X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=faebb1a76d2cd34b395337a7caec5ca52889c63c;hb=fc853e3c385e32591ceac07070d37932fcf87941;hp=49511ad41f0f7104ccd1063888cec9c27add88d0;hpb=e7a39cabfa0ee4eaf45fc999ceed3ed4674b8e46;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 49511ad..faebb1a 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,13 +1,13 @@ /* - * 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 * 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 @@ -18,20 +18,21 @@ package jalview.gui; import java.util.*; +import java.util.List; import java.awt.*; import java.awt.event.*; import javax.swing.*; import javax.swing.tree.DefaultMutableTreeNode; -import javax.swing.tree.MutableTreeNode; -import javax.swing.tree.TreeModel; + +import com.stevesoft.pat.Regex; import jalview.datamodel.*; import jalview.io.*; +import jalview.util.DBRefUtils; import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.seqfetcher.DbSourceProxy; - import java.awt.BorderLayout; public class SequenceFetcher extends JPanel implements Runnable @@ -139,6 +140,7 @@ public class SequenceFetcher extends JPanel implements Runnable Thread sf = new Thread(new Runnable() { + @Override public void run() { if (getSequenceFetcherSingleton(guiWindow) != null) @@ -149,6 +151,7 @@ public class SequenceFetcher extends JPanel implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { JOptionPane @@ -233,6 +236,7 @@ public class SequenceFetcher extends JPanel implements Runnable ok.setText("OK"); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(); @@ -241,6 +245,7 @@ public class SequenceFetcher extends JPanel implements Runnable clear.setText("Clear"); clear.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { clear_actionPerformed(); @@ -250,6 +255,7 @@ public class SequenceFetcher extends JPanel implements Runnable example.setText("Example"); example.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { example_actionPerformed(); @@ -258,6 +264,7 @@ public class SequenceFetcher extends JPanel implements Runnable close.setText("Close"); close.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { close_actionPerformed(e); @@ -267,6 +274,7 @@ public class SequenceFetcher extends JPanel implements Runnable textArea.setLineWrap(true); textArea.addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent e) { if (e.getKeyCode() == KeyEvent.VK_ENTER) @@ -286,9 +294,9 @@ public class SequenceFetcher extends JPanel implements Runnable database.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - DbSourceProxy db = null; try { databaseButt.setText(database.getSelectedItem() @@ -297,7 +305,17 @@ public class SequenceFetcher extends JPanel implements Runnable + " others)" : "")); String eq = database.getExampleQueries(); dbeg.setText("Example query: " + eq); - replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1)); + boolean enablePunct = !(eq != null && eq.indexOf(",") > -1); + for (DbSourceProxy dbs : database.getSelectedSources()) + { + if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource) + { + enablePunct = false; + break; + } + } + replacePunctuation.setEnabled(enablePunct); + } catch (Exception ex) { dbeg.setText(""); @@ -388,7 +406,8 @@ public class SequenceFetcher extends JPanel implements Runnable public void ok_actionPerformed() { - database.setEnabled(false); + databaseButt.setEnabled(false); + example.setEnabled(false); textArea.setEnabled(false); ok.setEnabled(false); close.setEnabled(false); @@ -399,12 +418,14 @@ public class SequenceFetcher extends JPanel implements Runnable private void resetDialog() { - database.setEnabled(true); + databaseButt.setEnabled(true); + example.setEnabled(true); textArea.setEnabled(true); ok.setEnabled(true); close.setEnabled(true); } + @Override public void run() { String error = ""; @@ -438,137 +459,265 @@ public class SequenceFetcher extends JPanel implements Runnable resetDialog(); return; } - ArrayList aresultq = new ArrayList(); - ArrayList aresult = new ArrayList(); - DbSourceProxy proxy = database.getSelectedSources().get(0); - Enumeration en = new StringTokenizer(textArea.getText(), ";"); - boolean isAliSource = false; - try - { - guiWindow.setProgressBar( - "Fetching Sequences from " + proxy.getDbName(), Thread - .currentThread().hashCode()); - isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB); - if (proxy.getAccessionSeparator() == null) + // indicate if successive sources should be merged into one alignment. + boolean addToLast = false; + ArrayList aresultq = new ArrayList(), presultTitle = new ArrayList(); + ArrayList presult = new ArrayList(), aresult = new ArrayList(); + Iterator proxies = database.getSelectedSources() + .iterator(); + String[] qries; + List nextfetch = Arrays.asList(qries = textArea.getText() + .split(";")); + Iterator en = Arrays.asList(new String[0]).iterator(); + int nqueries = qries.length; + while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0)) + { + if (!en.hasNext() && nextfetch.size() > 0) + { + en = nextfetch.iterator(); + nqueries = nextfetch.size(); + // save the remaining queries in the original array + qries = nextfetch.toArray(new String[nqueries]); + nextfetch = new ArrayList(); + } + + DbSourceProxy proxy = proxies.next(); + boolean isAliSource = false; + try { - while (en.hasMoreElements()) + // update status + guiWindow.setProgressBar("Fetching " + nqueries + + " sequence queries from " + proxy.getDbName(), Thread + .currentThread().hashCode()); + isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB); + if (proxy.getAccessionSeparator() == null) { - String item = (String) en.nextElement(); - try + while (en.hasNext()) { - if (aresult != null) + String item = en.next(); + try { + if (aresult != null) + { + try + { + // give the server a chance to breathe + Thread.sleep(5); + } catch (Exception e) + { + // + } + + } + + AlignmentI indres = null; try { - // give the server a chance to breathe - Thread.sleep(5); - } catch (Exception e) + indres = proxy.getSequenceRecords(item); + } catch (OutOfMemoryError oome) { - // + new OOMWarning("fetching " + item + " from " + + proxy.getDbName(), oome, this); } - + if (indres != null) + { + aresultq.add(item); + aresult.add(indres); + } + else + { + nextfetch.add(item); + } + } catch (Exception e) + { + jalview.bin.Cache.log.info("Error retrieving " + item + + " from " + proxy.getDbName(), e); + nextfetch.add(item); } - - AlignmentI indres = null; - try + } + } + else + { + StringBuffer multiacc = new StringBuffer(); + ArrayList tosend = new ArrayList(); + while (en.hasNext()) + { + String nel = en.next(); + tosend.add(nel); + multiacc.append(nel); + if (en.hasNext()) { - indres = proxy.getSequenceRecords(item); - } catch (OutOfMemoryError oome) + multiacc.append(proxy.getAccessionSeparator()); + } + } + try + { + AlignmentI rslt; + SequenceI[] rs; + List nores = new ArrayList(); + rslt = proxy.getSequenceRecords(multiacc.toString()); + if (rslt == null || rslt.getHeight() == 0) { - new OOMWarning("fetching " + item + " from " - + proxy.getDbName(), oome, this); + // no results - pass on all queries to next source + nextfetch.addAll(tosend); } - if (indres != null) + else { - aresultq.add(item); - aresult.add(indres); + aresultq.add(multiacc.toString()); + aresult.add(rslt); + + rs = rslt.getSequencesArray(); + // search for each query in the dbrefs associated with each + // sequence + // returned. + // ones we do not find will be used to query next source (if any) + for (String q : tosend) + { + DBRefEntry dbr = new DBRefEntry(), found[] = null; + dbr.setSource(proxy.getDbSource()); + dbr.setVersion(null); + if (proxy.getAccessionValidator() != null) + { + Regex vgr = proxy.getAccessionValidator(); + vgr.search(q); + if (vgr.numSubs() > 0) + { + dbr.setAccessionId(vgr.stringMatched(1)); + } + else + { + dbr.setAccessionId(vgr.stringMatched()); + } + } + else + { + dbr.setAccessionId(q); + } + boolean rfound = false; + for (int r = 0; r < rs.length; r++) + { + if (rs[r] != null + && (found = DBRefUtils.searchRefs( + rs[r].getDBRef(), dbr)) != null + && found.length > 0) + { + rfound = true; + rs[r] = null; + continue; + } + } + if (!rfound) + { + nextfetch.add(q); + } + } } - } catch (Exception e) + } catch (OutOfMemoryError oome) { - jalview.bin.Cache.log.info("Error retrieving " + item - + " from " + proxy.getDbName(), e); + new OOMWarning("fetching " + multiacc + " from " + + database.getSelectedItem(), oome, this); } } + + } catch (Exception e) + { + showErrorMessage("Error retrieving " + textArea.getText() + + " from " + database.getSelectedItem()); + // error + // +="Couldn't retrieve sequences from "+database.getSelectedItem(); + System.err.println("Retrieval failed for source ='" + + database.getSelectedItem() + "' and query\n'" + + textArea.getText() + "'\n"); + e.printStackTrace(); + } catch (OutOfMemoryError e) + { + // resets dialog box - so we don't use OOMwarning here. + showErrorMessage("Out of Memory when retrieving " + + textArea.getText() + + " from " + + database.getSelectedItem() + + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n"); + e.printStackTrace(); + } catch (Error e) + { + showErrorMessage("Serious Error retrieving " + textArea.getText() + + " from " + database.getSelectedItem()); + e.printStackTrace(); } - else + // Stack results ready for opening in alignment windows + if (aresult != null && aresult.size() > 0) { - StringBuffer multiacc = new StringBuffer(); - while (en.hasMoreElements()) + AlignmentI ar = null; + if (isAliSource) { - multiacc.append(en.nextElement()); - if (en.hasMoreElements()) + addToLast = false; + // new window for each result + while (aresult.size() > 0) { - multiacc.append(proxy.getAccessionSeparator()); + presult.add(aresult.remove(0)); + presultTitle.add(aresultq.remove(0) + " " + + getDefaultRetrievalTitle()); } } - try - { - aresultq.add(multiacc.toString()); - aresult.add(proxy.getSequenceRecords(multiacc.toString())); - } catch (OutOfMemoryError oome) + else { - new OOMWarning("fetching " + multiacc + " from " - + database.getSelectedItem(), oome, this); + String titl = null; + if (addToLast && presult.size() > 0) + { + ar = presult.remove(presult.size() - 1); + titl = presultTitle.remove(presultTitle.size() - 1); + } + // concatenate all results in one window + while (aresult.size() > 0) + { + if (ar == null) + { + ar = aresult.remove(0); + } + else + { + ar.append(aresult.remove(0)); + } + ; + } + addToLast = true; + presult.add(ar); + presultTitle.add(titl); } - } - - } catch (Exception e) - { - showErrorMessage("Error retrieving " + textArea.getText() + " from " - + database.getSelectedItem()); - // error +="Couldn't retrieve sequences from "+database.getSelectedItem(); - System.err.println("Retrieval failed for source ='" - + database.getSelectedItem() + "' and query\n'" - + textArea.getText() + "'\n"); - e.printStackTrace(); - } catch (OutOfMemoryError e) - { - // resets dialog box - so we don't use OOMwarning here. - showErrorMessage("Out of Memory when retrieving " - + textArea.getText() - + " from " - + database.getSelectedItem() - + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n"); - e.printStackTrace(); - } catch (Error e) - { - showErrorMessage("Serious Error retrieving " + textArea.getText() - + " from " + database.getSelectedItem()); - e.printStackTrace(); + guiWindow.setProgressBar("Finished querying", Thread.currentThread() + .hashCode()); } - if (aresult != null && aresult.size() > 0) + guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results." + : "Processing ..", Thread.currentThread().hashCode()); + // process results + while (presult.size() > 0) { - AlignmentI ar = null; - if (isAliSource) + parseResult(presult.remove(0), presultTitle.remove(0), null); + } + // only remove visual delay after we finished parsing. + guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); + if (nextfetch.size() > 0) + { + StringBuffer sb = new StringBuffer(); + sb.append("Didn't retrieve the following " + + (nextfetch.size() == 1 ? "query" : nextfetch.size() + + " queries") + ": \n"); + int l = sb.length(), lr = 0; + for (String s : nextfetch) { - // new window for each result - while (aresult.size() > 0) + if (l != sb.length()) { - parseResult(aresult.remove(0), aresultq.remove(0) + " " - + getDefaultRetrievalTitle(), null); + sb.append("; "); } - } - else - { - // concatenate all results in one window - while (aresult.size() > 0) + if (lr - sb.length() > 40) { - if (ar == null) - { - ar = aresult.remove(0); - } - else - { - ar.append(aresult.remove(0)); - } - ; + sb.append("\n"); } - parseResult(ar, null, null); + sb.append(s); } + showErrorMessage(sb.toString()); } - // only remove visual delay after we finished parsing. - guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); resetDialog(); } @@ -634,19 +783,21 @@ public class SequenceFetcher extends JPanel implements Runnable title = getDefaultRetrievalTitle(); } SequenceFeature[] sfs = null; - for (Enumeration sq = al.getSequences().elements(); sq - .hasMoreElements();) + List alsqs; + synchronized (alsqs = al.getSequences()) { - if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence() - .getSequenceFeatures()) != null) + for (SequenceI sq : alsqs) { - if (sfs.length > 0) + if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null) { - af.setShowSeqFeatures(true); - break; + if (sfs.length > 0) + { + af.setShowSeqFeatures(true); + break; + } } - } + } } Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -688,6 +839,7 @@ public class SequenceFetcher extends JPanel implements Runnable resetDialog(); javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, error,