X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=f8d3734dcee1eccc9ecbf8824ff3736ea56dc9da;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=af8c1083c2b41891208cce0b027f95eb29816b72;hpb=152aa52bc19a393141cfc19f5852d1fbcd239f16;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index af8c108..f8d3734 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,47 +1,99 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import MCview.*; -import jalview.datamodel.*; -import jalview.datamodel.xdb.embl.*; -import java.io.File; -import jalview.io.*; -import jalview.ws.DBRefFetcher; -import jalview.ws.ebi.EBIFetchClient; -import jalview.ws.seqfetcher.ASequenceFetcher; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.FormatAdapter; +import jalview.io.IdentifyFile; +import jalview.util.DBRefUtils; +import jalview.util.MessageManager; +import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.seqfetcher.DbSourceProxy; -import java.awt.Rectangle; import java.awt.BorderLayout; -import java.awt.Dimension; +import java.awt.Font; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Iterator; +import java.util.List; + +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JTextArea; +import javax.swing.SwingConstants; +import javax.swing.tree.DefaultMutableTreeNode; + +import com.stevesoft.pat.Regex; public class SequenceFetcher extends JPanel implements Runnable { - // ASequenceFetcher sfetch; + JLabel dbeg = new JLabel(); + + JDatabaseTree database; + + JButton databaseButt; + + JLabel jLabel1 = new JLabel(); + + JCheckBox replacePunctuation = new JCheckBox(); + + JButton ok = new JButton(); + + JButton clear = new JButton(); + + JButton example = new JButton(); + + JButton close = new JButton(); + + JPanel jPanel1 = new JPanel(); + + JTextArea textArea = new JTextArea(); + + JScrollPane jScrollPane1 = new JScrollPane(); + + JPanel jPanel2 = new JPanel(); + + JPanel jPanel3 = new JPanel(); + + JPanel jPanel4 = new JPanel(); + + BorderLayout borderLayout1 = new BorderLayout(); + + BorderLayout borderLayout2 = new BorderLayout(); + + BorderLayout borderLayout3 = new BorderLayout(); + JInternalFrame frame; IProgressIndicator guiWindow; @@ -52,16 +104,18 @@ public class SequenceFetcher extends JPanel implements Runnable final String noDbSelected = "-- Select Database --"; - Hashtable sources = new Hashtable(); - private static jalview.ws.SequenceFetcher sfetch = null; - private static String dasRegistry = null; + private static long lastDasSourceRegistry = -3; + + private static DasSourceRegistryI dasRegistry = null; private static boolean _initingFetcher = false; private static Thread initingThread = null; + int debounceTrap = 0; + /** * Blocking method that initialises and returns the shared instance of the * SequenceFetcher client @@ -77,9 +131,11 @@ public class SequenceFetcher extends JPanel implements Runnable { if (guiWindow != null) { - guiWindow.setProgressBar( - "Waiting for Sequence Database Fetchers to initialise", - Thread.currentThread().hashCode()); + guiWindow + .setProgressBar( + MessageManager + .getString("status.waiting_sequence_database_fetchers_init"), + Thread.currentThread().hashCode()); } // initting happening on another thread - so wait around to see if it // finishes. @@ -96,13 +152,19 @@ public class SequenceFetcher extends JPanel implements Runnable } if (guiWindow != null) { - guiWindow.setProgressBar( - "Waiting for Sequence Database Fetchers to initialise", - Thread.currentThread().hashCode()); + guiWindow + .setProgressBar( + MessageManager + .getString("status.waiting_sequence_database_fetchers_init"), + Thread.currentThread().hashCode()); } } if (sfetch == null - || dasRegistry != DasSourceBrowser.getDasRegistryURL()) + || dasRegistry != jalview.bin.Cache.getDasSourceRegistry() + || lastDasSourceRegistry != (jalview.bin.Cache + .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache + .getDasSourceRegistry().getLocalSourceString()) + .hashCode()) { _initingFetcher = true; initingThread = Thread.currentThread(); @@ -111,16 +173,20 @@ public class SequenceFetcher extends JPanel implements Runnable */ if (guiWindow != null) { - guiWindow.setProgressBar("Initialising Sequence Database Fetchers", + guiWindow.setProgressBar(MessageManager + .getString("status.init_sequence_database_fetchers"), Thread.currentThread().hashCode()); } - dasRegistry = DasSourceBrowser.getDasRegistryURL(); + dasRegistry = jalview.bin.Cache.getDasSourceRegistry(); + dasRegistry.refreshSources(); + jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher(); if (guiWindow != null) { - guiWindow.setProgressBar("Initialising Sequence Database Fetchers", - initingThread.hashCode()); + guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); } + lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry + .getLocalSourceString()).hashCode(); sfetch = sf; _initingFetcher = false; initingThread = null; @@ -128,31 +194,37 @@ public class SequenceFetcher extends JPanel implements Runnable return sfetch; } + private IProgressIndicator progressIndicator; + public SequenceFetcher(IProgressIndicator guiIndic) { - final IProgressIndicator guiWindow = guiIndic; + this.progressIndicator = guiIndic; final SequenceFetcher us = this; // launch initialiser thread Thread sf = new Thread(new Runnable() { + @Override public void run() { - if (getSequenceFetcherSingleton(guiWindow) != null) + if (getSequenceFetcherSingleton(progressIndicator) != null) { - us.initGui(guiWindow); + us.initGui(progressIndicator); } else { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { JOptionPane .showInternalMessageDialog( Desktop.desktop, - "Could not create the sequence fetcher client. Check error logs for details.", - "Couldn't create SequenceFetcher", + MessageManager + .getString("warn.couldnt_create_sequence_fetcher_client"), + MessageManager + .getString("label.couldnt_create_sequence_fetcher"), JOptionPane.ERROR_MESSAGE); } }); @@ -164,6 +236,16 @@ public class SequenceFetcher extends JPanel implements Runnable sf.start(); } + private class DatabaseAuthority extends DefaultMutableTreeNode + { + + }; + + private class DatabaseSource extends DefaultMutableTreeNode + { + + }; + /** * called by thread spawned by constructor * @@ -176,29 +258,7 @@ public class SequenceFetcher extends JPanel implements Runnable { alignFrame = (AlignFrame) guiWindow; } - - database.addItem(noDbSelected); - /* - * Dynamically generated database list will need a translation function from - * internal source to externally distinct names. UNIPROT and UP_NAME are - * identical DB sources, and should be collapsed. - */ - - String dbs[] = sfetch.getOrderedSupportedSources(); - for (int i = 0; i < dbs.length; i++) - { - if (!sources.containsValue(dbs[i])) - { - String name = sfetch.getSourceProxy(dbs[i]).getDbName(); - // duplicate source names are thrown away, here. - if (!sources.containsKey(name)) - { - database.addItem(name); - } - // overwrite with latest version of the retriever for this source - sources.put(name, dbs[i]); - } - } + database = new JDatabaseTree(sfetch); try { jbInit(); @@ -221,65 +281,75 @@ public class SequenceFetcher extends JPanel implements Runnable private String getFrameTitle() { - return ((alignFrame == null) ? "New " : "Additional ") - + "Sequence Fetcher"; + return ((alignFrame == null) ? MessageManager + .getString("label.new_sequence_fetcher") : MessageManager + .getString("label.additional_sequence_fetcher")); } private void jbInit() throws Exception { this.setLayout(borderLayout2); - database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + database.setFont(JvSwingUtils.getLabelFont()); 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(MessageManager + .getString("label.separate_multiple_accession_ids")); replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER); replacePunctuation .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); - replacePunctuation.setText("Replace commas with semi-colons"); - ok.setText("OK"); + replacePunctuation.setText(MessageManager + .getString("label.replace_commas_semicolons")); + ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(); } }); - clear.setText("Clear"); + clear.setText(MessageManager.getString("action.clear")); clear.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { clear_actionPerformed(); } }); - example.setText("Example"); + example.setText(MessageManager.getString("label.example")); example.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { example_actionPerformed(); } }); - close.setText("Close"); + close.setText(MessageManager.getString("action.close")); close.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { close_actionPerformed(e); } }); - textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + textArea.setFont(JvSwingUtils.getLabelFont()); textArea.setLineWrap(true); textArea.addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent e) { if (e.getKeyCode() == KeyEvent.VK_ENTER) + { ok_actionPerformed(); + } } }); jPanel3.setLayout(borderLayout1); @@ -290,30 +360,30 @@ public class SequenceFetcher extends JPanel implements Runnable jPanel1.add(close); jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER); jPanel2.setLayout(borderLayout3); - + databaseButt = database.getDatabaseSelectorButton(); + databaseButt.setFont(JvSwingUtils.getLabelFont()); database.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { - DbSourceProxy db = null; - try + debounceTrap++; + String currentSelection = database.getSelectedItem(); + if (!currentSelection.equalsIgnoreCase("pdb")) { - db = sfetch.getSourceProxy((String) sources.get(database - .getSelectedItem())); - String eq = db.getTestQuery(); - dbeg.setText("Example query: " + eq); - replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1)); - } catch (Exception ex) + otherSourceAction(); + } + if (currentSelection.equalsIgnoreCase("pdb") + && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0))) { - dbeg.setText(""); - replacePunctuation.setEnabled(true); + pdbSourceAction(); } - jPanel2.repaint(); + database.action = -1; } }); + dbeg.setText(""); - jPanel2.add(database, java.awt.BorderLayout.NORTH); + jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH); jPanel2.add(dbeg, java.awt.BorderLayout.CENTER); JPanel jPanel2a = new JPanel(new BorderLayout()); jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH); @@ -328,14 +398,49 @@ public class SequenceFetcher extends JPanel implements Runnable } + private void pdbSourceAction() + { + databaseButt.setText(database.getSelectedItem()); + new PDBSearchPanel(this); + frame.dispose(); + } + + private void otherSourceAction() + { + try + { + databaseButt.setText(database.getSelectedItem() + + (database.getSelectedSources().size() > 1 ? " (and " + + database.getSelectedSources().size() + " others)" + : "")); + String eq = database.getExampleQueries(); + dbeg.setText(MessageManager.formatMessage( + "label.example_query_param", new String[] { eq })); + 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(""); + replacePunctuation.setEnabled(true); + } + jPanel2.repaint(); + } + protected void example_actionPerformed() { DbSourceProxy db = null; try { - db = sfetch.getSourceProxy((String) sources.get(database - .getSelectedItem())); - textArea.setText(db.getTestQuery()); + textArea.setText(database.getExampleQueries()); } catch (Exception ex) { } @@ -348,40 +453,6 @@ public class SequenceFetcher extends JPanel implements Runnable jPanel3.repaint(); } - JLabel dbeg = new JLabel(); - - JComboBox database = new JComboBox(); - - JLabel jLabel1 = new JLabel(); - - JCheckBox replacePunctuation = new JCheckBox(); - - JButton ok = new JButton(); - - JButton clear = new JButton(); - - JButton example = new JButton(); - - JButton close = new JButton(); - - JPanel jPanel1 = new JPanel(); - - JTextArea textArea = new JTextArea(); - - JScrollPane jScrollPane1 = new JScrollPane(); - - JPanel jPanel2 = new JPanel(); - - JPanel jPanel3 = new JPanel(); - - JPanel jPanel4 = new JPanel(); - - BorderLayout borderLayout1 = new BorderLayout(); - - BorderLayout borderLayout2 = new BorderLayout(); - - BorderLayout borderLayout3 = new BorderLayout(); - public void close_actionPerformed(ActionEvent e) { try @@ -394,7 +465,8 @@ 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); @@ -405,16 +477,18 @@ 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 = ""; - if (database.getSelectedItem().equals(noDbSelected)) + if (!database.hasSelection()) { error += "Please select the source database\n"; } @@ -444,265 +518,280 @@ public class SequenceFetcher extends JPanel implements Runnable resetDialog(); 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()); - DbSourceProxy proxy = sfetch.getSourceProxy((String) sources - .get(source)); - 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(MessageManager.formatMessage( + "status.fetching_sequence_queries_from", + new String[] { + Integer.valueOf(nqueries).toString(), + 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 " - + database.getSelectedItem(), oome, this); + // no results - pass on all queries to next source + nextfetch.addAll(tosend); } - if (indres != null) + else { - if (aresult == null) - { - aresult = indres; - } - else + 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) { - aresult.append(indres); + 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 " + source, 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 - { - aresult = 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(MessageManager + .getString("status.finshed_querying"), Thread.currentThread() + .hashCode()); } - if (aresult != null) - { - parseResult(aresult, null, null); + guiWindow.setProgressBar( + (presult.size() > 0) ? MessageManager + .getString("status.parsing_results") : MessageManager + .getString("status.processing"), Thread.currentThread() + .hashCode()); + // process results + while (presult.size() > 0) + { + 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) + { + if (l != sb.length()) + { + sb.append("; "); + } + if (lr - sb.length() > 40) + { + sb.append("\n"); + } + sb.append(s); + } + showErrorMessage(sb.toString()); + } resetDialog(); } - /* - * result = new StringBuffer(); if - * (database.getSelectedItem().equals("Uniprot")) { - * getUniprotFile(textArea.getText()); } else if - * (database.getSelectedItem().equals("EMBL") || - * database.getSelectedItem().equals("EMBLCDS")) { String DBRefSource = - * database.getSelectedItem().equals("EMBLCDS") ? - * 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 = - * 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 - * 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 - * SequenceI[seqparts.length]; } else { newseqs = new - * SequenceI[seqs.length+seqparts.length]; - * - * for (;si0) { 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 - * 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; } } - * - * if (result == null || result.length() == 0) { showErrorMessage("Error - * retrieving " + textArea.getText() + " from " + database.getSelectedItem()); - * } - * - * resetDialog(); return; } - * - * void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient(); - * File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null); - * - * DBRefFetcher dbref = new DBRefFetcher(); Vector entries = - * dbref.getUniprotEntries(file); - * - * if (entries != null) { //First, make the new sequences Enumeration en = - * entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry = - * (UniprotEntry) en.nextElement(); - * - * StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot"); Enumeration - * en2 = entry.getAccession().elements(); while (en2.hasMoreElements()) { - * name.append("|"); name.append(en2.nextElement()); } en2 = - * entry.getName().elements(); while (en2.hasMoreElements()) { - * name.append("|"); name.append(en2.nextElement()); } - * - * if (entry.getProtein() != null) { name.append(" " + - * entry.getProtein().getName().elementAt(0)); } - * - * result.append(name + "\n" + entry.getUniprotSequence().getContent() + - * "\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(); - * i++) { UniprotEntry entry = (UniprotEntry) entries.elementAt(i); - * Enumeration e = entry.getDbReference().elements(); Vector onlyPdbEntries = - * new Vector(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry) - * e.nextElement(); if (!pdb.getType().equals("PDB")) { continue; } - * - * onlyPdbEntries.addElement(pdb); } - * - * Enumeration en2 = entry.getAccession().elements(); while - * (en2.hasMoreElements()) { - * al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry( - * DBRefSource.UNIPROT, "0", en2.nextElement().toString())); } - * - * - * - * - * al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries); if - * (entry.getFeature() != null) { e = entry.getFeature().elements(); while - * (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature) - * e.nextElement(); sf.setFeatureGroup("Uniprot"); - * 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, - * 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 - * pdbchain = (PDBChain) pdbfile.chains.elementAt(i); // Get the Chain's - * Sequence - who's dataset includes any special features added from the PDB - * file SequenceI sq = pdbchain.sequence; // Specially formatted name for the - * PDB chain sequences retrieved from the PDB - * sq.setName("PDB|"+id+"|"+sq.getName()); // Might need to add more metadata - * to the PDBEntry object // like below /* PDBEntry entry = new PDBEntry(); // - * 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 - * 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 " + - * textArea.getText() + " from " + database.getSelectedItem(), ex); return - * null; } - * - * - * SequenceI[] results = new SequenceI[result.size()]; for (int i = 0, j = - * result.size(); i < j; i++) { results[i] = (SequenceI) result.elementAt(i); - * result.setElementAt(null,i); } return results; } - */ AlignmentI parseResult(String result, String title) { String format = new IdentifyFile().Identify(result, "Paste"); - Alignment sequences = null; + AlignmentI sequences = null; if (FormatAdapter.isValidFormat(format)) { sequences = null; @@ -728,12 +817,26 @@ public class SequenceFetcher extends JPanel implements Runnable 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 (al != null && al.getHeight() > 0) { + if (title == null) + { + title = getDefaultRetrievalTitle(); + } if (alignFrame == null) { AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, @@ -746,29 +849,28 @@ public class SequenceFetcher extends JPanel implements Runnable // Alignments? } - if (title == null) - { - title = "Retrieved from " + database.getSelectedItem(); - } 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.getSequenceFeatures()) != null) { - af.setShowSeqFeatures(true); - break; + if (sfs.length > 0) + { + af.setShowSeqFeatures(true); + break; + } } - } + } } Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - af.statusBar.setText("Successfully pasted alignment file"); + af.statusBar.setText(MessageManager + .getString("label.successfully_pasted_alignment_file")); try { @@ -780,20 +882,7 @@ public class SequenceFetcher extends JPanel implements Runnable } else { - for (int i = 0; i < al.getHeight(); i++) - { - alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this - // also - // creates - // dataset - // sequence - // entries - } - alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment - .getHeight()); - alignFrame.viewport.alignment.getWidth(); - alignFrame.viewport.firePropertyChange("alignment", null, - alignFrame.viewport.getAlignment().getSequences()); + alignFrame.viewport.addAlignment(al, title); } } return al; @@ -804,11 +893,23 @@ public class SequenceFetcher extends JPanel implements Runnable resetDialog(); javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, error, - "Error Retrieving Data", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.error_retrieving_data"), + JOptionPane.WARNING_MESSAGE); } }); } + + public IProgressIndicator getProgressIndicator() + { + return progressIndicator; + } + + public void setProgressIndicator(IProgressIndicator progressIndicator) + { + this.progressIndicator = progressIndicator; + } }