReplace() != null)
{
// create link for this URL from description where regex matches
String[] urls = urlLink.makeUrls(descr, true);
if (urls != null)
{
for (int u = 0; u < urls.length; u += 2)
{
if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
linkset.addElement(urls[u] + "|" + urls[u + 1]);
addshowLink(linkMenu, label, urls[u + 1]);
}
}
}
}
}
else
{
if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
{
linkset.addElement(label + "|" + urlLink.getUrl_prefix());
// Add a non-dynamic link
addshowLink(linkMenu, label, urlLink.getUrl_prefix());
}
}
}
if (sequence != null)
{
sequenceMenu.add(linkMenu);
}
else
{
add(linkMenu);
}
}
}
/**
* Add annotation types to a 'Show annotations' or 'Hide annotations' menu.
* "All" is added first, followed by a separator. Then add any annotation
* types associated with the current selection.
*
* 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)
*/
protected void buildAnnotationTypesMenus()
{
final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
if (selectionGroup == null)
{
// this menu option is only for a selection
return;
}
showAnnotationsMenu.removeAll();
hideAnnotationsMenu.removeAll();
final List all = Arrays.asList(ALL_ANNOTATIONS);
addAnnotationTypeToShowHide(showAnnotationsMenu, "", all, true, true);
addAnnotationTypeToShowHide(hideAnnotationsMenu, "", all, true, false);
showAnnotationsMenu.addSeparator();
hideAnnotationsMenu.addSeparator();
final AlignmentAnnotation[] annotations = ap.getAlignment()
.getAlignmentAnnotation();
BitSet visibleGraphGroups = PopupMenu
.getVisibleLineGraphGroups(annotations);
/*
* Find shown/hidden annotations types, distinguished by source (calcId),
* and grouped by graphGroup.
*/
Map>> shownTypes = new HashMap>>();
Map>> hiddenTypes = new HashMap>>();
PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
visibleGraphGroups, annotations, selectionGroup);
for (String calcId : hiddenTypes.keySet())
{
for (List type : hiddenTypes.get(calcId))
{
addAnnotationTypeToShowHide(showAnnotationsMenu, calcId, type,
false, true);
}
}
for (String calcId : shownTypes.keySet())
{
for (List type : shownTypes.get(calcId))
{
addAnnotationTypeToShowHide(hideAnnotationsMenu, calcId, type,
false, false);
}
}
}
/**
* Helper method to populate lists of annotation types for the Show/Hide
* Annotations menus. If sequenceGroup is not null, this is restricted to
* annotations which are associated with sequences in the selection group.
*
* If an annotation row is currently visible, its type (label) is added (once
* only per type), to the shownTypes list. If it is currently hidden, it is
* added to the hiddenTypesList.
*
* For rows that belong to a line graph group, so are always rendered
* together:
*
* - Treat all rows in the group as visible, if at least one of them is
* - Build a comma-separated label with all the types that belong to the
* group
*
*
* @param shownTypes
* a map, keyed by calcId (annotation source), whose entries are the
* lists of annotation types found for the calcId; each annotation
* type in turn may be a list (in the case of grouped annotations)
* @param hiddenTypes
* a map, similar to shownTypes, but for hidden annotation types
* @param visibleGraphGroups
* a lookup keyed by graphGroup identifier
* @param annotations
* the annotations on the alignment to scan
* @param sequenceGroup
* the sequence group to restrict search to
*/
public static void getAnnotationTypesForShowHide(
Map>> shownTypes,
Map>> hiddenTypes,
BitSet visibleGraphGroups, AlignmentAnnotation[] annotations,
SequenceGroup sequenceGroup)
{
/*
* Build a lookup, by calcId (annotation source), of all annotation types in
* each graph group.
*/
Map>> groupLabels = new HashMap>>();
// trackers for which calcId!label combinations we have dealt with
List addedToShown = new ArrayList();
List addedToHidden = new ArrayList();
for (AlignmentAnnotation aa : annotations)
{
if (sequenceGroup == null
|| (aa.sequenceRef != null && sequenceGroup.getSequences()
.contains(aa.sequenceRef)))
{
String calcId = aa.getCalcId();
/*
* Build a 'composite label' for types in line graph groups.
*/
final List labelAsList = new ArrayList();
final String displayLabel = aa.label;
labelAsList.add(displayLabel);
if (aa.graph == AlignmentAnnotation.LINE_GRAPH
&& aa.graphGroup > -1)
{
if (!groupLabels.containsKey(calcId))
{
groupLabels.put(calcId, new HashMap>());
}
Map> groupLabelsForCalcId = groupLabels
.get(calcId);
if (groupLabelsForCalcId.containsKey(aa.graphGroup))
{
if (!groupLabelsForCalcId.get(aa.graphGroup).contains(
displayLabel))
{
groupLabelsForCalcId.get(aa.graphGroup).add(displayLabel);
}
}
else
{
groupLabelsForCalcId.put(aa.graphGroup, labelAsList);
}
}
else
/*
* 'Simple case' - not a grouped annotation type - list of one label
* only
*/
{
String rememberAs = calcId + "!" + displayLabel;
if (aa.visible && !addedToShown.contains(rememberAs))
{
if (!shownTypes.containsKey(calcId))
{
shownTypes.put(calcId, new ArrayList>());
}
shownTypes.get(calcId).add(labelAsList);
addedToShown.add(rememberAs);
}
else
{
if (!aa.visible && !addedToHidden.contains(rememberAs))
{
if (!hiddenTypes.containsKey(calcId))
{
hiddenTypes.put(calcId, new ArrayList>());
}
hiddenTypes.get(calcId).add(labelAsList);
addedToHidden.add(rememberAs);
}
}
}
}
}
/*
* finally add the 'composite group labels' to the appropriate lists,
* depending on whether the group is identified as visible or hidden
*/
for (String calcId : groupLabels.keySet())
{
for (int group : groupLabels.get(calcId).keySet())
{
final List groupLabel = groupLabels.get(calcId).get(group);
if (visibleGraphGroups.get(group))
{
if (!shownTypes.containsKey(calcId))
{
shownTypes.put(calcId, new ArrayList>());
}
shownTypes.get(calcId).add(groupLabel);
}
else
{
if (!hiddenTypes.containsKey(calcId))
{
hiddenTypes.put(calcId, new ArrayList>());
}
hiddenTypes.get(calcId).add(groupLabel);
}
}
}
}
/**
* Returns a BitSet (possibly empty) of those graphGroups for line graph
* annotations, which have at least one member annotation row marked visible.
* The logic is that only one row in the group is marked visible, but when it
* is drawn, so are all the other rows in the same group.
*
* This lookup set allows us to check whether rows marked not visible are in
* fact shown.
*
* @see AnnotationRenderer#drawComponent
* @param annotations
* @return
*/
public static BitSet getVisibleLineGraphGroups(
AlignmentAnnotation[] annotations)
{
// todo move to a utility class
BitSet result = new BitSet();
for (AlignmentAnnotation ann : annotations)
{
if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible)
{
int gg = ann.graphGroup;
if (gg > -1)
{
result.set(gg);
}
}
}
return result;
}
/**
* Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
* menus.
*
* @param showOrHideMenu
* the menu to add to
* @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,
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);
final JMenuItem item = new JMenuItem(label);
item.setToolTipText(calcId);
item.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
showHideAnnotation_actionPerformed(types, allTypes, actionIsShow);
}
});
showOrHideMenu.add(item);
}
/**
* Action on selecting a list of annotation type (or the 'all types' values)
* to show or hide for the selection.
*
* @param types
* @param anyType
* @param doShow
*/
protected void showHideAnnotation_actionPerformed(
Collection types, boolean anyType, boolean doShow)
{
for (AlignmentAnnotation aa : ap.getAlignment()
.getAlignmentAnnotation())
{
// TODO: select by calcId (source of annotation) as well as label
// e.g. by refactoring of buildAnnotationTypeMenus to as
// to construct the actionPerformed methods as the calcId/labels are found
if (anyType || types.contains(aa.label))
{
if ((aa.sequenceRef != null)
&& ap.av.getSelectionGroup().getSequences()
.contains(aa.sequenceRef))
{
aa.visible = doShow;
}
}
}
refresh();
}
private void buildGroupURLMenu(SequenceGroup sg, Vector 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"));
JMenu[] linkMenus = new JMenu[]
{ null, new JMenu(MessageManager.getString("action.ids")),
new JMenu(MessageManager.getString("action.sequences")),
new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
// types
// of url
// that
// might
// be
// created.
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.getDBRef();
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 = (Object[]) 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 (int i = 0; i < groupLinks.size(); i++)
{
String link = groupLinks.elementAt(i).toString();
GroupUrlLink urlLink = null;
try
{
urlLink = new GroupUrlLink(link);
} catch (Exception foo)
{
jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+ "'", foo);
continue;
}
;
if (!urlLink.isValid())
{
jalview.bin.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 = (Object[]) 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;
// System.out.println(urlLink.getGroupURLType()
// +" "+((String[])urlset[3])[0]);
// 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);
}
}
/**
* 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 String[]
{ url }));
item.addActionListener(new java.awt.event.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 java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
@Override
public void run()
{
try
{
showLink(urlgenerator.constructFrom(urlstub));
} catch (UrlStringTooLongException e)
{
}
}
}).start();
}
});
linkMenu.add(item);
}
/**
* DOCUMENT ME!
*
* @throws Exception
* DOCUMENT ME!
*/
private void jbInit() throws Exception
{
groupMenu.setText(MessageManager.getString("label.group"));
groupMenu.setText(MessageManager.getString("label.selection"));
groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new java.awt.event.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 java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sequenceName_actionPerformed();
}
});
chooseAnnotations.setText(MessageManager
.getString("label.choose_annotations") + "...");
chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
chooseAnnotations_actionPerformed(e);
}
});
sequenceDetails.setText(MessageManager
.getString("label.sequence_details") + "...");
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sequenceDetails_actionPerformed();
}
});
sequenceSelDetails.setText(MessageManager
.getString("label.sequence_details") + "...");
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sequenceSelectionDetails_actionPerformed();
}
});
PIDColour.setFocusPainted(false);
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
unGroupMenuItem_actionPerformed();
}
});
createGroupMenuItem.setText(MessageManager
.getString("action.create_group"));
createGroupMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
createGroupMenuItem_actionPerformed();
}
});
outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
outline_actionPerformed();
}
});
nucleotideMenuItem
.setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
nucleotideMenuItem_actionPerformed();
}
});
colourMenu.setText(MessageManager.getString("label.group_colour"));
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_conversed"));
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);
}
});
pdbMenu.setText(MessageManager
.getString("label.associate_structure_with_sequence"));
pdbFromFile.setText(MessageManager.getString("label.from_file"));
pdbFromFile.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
pdbFromFile_actionPerformed();
}
});
// RNAFold.setText("From RNA Fold with predict2D");
// RNAFold.addActionListener(new ActionListener()
// {
// public void actionPerformed(ActionEvent e)
// {
// try {
// RNAFold_actionPerformed();
// } catch (Exception e1) {
// // TODO Auto-generated catch block
// e1.printStackTrace();
// }
// }
// });
// ContraFold.setText("From Contra Fold with predict2D");
// ContraFold.addActionListener(new ActionListener()
// {
// public void actionPerformed(ActionEvent e)
// {
// try {
// ContraFold_actionPerformed();
// } catch (Exception e1) {
// // TODO Auto-generated catch block
// e1.printStackTrace();
// }
// }
// });
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
enterPDB_actionPerformed();
}
});
discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
discoverPDB.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
discoverPDB_actionPerformed();
}
});
outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ "...");
showAnnotationsMenu.setText(MessageManager
.getString("label.show_annotations"));
hideAnnotationsMenu.setText(MessageManager
.getString("label.hide_annotations"));
configureReferenceAnnotationsMenu();
sequenceFeature.setText(MessageManager
.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
}
});
textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed();
}
});
jMenu1.setText(MessageManager.getString("label.group"));
structureMenu.setText(MessageManager.getString("label.structure"));
viewStructureMenu.setText(MessageManager
.getString("label.view_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);
}
});
/*
* annotationMenuItem.setText("By Annotation");
* annotationMenuItem.addActionListener(new ActionListener() { public void
* actionPerformed(ActionEvent actionEvent) {
* annotationMenuItem_actionPerformed(actionEvent); } });
*/
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
this.add(structureMenu);
// groupMenu.add(chooseAnnotations);
groupMenu.add(showAnnotationsMenu);
groupMenu.add(hideAnnotationsMenu);
groupMenu.add(addDatasequenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
groupMenu.add(createGroupMenuItem);
groupMenu.add(unGroupMenuItem);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
sequenceMenu.add(sequenceDetails);
colourMenu.add(textColour);
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
colourMenu.add(BLOSUM62Colour);
colourMenu.add(PIDColour);
colourMenu.add(zappoColour);
colourMenu.add(taylorColour);
colourMenu.add(hydrophobicityColour);
colourMenu.add(helixColour);
colourMenu.add(strandColour);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
if (ap.getAlignment().isNucleotide())
{
// JBPNote - commented since the colourscheme isn't functional
// colourMenu.add(RNAInteractionColour);
colourMenu.add(purinePyrimidineColour);
}
// colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
{
java.util.Enumeration userColours = jalview.gui.UserDefinedColours
.getUserColourSchemes().keys();
while (userColours.hasMoreElements())
{
JMenuItem item = new JMenuItem(userColours.nextElement().toString());
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
}
});
colourMenu.add(item);
}
}
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
// colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
editMenu.add(upperCase);
editMenu.add(lowerCase);
editMenu.add(toggle);
pdbMenu.add(pdbFromFile);
// 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);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
jMenu1.add(colourMenu);
jMenu1.add(showBoxes);
jMenu1.add(showText);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed();
}
});
clustalColour.setText(MessageManager
.getString("label.clustalx_colours"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
clustalColour_actionPerformed();
}
});
zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed();
}
});
taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed();
}
});
hydrophobicityColour.setText(MessageManager
.getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
hydrophobicityColour_actionPerformed();
}
});
helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed();
}
});
strandColour.setText(MessageManager
.getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed();
}
});
turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed();
}
});
buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed();
}
});
abovePIDColour.setText(MessageManager
.getString("label.above_identity_percentage"));
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
abovePIDColour_actionPerformed();
}
});
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.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed();
}
});
BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed();
}
});
purinePyrimidineColour.setText(MessageManager
.getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
purinePyrimidineColour_actionPerformed();
}
});
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
conservationMenuItem.setText(MessageManager
.getString("label.conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed();
}
});
}
/**
* 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 annotation that matches on
* sequenceRef.datasetSequence, calcId and label.
*/
protected void configureReferenceAnnotationsMenu()
{
addDatasequenceAnnotations.setText(MessageManager
.getString("label.add_reference_annotations"));
addDatasequenceAnnotations.setEnabled(false);
/*
* Temporary store so we can write distinct calcId / type pairs on the
* tooltip.
*/
Map tipEntries = new HashMap();
StringBuilder tooltip = new StringBuilder(64);
tooltip.append(MessageManager.getString("label.add_annotations_for"));
// this menu option only applies for a Selection
if (this.ap.av.getSelectionGroup() == null)
{
return;
}
/*
* For each sequence selected in the alignment, make a list of any
* annotations on the underlying dataset sequence which are not already on
* the sequence in the alignment.
*
* Build a map of { alignmentSequence, }
*/
final Map> candidates = new HashMap>();
for (SequenceI seq : this.ap.av.getSelectionGroup().getSequences())
{
SequenceI dataset = seq.getDatasetSequence();
if (dataset == null)
{
continue;
}
AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
if (datasetAnnotations == null)
{
continue;
}
final List result = new ArrayList();
for (AlignmentAnnotation dsann : datasetAnnotations)
{
/*
* If the sequence has no annotation that matches this one, then add
* this one to the results list.
*/
if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label)
.isEmpty())
{
result.add(dsann);
tipEntries.put(dsann.getCalcId(), dsann.label);
}
}
/*
* Save any addable annotations for this sequence
*/
if (!result.isEmpty())
{
candidates.put(seq, result);
}
}
if (!candidates.isEmpty())
{
/*
* Found annotations that could be added. Enable the menu item, and
* configure its tooltip and action.
*/
addDatasequenceAnnotations.setEnabled(true);
for (String calcId : tipEntries.keySet())
{
tooltip.append("
" + calcId + "/" + tipEntries.get(calcId));
}
String tooltipText = JvSwingUtils.wrapTooltip(true,
tooltip.toString());
addDatasequenceAnnotations.setToolTipText(tooltipText);
addDatasequenceAnnotations.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)
{
for (SequenceI seq : candidates.keySet())
{
for (AlignmentAnnotation ann : candidates.get(seq))
{
AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
int startRes = 0;
int endRes = ann.annotations.length;
final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
if (selectionGroup != null)
{
startRes = selectionGroup.getStartRes();
endRes = selectionGroup.getEndRes();
}
copyAnn.restrict(startRes, endRes);
// add to the sequence (sets correct copyAnn.datasetSequence)
seq.addAlignmentAnnotation(copyAnn);
// adjust for gaps
copyAnn.adjustForAlignment();
// add to the alignment and set visible
this.ap.getAlignment().addAnnotation(copyAnn);
copyAnn.visible = true;
}
}
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();
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
contents.append(""
+ MessageManager
.formatMessage(
"label.create_sequence_details_report_annotation_for",
new String[]
{ seq.getDisplayId(true) }) + "
");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
contents,
seq,
true,
true,
false,
(ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
: null);
contents.append("
");
}
cap.setText("" + contents.toString() + "");
Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
"label.sequece_details_for",
(sequences.length == 1 ? new String[]
{ sequences[0].getDisplayId(true) } : new String[]
{ 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());
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void zappoColour_actionPerformed()
{
getGroup().cs = new ZappoColourScheme();
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void taylorColour_actionPerformed()
{
getGroup().cs = new TaylorColourScheme();
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void hydrophobicityColour_actionPerformed()
{
getGroup().cs = new HydrophobicColourScheme();
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void helixColour_actionPerformed()
{
getGroup().cs = new HelixColourScheme();
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void strandColour_actionPerformed()
{
getGroup().cs = new StrandColourScheme();
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void turnColour_actionPerformed()
{
getGroup().cs = new TurnColourScheme();
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void buriedColour_actionPerformed()
{
getGroup().cs = new BuriedColourScheme();
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void nucleotideMenuItem_actionPerformed()
{
getGroup().cs = new NucleotideColourScheme();
refresh();
}
protected void purinePyrimidineColour_actionPerformed()
{
getGroup().cs = new PurinePyrimidineColourScheme();
refresh();
}
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
*/
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void abovePIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
{
return;
}
if (abovePIDColour.isSelected())
{
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
else
// remove PIDColouring
{
sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
}
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void userDefinedColour_actionPerformed(ActionEvent e)
{
SequenceGroup sg = getGroup();
if (e.getSource().equals(userDefinedColour))
{
new UserDefinedColours(ap, sg);
}
else
{
UserColourScheme udc = (UserColourScheme) UserDefinedColours
.getUserColourSchemes().get(e.getActionCommand());
sg.cs = udc;
}
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!
*/
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void BLOSUM62Colour_actionPerformed()
{
SequenceGroup sg = getGroup();
sg.cs = new Blosum62ColourScheme();
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void noColourmenuItem_actionPerformed()
{
getGroup().cs = null;
refresh();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void conservationMenuItem_actionPerformed()
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
{
return;
}
if (conservationMenuItem.isSelected())
{
// JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3, 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.cs, sg.getName());
SliderPanel.showConservationSlider();
}
else
// remove ConservationColouring
{
sg.cs.setConservation(null);
}
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.cs = 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)
{
JOptionPane
.showMessageDialog(
ap,
MessageManager
.getString("label.spaces_converted_to_backslashes"),
MessageManager
.getString("label.no_spaces_allowed_sequence_name"),
JOptionPane.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)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
void hideSequences(boolean representGroup)
{
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null || sg.getSize() < 1)
{
ap.av.hideSequence(new SequenceI[]
{ sequence });
return;
}
ap.av.setSelectionGroup(null);
if (representGroup)
{
ap.av.hideRepSequences(sequence, sg);
return;
}
int gsize = sg.getSize();
SequenceI[] hseqs;
hseqs = new SequenceI[gsize];
int index = 0;
for (int i = 0; i < gsize; i++)
{
hseqs[index++] = sg.getSequenceAt(i);
}
ap.av.hideSequence(hseqs);
// refresh(); TODO: ? needed ?
ap.av.sendSelection();
}
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)
{
int[][] 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 String[]
{ 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
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
ap.av, true));
}
public void pdbFromFile_actionPerformed()
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(MessageManager.formatMessage(
"label.select_pdb_file_for", new String[]
{ sequence.getDisplayId(false) }));
chooser.setToolTipText(MessageManager.formatMessage(
"label.load_pdb_file_associate_with_sequence", new String[]
{ sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
jalview.io.AppletFormatAdapter.FILE, sequence, true);
}
}
// JBNote: commented out - these won't be instantiated here...!
// public void RNAFold_actionPerformed() throws Exception
// {
// Predict2D P2D = new Predict2D();
// P2D.getStructure2DFromRNAFold("toto");
// }
//
// public void ContraFold_actionPerformed() throws Exception
// {
// Predict2D P2D = new Predict2D();
// P2D.getStructure2DFromContraFold("toto");
// }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
MessageManager.getString("label.enter_pdb_id"),
MessageManager.getString("label.enter_pdb_id"),
JOptionPane.QUESTION_MESSAGE);
if (id != null && id.length() > 0)
{
PDBEntry entry = new PDBEntry();
entry.setId(id.toUpperCase());
sequence.getDatasetSequence().addPDBId(entry);
}
}
public void discoverPDB_actionPerformed()
{
final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
{ sequence }
: ap.av.getSequenceSelection());
Thread discpdb = new Thread(new Runnable()
{
@Override
public void run()
{
new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
.fetchDBRefs(false);
}
});
discpdb.start();
}
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.seqPanel.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"),
EditCommand.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());
}
}
}
}