/*
- * 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 2.6)
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
private static String dasRegistry = null;
+ private static boolean _initingFetcher = false;
+
+ private static Thread initingThread = 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 (_initingFetcher && initingThread != null && initingThread.isAlive())
+ {
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ "Waiting for Sequence Database Fetchers to initialise",
+ Thread.currentThread().hashCode());
+ }
+ // initting happening on another thread - so wait around to see if it
+ // finishes.
+ while (_initingFetcher && initingThread != null
+ && initingThread.isAlive())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ "Waiting for Sequence Database Fetchers to initialise",
+ Thread.currentThread().hashCode());
+ }
+ }
+ if (sfetch == null
+ || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ {
+ _initingFetcher = true;
+ initingThread = Thread.currentThread();
+ /**
+ * 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",
+ initingThread.hashCode());
+ }
+ sfetch = sf;
+ _initingFetcher = false;
+ initingThread = null;
+ }
+ 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();
frame.setContentPane(this);
if (new jalview.util.Platform().isAMac())
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
}
else
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
}
}
dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1
- .setText("Separate multiple accession ids with semi colon \";\"");
+ jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+
+ replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
+ replacePunctuation
+ .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ replacePunctuation.setText("Replace commas with semi-colons");
ok.setText("OK");
ok.addActionListener(new ActionListener()
{
{
db = sfetch.getSourceProxy((String) sources.get(database
.getSelectedItem()));
- dbeg.setText("Example query: " + db.getTestQuery());
+ String eq = db.getTestQuery();
+ dbeg.setText("Example query: " + eq);
+ replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
} catch (Exception ex)
{
dbeg.setText("");
+ replacePunctuation.setEnabled(true);
}
jPanel2.repaint();
}
dbeg.setText("");
jPanel2.add(database, java.awt.BorderLayout.NORTH);
jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
- jPanel2.add(jLabel1, java.awt.BorderLayout.SOUTH);
+ JPanel jPanel2a = new JPanel(new BorderLayout());
+ jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
+ jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
// jPanel2.setPreferredSize(new Dimension())
jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
this.add(jPanel1, java.awt.BorderLayout.SOUTH);
JLabel jLabel1 = new JLabel();
+ JCheckBox replacePunctuation = new JCheckBox();
+
JButton ok = new JButton();
JButton clear = new JButton();
{
error += "Please select the source database\n";
}
- com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
+ // TODO: make this transformation more configurable
+ com.stevesoft.pat.Regex empty;
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ empty = new com.stevesoft.pat.Regex(
+ // replace commas and spaces with a semicolon
+ "(\\s|[,; ])+", ";");
+ }
+ else
+ {
+ // just turn spaces and semicolons into single semicolons
+ empty = new com.stevesoft.pat.Regex("(\\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)";
}
resetDialog();
return;
}
- AlignmentI aresult = null;
+ ArrayList<String> aresultq=new ArrayList<String>();
+ ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
+ Object source = database.getSelectedItem();
+ Enumeration en = new StringTokenizer(textArea.getText(), ";");
+ boolean isAliSource=false;
try
{
- guiWindow.setProgressBar("Fetching Sequences from "
- + database.getSelectedItem(), Thread.currentThread()
- .hashCode());
- aresult = sfetch.getSourceProxy(
- (String) sources.get(database.getSelectedItem()))
- .getSequenceRecords(textArea.getText());
+ guiWindow.setProgressBar(
+ "Fetching Sequences from " + database.getSelectedItem(),
+ Thread.currentThread().hashCode());
+ DbSourceProxy proxy = sfetch.getSourceProxy((String) sources
+ .get(source));
+ isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+ 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 = null;
+ try
+ {
+ indres = proxy.getSequenceRecords(item);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + item + " from "
+ + database.getSelectedItem(), oome, this);
+ }
+ if (indres != null)
+ {
+ aresultq.add(item);
+ aresult.add(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());
+ }
+ }
+ try
+ {
+ aresultq.add(multiacc.toString());
+ aresult.add(proxy.getSequenceRecords(multiacc.toString()));
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
+ }
+
+ }
} 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)
+ if (aresult != null && aresult.size()>0)
{
- parseResult(aresult, null, null);
+ AlignmentI ar=null;
+ if (isAliSource) {
+ // new window for each result
+ while (aresult.size()>0)
+ {
+ parseResult(aresult.remove(0), aresultq.remove(0)+" "+getDefaultRetrievalTitle(), null);
+ }
+ } else {
+ // concatenate all results in one window
+ while (aresult.size()>0)
+ {
+ if (ar==null) { ar = aresult.remove(0);}
+ else { ar.append(aresult.remove(0)); };
+ }
+ parseResult(ar, null, null);
+ }
}
+ // only remove visual delay after we finished parsing.
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
resetDialog();
}
* 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
* 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)) {
* 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<seqparts.length;
- * i++, j++) { newseqs[i] = seqparts[j]; } seqs=newseqs; } result.append("#
- * Success for "+query.toUpperCase()+"\n"); } } if (seqs != null &&
- * seqs.length > 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<seqparts.length; i++, j++) { newseqs[i] = seqparts[j]; }
+ * seqs=newseqs; } result.append("# Success for "+query.toUpperCase()+"\n"); }
+ * } if (seqs != null && seqs.length > 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; }
*
* 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();
* (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
* 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; }
*
return null;
}
+ /**
+ *
+ * @return a standard title for any results retrieved using the currently selected source and settings
+ */
+ public String getDefaultRetrievalTitle() {
+ return "Retrieved from " + database.getSelectedItem();
+ }
AlignmentI parseResult(AlignmentI al, String title,
String currentFileFormat)
{
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();
+ title = getDefaultRetrievalTitle();
}
+ 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