/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
private static String dasRegistry = null;
+ /**
+ * Blocking method that initialises and returns the shared instance of the
+ * SequenceFetcher client
+ *
+ * @param guiWindow -
+ * where the initialisation delay message should be shown
+ * @return the singleton instance of the sequence fetcher client
+ */
+ public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
+ final IProgressIndicator guiWindow)
+ {
+ if (sfetch == null
+ || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ {
+ /**
+ * give a visual indication that sequence fetcher construction is occuring
+ */
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ Thread.currentThread().hashCode());
+ }
+ dasRegistry = DasSourceBrowser.getDasRegistryURL();
+ jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ Thread.currentThread().hashCode());
+ }
+ sfetch = sf;
+
+ }
+ return sfetch;
+ }
+
public SequenceFetcher(IProgressIndicator guiIndic)
{
final IProgressIndicator guiWindow = guiIndic;
public void run()
{
- if (sfetch == null
- || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ if (getSequenceFetcherSingleton(guiWindow) != null)
{
- /**
- * give a visual indication that sequence fetcher construction is
- * occuring
- */
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(
- "Initialising Sequence Database Fetchers", this
- .hashCode());
- }
- dasRegistry = DasSourceBrowser.getDasRegistryURL();
- jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
- if (guiWindow != null)
+ us.initGui(guiWindow);
+ }
+ else
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- guiWindow.setProgressBar(
- "Initialising Sequence Database Fetchers", this
- .hashCode());
- }
- sfetch = sf;
-
+ public void run()
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Could not create the sequence fetcher client. Check error logs for details.",
+ "Couldn't create SequenceFetcher",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ });
+
+ // raise warning dialog
}
- us.initGui(guiWindow);
}
});
sf.start();
return;
}
AlignmentI aresult = null;
+ Object source = database.getSelectedItem();
+ Enumeration en = new StringTokenizer(textArea.getText(), ";");
try
{
guiWindow.setProgressBar("Fetching Sequences from "
+ database.getSelectedItem(), Thread.currentThread()
.hashCode());
- aresult = sfetch.getSourceProxy(
- (String) sources.get(database.getSelectedItem()))
- .getSequenceRecords(textArea.getText());
+ DbSourceProxy proxy = sfetch.getSourceProxy(
+ (String) sources.get(source));
+ if (proxy.getAccessionSeparator()==null)
+ {
+ while (en.hasMoreElements())
+ {
+ String item = (String) en.nextElement();
+ try {
+ if (aresult!=null)
+ {
+ try {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
+ }
+
+ }
+ AlignmentI indres = proxy.getSequenceRecords(item);
+ if (indres!=null)
+ {
+ if (aresult == null)
+ {
+ aresult = indres;
+ } else {
+ aresult.append(indres);
+ }
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.info("Error retrieving "+item+" from "+source,e);
+ }
+ }
+ } else {
+ StringBuffer multiacc = new StringBuffer();
+ while (en.hasMoreElements())
+ {
+ multiacc.append(en.nextElement());
+ if (en.hasMoreElements())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
+ aresult = proxy
+ .getSequenceRecords(multiacc.toString());
+ }
} catch (Exception e)
{
e.printStackTrace();
} catch (OutOfMemoryError e)
{
+ // resets dialog box - so we don't use OOMwarning here.
showErrorMessage("Out of Memory when retrieving "
+ textArea.getText()
+ " from "
+ " from " + database.getSelectedItem());
e.printStackTrace();
}
- guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
if (aresult != null)
{
parseResult(aresult, null, null);
}
+ // only remove visual delay after we finished parsing.
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
resetDialog();
}
* for (;si<seqs.length; si++) { newseqs[si] = seqs[si]; seqs[si] = null; } }
* for (int j=0;j<seqparts.length; si++, j++) { newseqs[si] =
* seqparts[j].deriveSequence(); // place DBReferences on dataset and refer }
- * seqs=newseqs;
- * } } } else { result.append("# no response for "+qry); } } if (seqs!=null &&
- * seqs.length>0) { if (parseResult(new Alignment(seqs), null, null)!=null) {
- * result.append("# Successfully parsed the "+database.getSelectedItem()+"
- * Queries into an Alignment"); } } } else if
+ * seqs=newseqs; } } } else { result.append("# no response for "+qry); } } if
+ * (seqs!=null && seqs.length>0) { if (parseResult(new Alignment(seqs), null,
+ * null)!=null) { result.append("# Successfully parsed the
+ * "+database.getSelectedItem()+" Queries into an Alignment"); } } } else if
* (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
* StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
* null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
* textArea.getText().toUpperCase(), "URL").print() );
*
* if(result.length()>0) { parseResult( result.toString(),
- * textArea.getText().toUpperCase() ); }
- * } catch (java.io.IOException ex) { result = null; } }
+ * textArea.getText().toUpperCase() ); } } catch (java.io.IOException ex) {
+ * result = null; } }
*
* if (result == null || result.length() == 0) { showErrorMessage("Error
* retrieving " + textArea.getText() + " from " + database.getSelectedItem()); }
* entry.getProtein().getName().elementAt(0)); }
*
* result.append(name + "\n" + entry.getUniprotSequence().getContent() +
- * "\n");
- * }
+ * "\n"); }
*
* //Then read in the features and apply them to the dataset Alignment al =
* parseResult(result.toString(), null); for (int i = 0; i < entries.size();
* Construct the PDBEntry entry.setId(id); if (entry.getProperty() == null)
* entry.setProperty(new Hashtable()); entry.getProperty().put("chains",
* pdbchain.id + "=" + sq.getStart() + "-" + sq.getEnd());
- * sq.getDatasetSequence().addPDBId(entry);
- * // Add PDB DB Refs // We make a DBRefEtntry because we have obtained the
- * PDB file from a verifiable source // JBPNote - PDB DBRefEntry should also
- * carry the chain and mapping information DBRefEntry dbentry = new
+ * sq.getDatasetSequence().addPDBId(entry); // Add PDB DB Refs // We make a
+ * DBRefEtntry because we have obtained the PDB file from a verifiable source //
+ * JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ * information DBRefEntry dbentry = new
* DBRefEntry(jalview.datamodel.DBRefSource.PDB, "0", id + pdbchain.id);
* sq.addDBRef(dbentry); // and add seuqence to the retrieved set
* result.addElement(sq.deriveSequence()); } }
if (currentFileFormat != null)
{
af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
- // FORMAT FOR
- // NON-FormatAdapter Sourced
- // Alignments?
+ // FORMAT FOR
+ // NON-FormatAdapter Sourced
+ // Alignments?
}
if (title == null)
{
title = "Retrieved from " + database.getSelectedItem();
}
-
+ SequenceFeature[] sfs=null;
+ for (Enumeration sq=al.getSequences().elements(); sq.hasMoreElements();)
+ {
+ if ((sfs=((SequenceI)sq.nextElement()).getDatasetSequence().getSequenceFeatures())!=null)
+ {
+ if (sfs.length>0)
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
+ }
+
+ }
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
for (int i = 0; i < al.getHeight(); i++)
{
alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this
- // also
- // creates
- // dataset
- // sequence
- // entries
+ // also
+ // creates
+ // dataset
+ // sequence
+ // entries
}
alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment
.getHeight());
git://source.jalview.org / jalview.git / blobdiff