X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=36a7679262259a2c8f5ef0dacb845a5a58d649ce;hb=a10a465359de7b8c0baff4925d4b267a28eb0071;hp=3a07bd1b6aa2b3b3b286d917df65991aa4c5b5e9;hpb=c9a404d43d8ab221b0ac1f0b3a7d05c7c769c71c;p=jalview.git
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 3a07bd1..36a7679 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
+ * 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
+ * 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 .
*/
package jalview.gui;
@@ -59,6 +58,41 @@ public class SequenceFetcher extends JPanel implements Runnable
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;
@@ -69,31 +103,27 @@ public class SequenceFetcher extends JPanel implements Runnable
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();
@@ -146,11 +176,11 @@ public class SequenceFetcher extends JPanel implements Runnable
frame.setContentPane(this);
if (new jalview.util.Platform().isAMac())
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 200);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
}
else
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
}
}
@@ -341,9 +371,13 @@ public class SequenceFetcher extends JPanel implements Runnable
{
error += "Please select the source database\n";
}
- com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
+ // TODO: make this transformation optional and configurable
+ com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex(
+ "(\\s|[,; ])+", ";"); // \\s+", "");
textArea.setText(empty.replaceAll(textArea.getText()));
- if (textArea.getText().length() == 0)
+ // see if there's anthing to search with
+ if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
+ .getText()))
{
error += "Please enter a (semi-colon separated list of) database id(s)";
}
@@ -354,14 +388,66 @@ public class SequenceFetcher extends JPanel implements Runnable
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)
{
@@ -374,6 +460,7 @@ public class SequenceFetcher extends JPanel implements Runnable
e.printStackTrace();
} catch (OutOfMemoryError e)
{
+ // resets dialog box - so we don't use OOMwarning here.
showErrorMessage("Out of Memory when retrieving "
+ textArea.getText()
+ " from "
@@ -386,11 +473,12 @@ public class SequenceFetcher extends JPanel implements Runnable
+ " 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();
}
@@ -404,15 +492,15 @@ public class SequenceFetcher extends JPanel implements Runnable
* jalview.datamodel.DBRefSource.EMBLCDS : jalview.datamodel.DBRefSource.EMBL;
*
* StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
- * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch =
- * new EBIFetchClient(); String qry =
+ * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch
+ * = new EBIFetchClient(); String qry =
* database.getSelectedItem().toString().toLowerCase( ) + ":" +
* st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "emblxml",null);
*
* jalview.datamodel.xdb.embl.EmblFile efile=null; if (reply != null &&
* reply.exists()) { efile =
- * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null) {
- * for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
+ * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null)
+ * { for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
* entry = (EmblEntry) i.next(); SequenceI[] seqparts =
* entry.getSequences(false,true, DBRefSource); if (seqparts!=null) {
* SequenceI[] newseqs = null; int si=0; if (seqs==null) { newseqs = new
@@ -422,33 +510,34 @@ public class SequenceFetcher extends JPanel implements Runnable
* for (;si0) { 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)) {
* SequenceI[] seqparts = getPDBFile(query.toUpperCase()); if (seqparts !=
* null) { if (seqs == null) { seqs = seqparts; } else { SequenceI[] newseqs =
* new SequenceI[seqs.length+seqparts.length]; int i=0; for (; i <
- * seqs.length; i++) { newseqs[i] = seqs[i]; seqs[i] = null; } for (int j=0;j 0) { if (parseResult(new Alignment(seqs), null, null)!=null) {
- * result.append( "# Successfully parsed the PDB File Queries into an
+ * seqs.length; i++) { newseqs[i] = seqs[i]; seqs[i] = null; } for (int
+ * j=0;j 0) { if (parseResult(new
+ * Alignment(seqs), null, null)!=null) { result.append( "# Successfully parsed
+ * the PDB File Queries into an
* Alignment"); } } } else if( database.getSelectedItem().equals("PFAM")) {
* try { result.append(new FastaFile(
* "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=" +
* 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()); }
+ * retrieving " + textArea.getText() + " from " + database.getSelectedItem());
+ * }
*
* resetDialog(); return; }
*
@@ -472,8 +561,7 @@ public class SequenceFetcher extends JPanel implements Runnable
* 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();
@@ -496,15 +584,16 @@ public class SequenceFetcher extends JPanel implements Runnable
* (entry.getFeature() != null) { e = entry.getFeature().elements(); while
* (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature)
* e.nextElement(); sf.setFeatureGroup("Uniprot");
- * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } } }
+ * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } }
+ * }
*
* SequenceI[] getPDBFile(String id) { Vector result = new Vector(); String
* chain = null; if (id.indexOf(":") > -1) { chain =
* id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); }
*
* EBIFetchClient ebi = new EBIFetchClient(); String file =
- * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file ==
- * null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
+ * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file
+ * == null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
* jalview.io.AppletFormatAdapter.FILE); for (int i = 0; i <
* pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain)
* pdbfile.chains.elementAt(i)).id. toUpperCase().equals(chain)) { PDBChain
@@ -517,17 +606,17 @@ public class SequenceFetcher extends JPanel implements Runnable
* 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 (result.size() < 1) { throw new Exception("WsDBFetch for PDB id resulted
- * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file {
- * jalview.bin.Cache.log.warn("Exception when retrieving " +
+ * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file
+ * { jalview.bin.Cache.log.warn("Exception when retrieving " +
* textArea.getText() + " from " + database.getSelectedItem(), ex); return
* null; }
*
@@ -578,16 +667,30 @@ public class SequenceFetcher extends JPanel implements Runnable
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);
@@ -606,11 +709,11 @@ public class SequenceFetcher extends JPanel implements Runnable
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());