/*
- * 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
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
import jalview.schemes.ZappoColourScheme;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
/**
* Creates a new AlignFrame object with specific width and height.
- *
+ *
* @param al
* @param width
* @param height
/**
* Creates a new AlignFrame object with specific width, height and
* sequenceSetId
- *
+ *
* @param al
* @param width
* @param height
/**
* Creates a new AlignFrame object with specific width, height and
* sequenceSetId
- *
+ *
* @param al
* @param width
* @param height
/**
* new alignment window with hidden columns
- *
+ *
* @param al
* AlignmentI
* @param hiddenColumns
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
- *
+ *
* @param al
* @param hiddenColumns
* @param width
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
- *
+ *
* @param al
* @param hiddenColumns
* @param width
/**
* Make a new AlignFrame from exisiting alignmentPanels
- *
+ *
* @param ap
* AlignmentPanel
* @param av
/**
* Change the filename and format for the alignment, and enable the 'reload'
* button functionality.
- *
+ *
* @param file
* valid filename
* @param format
/**
* Need to call this method when tabs are selected for multiple views, or when
* loading from Jalview2XML.java
- *
+ *
* @param av
* AlignViewport
*/
updateEditMenuBar();
}
+
// methods for implementing IProgressIndicator
// need to refactor to a reusable stub class
Hashtable progressBars, progressBarHandlers;
/*
* (non-Javadoc)
- *
+ *
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
@Override
}
/**
- *
+ *
* @return true if any progress bars are still active
*/
@Override
for (int i = 0; i < frames.length; i++)
{
if (frames[i] instanceof AlignFrame && frames[i] != this
- && ((AlignFrame) frames[i]).fileName!=null && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ && ((AlignFrame) frames[i]).fileName != null
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
try
{
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
}
}
FormatAdapter f = new FormatAdapter();
- String output = f.formatSequences(
- format,
+ String output = f.formatSequences(format,
viewport.getAlignment(), // class cast exceptions will
// occur in the distant future
omitHidden, f.getCacheSuffixDefault(format),
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* Close the current view or all views in the alignment frame. If the frame
* only contains one view then the alignment will be removed from memory.
- *
+ *
* @param closeAllTabs
*/
@Override
/**
* close alignPanel2 and shuffle tabs appropriately.
- *
+ *
* @param alignPanel2
*/
public void closeView(AlignmentPanel alignPanel2)
}
/**
- *
+ *
* @return alignment objects for all views
*/
AlignmentI[] getViewAlignments()
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param up
* DOCUMENT ME!
*/
{
return;
}
- viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* Paste contents of Jalview clipboard
- *
+ *
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
*/
}
int alwidth = 0;
- ArrayList<Integer> newGraphGroups=new ArrayList<Integer>();
- int fgroup=-1;
+ ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+ int fgroup = -1;
if (newAlignment)
{
{
newDs.clear(); // tidy up
}
- if (alignment.getAlignmentAnnotation()!=null)
+ if (alignment.getAlignmentAnnotation() != null)
{
- for (AlignmentAnnotation alan:alignment.getAlignmentAnnotation())
+ for (AlignmentAnnotation alan : alignment
+ .getAlignmentAnnotation())
{
- if (alan.graphGroup>fgroup)
+ if (alan.graphGroup > fgroup)
{
- fgroup=alan.graphGroup;
+ fgroup = alan.graphGroup;
}
}
}
if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
{
AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
- if (newann.graphGroup>-1)
+ if (newann.graphGroup > -1)
{
- if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
{
- for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
{
newGraphGroups.add(q, null);
}
- newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
}
- newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
}
newann.padAnnotation(alwidth);
for (int a = 0; a < sequences[i].getAnnotation().length; a++)
{
annotationAdded = true;
- newann=sequences[i].getAnnotation()[a];
+ newann = sequences[i].getAnnotation()[a];
newann.adjustForAlignment();
newann.padAnnotation(alwidth);
- if (newann.graphGroup>-1)
+ if (newann.graphGroup > -1)
{
- if (newann.graphGroup>-1)
+ if (newann.graphGroup > -1)
{
- if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
{
- for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
{
newGraphGroups.add(q, null);
}
- newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
}
- newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
}
}
alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
newann.padAnnotation(avwidth);
alview[avnum].addAnnotation(newann); // annotation was
// duplicated earlier
- // TODO JAL-1145 graphGroups are not updated for sequence annotation added to several views. This may cause strangeness
+ // TODO JAL-1145 graphGroups are not updated for sequence
+ // annotation added to several views. This may cause
+ // strangeness
alview[avnum].setAnnotationIndex(newann, a);
}
}
}
viewport.firePropertyChange("alignment", null,
alignment.getSequences());
- if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector<AlignmentPanel>)alignPanels))
+ if (alignPanels != null)
+ {
+ for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+ {
+ ap.validateAnnotationDimensions(false);
+ }
+ }
+ else
{
- ap.validateAnnotationDimensions(false);
- }} else { alignPanel.validateAnnotationDimensions(false);}
+ alignPanel.validateAnnotationDimensions(false);
+ }
}
else
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
addHistoryItem(trimRegion);
- for (SequenceGroup sg :viewport.getAlignment().getGroups())
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
}
/**
- *
+ *
* @param copyAnnotation
* if true then duplicate all annnotation, groups and settings
* @return new alignment panel, already displayed.
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @return new alignment panel, already displayed.
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @param copyAnnotation
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/*
* (non-Javadoc)
- *
+ *
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
@Override
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* called by key handler and the hide all/show all menu items
- *
+ *
* @param toggleSeqs
* @param toggleCols
*/
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* Set or clear 'Show Sequence Features'
- *
+ *
* @param evt
* DOCUMENT ME!
*/
/**
* Set or clear 'Show Sequence Features'
- *
+ *
* @param evt
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@Override
public void clustalColour_actionPerformed(ActionEvent e)
{
- changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+ viewport.getHiddenRepSequences()));
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param cs
* DOCUMENT ME!
*/
if (viewport.getColourAppliesToAllGroups())
{
-
- for (SequenceGroup sg:viewport.getAlignment().getGroups())
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
if (cs == null)
{
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg, viewport
- .getHiddenRepSequences());
+ sg.cs = new ClustalxColourScheme(sg,
+ viewport.getHiddenRepSequences());
}
else if (cs instanceof UserColourScheme)
{
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param type
* DOCUMENT ME!
* @param pwType
{
TreePanel tp;
- if (viewport.getSelectionGroup() != null)
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 0)
{
if (viewport.getSelectionGroup().getSize() < 3)
{
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- for (SequenceI _s:sg.getSequences())
+ for (SequenceI _s : sg.getSequences())
{
- if (_s.getLength() < sg
- .getEndRes())
+ if (_s.getLength() < sg.getEndRes())
{
JOptionPane
.showMessageDialog(
/**
* DOCUMENT ME!
- *
+ *
* @param title
* DOCUMENT ME!
* @param order
/**
* Add a new sort by annotation score menu item
- *
+ *
* @param sort
* the menu to add the option to
* @param scoreLabel
* search the alignment and rebuild the sort by annotation score submenu the
* last alignment annotation vector hash is stored to minimize cost of
* rebuilding in subsequence calls.
- *
+ *
*/
@Override
public void buildSortByAnnotationScoresMenu()
// almost certainly a quicker way to do this - but we keep it simple
Hashtable scoreSorts = new Hashtable();
AlignmentAnnotation aann[];
- for (SequenceI sqa:viewport.getAlignment().getSequences())
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
{
aann = sqa.getAnnotation();
for (int i = 0; aann != null && i < aann.length; i++)
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
- *
+ *
* @param treePanel
* Displayed tree window.
* @param title
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
- *
+ *
*/
public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
{
/*
* SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
* SequenceI[sz = seqs.getSize(false)];
- *
+ *
* for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
* seqs.getSequenceAt(i); }
*/
{
/*
* Vector seqs = viewport.getAlignment().getSequences();
- *
+ *
* if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
- *
+ *
* for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
* seqs.elementAt(i); } }
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* Add a treeviewer for the tree extracted from a newick file object to the
* current alignment view
- *
+ *
* @param nf
* the tree
* @param title
/**
* Generates menu items and listener event actions for web service clients
- *
+ *
*/
public void BuildWebServiceMenu()
{
@Override
public void run()
{
+ final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
try
{
System.err.println("Building ws menu again "
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// stored or retrieved from elsewhere
- Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+ // No MSAWS used any more:
+ // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
- 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,
- // alignframe)
- if (msaws != null)
- {
- // Add any Multiple Sequence Alignment Services
- for (int i = 0, j = msaws.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, me);
-
- }
- }
if (secstrpr != null)
{
// Add any secondary structure prediction services
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
+ int p=secstrmenu.getItemCount();
impl.attachWSMenuEntry(secstrmenu, me);
- }
- }
- if (seqsrch != null)
- {
- // Add any sequence search services
- for (int i = 0, j = seqsrch.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, me);
+ int q=secstrmenu.getItemCount();
+ for (int litm=p;litm<q; litm++)
+ {
+ legacyItems.add(secstrmenu.getItem(litm));
+ }
}
}
}
-
+
// Add all submenus in the order they should appear on the web
// services menu
wsmenu.add(msawsmenu);
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
- // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
- // submens.add(msawsmenu);
- // submens.add(secstrmenu);
- // submens.add(dismenu);
- // submens.add(analymenu);
-
// No search services yet
// wsmenu.add(seqsrchmenu);
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
+ boolean new_sspred=false;
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs.hasServices())
{
jws2servs.attachWSMenuEntry(webService, me);
+ for (Jws2Instance sv:jws2servs.getServices()) {
+ if (sv.description.toLowerCase().contains("jpred"))
+ {
+ for (JMenuItem jmi:legacyItems)
+ {
+ jmi.setVisible(false);
+ }
+ }
+ }
+
}
if (jws2servs.isRunning())
{
}
}
}
-
build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
}
} catch (Exception e)
{
- Cache.log.debug("Exception during web service menu building process.",e);
+ Cache.log
+ .debug("Exception during web service menu building process.",
+ e);
}
;
}
/**
* construct any groupURL type service menu entries.
- *
+ *
* @param webService
*/
private void build_urlServiceMenu(JMenu webService)
/*
* JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
* AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
- *
+ *
* @Override public void actionPerformed(ActionEvent e) {
* jalview.datamodel.AlignmentView
* .testSelectionViews(af.viewport.getAlignment(),
* af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
- *
+ *
* }); webService.add(testAlView);
*/
// TODO: refactor to RestClient discoverer and merge menu entries for
* public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
* chooser = new JalviewFileChooser(jalview.bin.Cache.
* getProperty("LAST_DIRECTORY"));
- *
+ *
* chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
* to Vamsas file"); chooser.setToolTipText("Export");
- *
+ *
* int value = chooser.showSaveDialog(this);
- *
+ *
* if (value == JalviewFileChooser.APPROVE_OPTION) {
* jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
* //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
*/
/**
* prototype of an automatically enabled/disabled analysis function
- *
+ *
*/
protected void setShowProductsEnabled()
{
/**
* search selection for sequence xRef products and build the show products
* menu.
- *
+ *
* @param selection
* @param dataset
* @return true if showProducts menu should be enabled.
} catch (Exception ex)
{
al = null;
- jalview.bin.Cache.log.debug("Exception during translation.", ex);
+ jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.",
+ "Implementation error: Translation Failed", JOptionPane.ERROR_MESSAGE);
+ return;
}
if (al == null)
{
/**
* Try to load a features file onto the alignment.
- *
+ *
* @param file
* contents or path to retrieve file
* @param type
* it's and Annotation file, then a JNet file, and finally a features file. If
* all are false then the user may have dropped an alignment file onto this
* AlignFrame.
- *
+ *
* @param file
* either a filename or a URL string.
*/
}
else
{
- // some problem - if no warning its probable that the ID matching process didn't work
- JOptionPane.showMessageDialog(Desktop.desktop,
- tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
- "Problem reading T-COFFEE score file",
- JOptionPane.WARNING_MESSAGE);
+ // some problem - if no warning its probable that the ID matching
+ // process didn't work
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ tcf.getWarningMessage() == null ? "Check that the file matches sequence IDs in the alignment."
+ : tcf.getWarningMessage(),
+ "Problem reading T-COFFEE score file",
+ JOptionPane.WARNING_MESSAGE);
}
}
else
}
} catch (Exception x)
{
- Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+ Cache.log
+ .debug("Exception when processing data source as T-COFFEE score file",
+ x);
tcf = null;
}
if (tcf == null)
{
/*
* if (format.equalsIgnoreCase("PDB")) {
- *
+ *
* String pdbfn = ""; // try to match up filename with sequence id
* try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
* new File(file); pdbfn = fl.getName(); } else if (protocol ==
} catch (Exception ex)
{
ex.printStackTrace();
- }
- catch (OutOfMemoryError oom)
+ } catch (OutOfMemoryError oom)
{
- try {
+ try
+ {
System.gc();
- } catch (Exception x){};
- new OOMWarning("loading data "+(protocol!=null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." : "using "+protocol+" from "+file) : ".")+(format!=null ? "(parsing as '"+format+"' file)" :""), oom, Desktop.desktop);
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "loading data "
+ + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+ : "using " + protocol + " from " + file)
+ : ".")
+ + (format != null ? "(parsing as '" + format
+ + "' file)" : ""), oom, Desktop.desktop);
}
}
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
/*
* (non-Javadoc)
- *
+ *
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
/**
* find the viewport amongst the tabs in this alignment frame and close that
* tab
- *
+ *
* @param av
*/
public boolean closeView(AlignViewport av)
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
col = col.brighter();
- for (SequenceI s:gps[g].getSequences())
- viewport.setSequenceColour(
- s, col)
- ;
+ for (SequenceI s : gps[g].getSequences())
+ viewport.setSequenceColour(s, col);
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
/**
* make the given alignmentPanel the currently selected tab
- *
+ *
* @param alignmentPanel
*/
public void setDisplayedView(AlignmentPanel alignmentPanel)
git://source.jalview.org / jalview.git / blobdiff