/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
+import jalview.ws.WSMenuEntryProviderI;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
|| evt.isShiftDown() || evt.isAltDown());
}
break;
-
+
+ //case KeyEvent.VK_A:
+ // if (viewport.cursorMode)
+ // {
+ // alignPanel.seqPanel.insertNucAtCursor(false,"A");
+ // //System.out.println("A");
+ // }
+ // break;
+ /*
+ case KeyEvent.VK_CLOSE_BRACKET:
+ if (viewport.cursorMode)
+ {
+ System.out.println("closing bracket");
+ }
+ break;
+ */
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
}
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
}
}
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
+ rnahelicesColour.setEnabled(nucleotide);
+ purinePyrimidineColour.setEnabled(nucleotide);
// Remember AlignFrame always starts as protein
- if (!nucleotide)
- {
- calculateMenu.remove(calculateMenu.getItemCount() - 2);
- }
+ //if (!nucleotide)
+ // {
+ // showTr
+ // calculateMenu.remove(calculateMenu.getItemCount() - 2);
+ // }
}
/**
applyToAllGroups.setState(av.colourAppliesToAllGroups);
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
showDbRefsMenuitem.setSelected(av.isShowDbRefs());
-
+ autoCalculate.setSelected(av.autoCalculateConsensus);
+ sortByTree.setSelected(av.sortByTree);
+ listenToViewSelections.setSelected(av.followSelection);
+ rnahelicesColour.setEnabled(av.alignment.hasRNAStructure());
+ rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
setShowProductsEnabled();
updateEditMenuBar();
progressBars.put(lId, progressPanel);
}
// update GUI
- setMenusForViewport();
+ // setMenusForViewport();
validate();
}
changeColour(new NucleotideColourScheme());
}
+ public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+ /*
+ public void covariationColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new CovariationColourScheme(viewport.alignment.getAlignmentAnnotation()[0]));
+ }
+ */
public void annotationColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
+
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
/**
* DOCUMENT ME!
.getAlignment().getSequences());
}
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+ viewport.sortByTree = sortByTree.isSelected();
+ }
+ @Override
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ viewport.followSelection = listenToViewSelections.isSelected();
+ }
/**
* DOCUMENT ME!
*
for (i = 0; i < treePanels.size(); i++)
{
- TreePanel tp = (TreePanel) treePanels.elementAt(i);
+ final TreePanel tp = (TreePanel) treePanels.elementAt(i);
final JMenuItem item = new JMenuItem(tp.getTitle());
final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- SequenceI[] oldOrder = viewport.getAlignment()
- .getSequencesArray();
- AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
-
- addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
- viewport.alignment));
-
- alignPanel.paintAlignment(true);
+ tp.sortByTree_actionPerformed(null);
+ addHistoryItem(tp.sortAlignmentIn(alignPanel));
+
}
});
}
}
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.alignment));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
// object broker mechanism.
final Vector wsmenu = new Vector();
final IProgressIndicator af = me;
- if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
- && Discoverer.services != null
+ final JMenu msawsmenu = new JMenu("Alignment");
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ final JMenu seqsrchmenu = new JMenu(
+ "Sequence Database Search");
+ final JMenu analymenu = new JMenu(
+ "Analysis");
+ // JAL-940 - only show secondary structure prediction services from the legacy server
+ if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
+ // &&
+ Discoverer.services != null
&& (Discoverer.services.size() > 0))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// stored or retrieved from elsewhere
- Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
- Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
+ Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch");
// TODO: move GUI generation code onto service implementation - so a
// client instance attaches itself to the GUI with method call like
// jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
if (msaws != null)
{
// Add any Multiple Sequence Alignment Services
- final JMenu msawsmenu = new JMenu("Alignment");
for (int i = 0, j = msaws.size(); i < j; i++)
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
impl.attachWSMenuEntry(msawsmenu, me);
}
- wsmenu.add(msawsmenu);
}
if (secstrpr != null)
{
// Add any secondary structure prediction services
- final JMenu secstrmenu = new JMenu(
- "Secondary Structure Prediction");
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
.getServiceClient(sh);
impl.attachWSMenuEntry(secstrmenu, me);
}
- wsmenu.add(secstrmenu);
}
if (seqsrch != null)
{
// Add any sequence search services
- final JMenu seqsrchmenu = new JMenu(
- "Sequence Database Search");
for (int i = 0, j = seqsrch.size(); i < j; i++)
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
.getServiceClient(sh);
impl.attachWSMenuEntry(seqsrchmenu, me);
}
- wsmenu.add(seqsrchmenu);
}
}
{
if (jws2servs.hasServices())
{
- JMenu jws2men = new JMenu("Jaba Web Services");
- jws2servs.attachWSMenuEntry(jws2men, me);
- for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
- {
- wsmenu.add(jws2men.getMenuComponent(i));
- }
+ jws2servs.attachWSMenuEntry(msawsmenu, me);
}
}
}
+ // Add all submenus in the order they should appear on the web services menu
+ wsmenu.add(msawsmenu);
+ wsmenu.add(secstrmenu);
+ wsmenu.add(analymenu);
+ // No search services yet
+ // wsmenu.add(seqsrchmenu);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
{
try
{
-
- resetWebServiceMenu();
- // finally, add the whole shebang onto the webservices menu
+ webService.removeAll();
+ // first, add discovered services onto the webservices menu
if (wsmenu.size() > 0)
{
for (int i = 0, j = wsmenu.size(); i < j; i++)
}
else
{
- me.webService.add(me.webServiceNoServices);
+ webService.add(me.webServiceNoServices);
}
+ build_urlServiceMenu(me.webService);
+ build_fetchdbmenu(webService);
} catch (Exception e)
{
}
}
- /**
- * empty the web service menu and add any ad-hoc functions not dynamically
- * discovered.
- *
- */
- private void resetWebServiceMenu()
- {
- webService.removeAll();
- build_fetchdbmenu(webService);
- build_urlServiceMenu(webService);
- }
/**
* construct any groupURL type service menu entries.
*/
private void build_urlServiceMenu(JMenu webService)
{
- if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
- {
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
- webService, this);
- }
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
/*
// TODO: refactor to RestClient discoverer and merge menu entries for
// rest-style services with other types of analysis/calculation service
// SHmmr test client - still being implemented.
- jalview.ws.rest.RestClient.makeShmmrRestClient().attachWSMenuEntry(
- webService, this);
// DEBUG - alignmentView
+
+ for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
+ client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
+ }
+
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ {
+ jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
+ webService, this);
+ }
}
/*
featuresFile = new FeaturesFile(file, type)
.parse(viewport.alignment.getDataset(),
alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
- false);
+ false, jalview.bin.Cache.getDefault(
+ "RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
ex.printStackTrace();
if (pdbfn.length() > 0)
{
// attempt to find a match in the alignment
- SequenceI mtch = idm.findIdMatch(pdbfn);
+ SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
int l = 0, c = pdbfn.indexOf(".");
while (mtch == null && c != -1)
{
- while ((c = pdbfn.indexOf(".", l)) > l)
+ do
{
l = c;
- }
+ } while ((c = pdbfn.indexOf(".", l)) > l);
if (l > -1)
{
pdbfn = pdbfn.substring(0, l);
}
- mtch = idm.findIdMatch(pdbfn);
+ mtch = idm.findAllIdMatches(pdbfn);
}
if (mtch != null)
{
// try and associate
// TODO: may want to set a standard ID naming formalism for
// associating PDB files which have no IDs.
+ for (SequenceI toassoc: (SequenceI[])fm[2]) {
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0], (String) fm[1],
- (SequenceI) fm[2], false);
+ toassoc, false);
if (pe != null)
{
System.err
.println("Associated file : " + ((String) fm[0])
+ " with "
- + ((SequenceI) fm[2]).getDisplayId(true));
+ + toassoc.getDisplayId(true));
assocfiles++;
}
+ }
alignPanel.paintAlignment(true);
}
}
alignPanel.paintAlignment(true);
}
}
+
+ /**
+ * make the given alignmentPanel the currently selected tab
+ *
+ * @param alignmentPanel
+ */
+ public void setDisplayedView(AlignmentPanel alignmentPanel)
+ {
+ if (!viewport.getSequenceSetId().equals(
+ alignmentPanel.av.getSequenceSetId()))
+ {
+ throw new Error(
+ "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+ }
+ if (tabbedPane != null
+ & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
+ {
+ tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
+ }
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff