) sq.getDatasetSequence()
.getPDBId();
if (pes != null)
{
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()]);
final JMenuItem gpdbview;
if (pdbe.size() == 1)
{
structureMenu.add(gpdbview = new JMenuItem("View structure for "
+ sqass.getDisplayId(false)));
}
else
{
structureMenu.add(gpdbview = new JMenuItem("View all "
+ pdbe.size() + " structures."));
}
gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
gpdbview.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
new AppJmol(ap, pe, ap.av.collateForPDB(pe));
}
});
}
}
else
{
groupMenu.setVisible(false);
editMenu.setVisible(false);
}
if (!ap.av.getAlignment().getGroups().contains(sg))
{
unGroupMenuItem.setVisible(false);
}
if (seq == null)
{
sequenceMenu.setVisible(false);
structureMenu.setVisible(false);
}
if (links != null && links.size() > 0)
{
JMenu linkMenu = new JMenu("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);
}
}
}
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("Group Link");
JMenu[] linkMenus = new JMenu[]
{ null, new JMenu("IDS"), new JMenu("Sequences"),
new JMenu("IDS and 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("Group Links");
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("open URL: " + url);
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
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("open URL (" + urlgenerator.getUrl_prefix()
+ "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
// put
// in
// info
// about
// what
// is
// being
// sent.
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
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("Group");
groupMenu.setText("Selection");
groupName.setText("Name");
groupName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
groupName_actionPerformed();
}
});
sequenceMenu.setText("Sequence");
sequenceName.setText("Edit Name/Description");
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
sequenceName_actionPerformed();
}
});
sequenceDetails.setText("Sequence Details ...");
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
sequenceDetails_actionPerformed();
}
});
sequenceSelDetails.setText("Sequence Details ...");
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
sequenceSelectionDetails_actionPerformed();
}
});
PIDColour.setFocusPainted(false);
unGroupMenuItem.setText("Remove Group");
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
unGroupMenuItem_actionPerformed();
}
});
outline.setText("Border colour");
outline.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
outline_actionPerformed();
}
});
nucleotideMenuItem.setText("Nucleotide");
nucleotideMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
nucleotideMenuItem_actionPerformed();
}
});
colourMenu.setText("Group Colour");
showBoxes.setText("Boxes");
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
showBoxes_actionPerformed();
}
});
showText.setText("Text");
showText.setState(true);
showText.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
}
});
showColourText.setText("Colour Text");
showColourText.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
}
});
displayNonconserved.setText("Show Nonconserved");
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
showNonconserved_actionPerformed();
}
});
editMenu.setText("Edit");
cut.setText("Cut");
cut.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed();
}
});
upperCase.setText("To Upper Case");
upperCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
copy.setText("Copy");
copy.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
}
});
lowerCase.setText("To Lower Case");
lowerCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
toggle.setText("Toggle Case");
toggle.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
pdbMenu.setText("Associate Structure with Sequence");
pdbFromFile.setText("From File");
pdbFromFile.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
pdbFromFile_actionPerformed();
}
});
enterPDB.setText("Enter PDB Id");
enterPDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
enterPDB_actionPerformed();
}
});
discoverPDB.setText("Discover PDB ids");
discoverPDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
discoverPDB_actionPerformed();
}
});
outputMenu.setText("Output to Textbox...");
sequenceFeature.setText("Create Sequence Feature");
sequenceFeature.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
}
});
textColour.setText("Text Colour");
textColour.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed();
}
});
jMenu1.setText("Group");
structureMenu.setText("Structure");
viewStructureMenu.setText("View Structure");
// colStructureMenu.setText("Colour By Structure");
editSequence.setText("Edit Sequence...");
editSequence.addActionListener(new ActionListener()
{
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(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
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())
{
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()
{
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);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
jMenu1.add(unGroupMenuItem);
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("None");
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed();
}
});
clustalColour.setText("Clustalx colours");
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
clustalColour_actionPerformed();
}
});
zappoColour.setText("Zappo");
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed();
}
});
taylorColour.setText("Taylor");
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed();
}
});
hydrophobicityColour.setText("Hydrophobicity");
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
hydrophobicityColour_actionPerformed();
}
});
helixColour.setText("Helix propensity");
helixColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed();
}
});
strandColour.setText("Strand propensity");
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed();
}
});
turnColour.setText("Turn propensity");
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed();
}
});
buriedColour.setText("Buried Index");
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed();
}
});
abovePIDColour.setText("Above % Identity");
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
abovePIDColour_actionPerformed();
}
});
userDefinedColour.setText("User Defined...");
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
}
});
PIDColour.setText("Percentage Identity");
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed();
}
});
BLOSUM62Colour.setText("BLOSUM62");
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed();
}
});
purinePyrimidineColour.setText("Purine/Pyrimidine");
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
purinePyrimidineColour_actionPerformed();
}
});
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
conservationMenuItem.setText("Conservation");
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed();
}
});
}
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("Annotation for " + 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, "Sequence Details for "
+ (sequences.length == 1 ? sequences[0].getDisplayId(true)
: "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.getActionCommand().equals("User Defined..."))
{
new UserDefinedColours(ap, sg);
}
else
{
UserColourScheme udc = (UserColourScheme) UserDefinedColours
.getUserColourSchemes().get(e.getActionCommand());
sg.cs = udc;
}
refresh();
}
/**
* 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())
{
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.predefinedColours = 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(), " Group Name ",
"Group Description ", "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(), " Sequence Name ",
"Sequence Description ", "Edit Sequence Name/Description",
ap.alignFrame);
if (!dialog.accept)
{
return;
}
if (dialog.getName() != null)
{
if (dialog.getName().indexOf(" ") > -1)
{
JOptionPane.showMessageDialog(ap,
"Spaces have been converted to \"_\"",
"No spaces allowed in 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();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
Color col = JColorChooser.showDialog(this, "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,
"Unixers: Couldn't find default web browser."
+ "\nAdd the full path to your browser in Preferences.",
"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 = "Toggle Case";
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
description = "To Upper Case";
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
description = "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,
"Alignment output - " + 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
SequenceGroup sg = ap.av.getSelectionGroup();
ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
omitHidden = ap.av.getViewAsString(true);
Alignment oal = new Alignment(ap.av.getSequenceSelection());
AlignmentAnnotation[] nala = ap.av.getAlignment()
.getAlignmentAnnotation();
if (nala != null)
{
for (int i = 0; i < nala.length; i++)
{
AlignmentAnnotation na = nala[i];
oal.addAnnotation(na);
}
}
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
oal, omitHidden, csel, sg));
oal = null;
}
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("Select a PDB file for "
+ sequence.getDisplayId(false));
chooser.setToolTipText("Load a PDB file and associate it with sequence '"
+ 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);
}
}
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
"Enter PDB Id", "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()
{
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 = (Sequence) sg.getSequenceAt(0);
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
sg.getEndRes() + 1), null, "Edit Sequence ", null,
"Edit Sequence", ap.alignFrame);
if (dialog.accept)
{
EditCommand editCommand = new EditCommand("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());
}
}
}
}