X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=5d4ea68a863e834bc0555547eb94f40354330b6d;hb=d2164f857e0729b86b1e0ffa4c858487f0a3298f;hp=2f92333a679a3e4a76ecd58f1d510b5fa153e303;hpb=20468f2b9a2938c35692d979f764b15bf878b882;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 2f92333..5d4ea68 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,180 +1,590 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 jalview.api.FeatureSettingsModelI; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.fts.service.pdb.PDBFTSPanel; +import jalview.fts.service.uniprot.UniprotFTSPanel; +import jalview.io.gff.SequenceOntologyI; +import jalview.util.DBRefUtils; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.dbsources.das.api.DasSourceRegistryI; +import jalview.ws.seqfetcher.DbSourceProxy; -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.EBIFetchClient; - -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.Collections; +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; -public class SequenceFetcher -extends JPanel implements Runnable +public class SequenceFetcher extends JPanel implements Runnable { - jalview.ws.SequenceFetcher 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; + AlignFrame alignFrame; + StringBuffer result; + final String noDbSelected = "-- Select Database --"; - public SequenceFetcher(AlignFrame af) + + private static jalview.ws.SequenceFetcher sfetch = null; + + private static long lastDasSourceRegistry = -3; + + private static DasSourceRegistryI dasRegistry = null; + + private static boolean _initingFetcher = false; + + private static Thread initingThread = null; + + public JTextArea getTextArea() { - alignFrame = af; - sfetch = new jalview.ws.SequenceFetcher(); - 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.getSupportedDb(); - for (int i=0; i newAlframes = null; + + public SequenceFetcher(IProgressIndicator guiIndic) + { + this(guiIndic, null, null); + } + + public SequenceFetcher(IProgressIndicator guiIndic, + final String selectedDb, final String queryString) + { + this._isConstructing=true; + this.progressIndicator = guiIndic; + final SequenceFetcher us = this; + // launch initialiser thread + Thread sf = new Thread(new Runnable() + { + + @Override + public void run() + { + if (getSequenceFetcherSingleton(progressIndicator) != null) + { + us.initGui(progressIndicator, selectedDb, queryString); + us._isConstructing=false; + } + else + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + MessageManager + .getString("warn.couldnt_create_sequence_fetcher_client"), + MessageManager + .getString("label.couldnt_create_sequence_fetcher"), + JOptionPane.ERROR_MESSAGE); + } + }); + + // raise warning dialog + } + } + }); + sf.start(); + } + /** + * blocking call which creates a new sequence fetcher panel, configures it and presses the OK button with the given database and query. + * @param database + * @param query + */ + public static List fetchAndShow(String database, String query) + { + final SequenceFetcher sf = new SequenceFetcher(Desktop.instance, database, query); + while (sf._isConstructing) + { + try { Thread.sleep(50); + } catch (Exception q) + { + return Collections.emptyList(); + } + } + sf.newAlframes = new ArrayList(); + sf.run(); + return sf.newAlframes; + } + + private class DatabaseAuthority extends DefaultMutableTreeNode + { + + }; + + private class DatabaseSource extends DefaultMutableTreeNode + { + + }; + + /** + * initialise the database and query for this fetcher panel + * + * @param selectedDb + * - string that should correspond to a sequence fetcher + * @param queryString + * - string that will be entered in the query dialog + * @return true if UI was configured with valid database and query string + */ + protected boolean setInitialQuery(String selectedDb, String queryString) + { + if (selectedDb == null || selectedDb.trim().length() == 0) + { + return false; + } try { - jbInit(); + List sp = sfetch.getSourceProxy(selectedDb); + for (DbSourceProxy sourcep : sp) + { + if (sourcep.getTier() == 0) + { + database.selection = Arrays + .asList(new DbSourceProxy[] { sourcep }); + break; + } + } + if (database.selection == null || database.selection.size() == 0) + { + System.err.println("Ignoring fetch parameter db='" + selectedDb + + "'"); + return false; + } + textArea.setText(queryString); + } catch (Exception q) + { + System.err.println("Ignoring fetch parameter db='" + selectedDb + + "' and query='" + queryString + "'"); + return false; } - catch (Exception ex) + return true; + } + + /** + * called by thread spawned by constructor + * + * @param guiWindow + * @param queryString + * @param selectedDb + */ + private void initGui(IProgressIndicator guiWindow, String selectedDb, + String queryString) + { + this.guiWindow = guiWindow; + if (guiWindow instanceof AlignFrame) + { + alignFrame = (AlignFrame) guiWindow; + } + database = new JDatabaseTree(sfetch); + try + { + jbInit(); + /* + * configure the UI with any query parameters we were called with + */ + if (!setInitialQuery(selectedDb, queryString)) + { + /* + * none provided, so show the database chooser + */ + database.waitForInput(); + } + } catch (Exception ex) { ex.printStackTrace(); } frame = new JInternalFrame(); frame.setContentPane(this); - if (System.getProperty("os.name").startsWith("Mac")) + if (Platform.isAMac()) { - Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140); + Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240); } else { - Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125); + Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180); } } 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 + 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 \";\""); - ok.setText("OK"); + 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(MessageManager + .getString("label.replace_commas_semicolons")); + ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(); } }); - close.setText("Close"); + clear.setText(MessageManager.getString("action.clear")); + clear.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + clear_actionPerformed(); + } + }); + + example.setText(MessageManager.getString("label.example")); + example.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + example_actionPerformed(); + } + }); + 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) + if (e.getKeyCode() == KeyEvent.VK_ENTER) + { ok_actionPerformed(); + } } }); jPanel3.setLayout(borderLayout1); borderLayout1.setVgap(5); jPanel1.add(ok); + jPanel1.add(example); + jPanel1.add(clear); jPanel1.add(close); - jPanel3.add(jPanel2, java.awt.BorderLayout.WEST); - jPanel2.add(database); + jPanel2.setLayout(borderLayout3); + databaseButt = /*database.getDatabaseSelectorButton(); + final JButton viewdbs =*/new JButton( + MessageManager.getString("action.select_ddbb")); + databaseButt.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent arg0) + { + hidePanel(); + database.showDialog(); + } + }); + databaseButt.setFont(JvSwingUtils.getLabelFont()); + database.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + String currentSelection = database.getSelectedItem(); + if (currentSelection == null) + { + close_actionPerformed(null); + } + + showPanel(); + + if ("pdb".equalsIgnoreCase(currentSelection)) + { + pdbSourceAction(); + } + else if ("uniprot".equalsIgnoreCase(currentSelection)) + { + uniprotSourceAction(); + } + else + { + otherSourceAction(); + } + database.action = -1; + } + }); + + dbeg.setText(""); + 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); + 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); - jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH); this.add(jPanel1, java.awt.BorderLayout.SOUTH); this.add(jPanel3, java.awt.BorderLayout.CENTER); + this.add(jPanel2, java.awt.BorderLayout.NORTH); jScrollPane1.getViewport().add(textArea); + } + private void pdbSourceAction() + { + databaseButt.setText(database.getSelectedItem()); + new PDBFTSPanel(this); + frame.dispose(); + } + + private void uniprotSourceAction() + { + databaseButt.setText(database.getSelectedItem()); + new UniprotFTSPanel(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 + { + textArea.setText(database.getExampleQueries()); + } catch (Exception ex) + { + } + jPanel3.repaint(); + } + + protected void clear_actionPerformed() + { + textArea.setText(""); + jPanel3.repaint(); } - JComboBox database = new JComboBox(); - JLabel jLabel1 = new JLabel(); - JButton ok = 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(); - BorderLayout borderLayout1 = new BorderLayout(); - BorderLayout borderLayout2 = new BorderLayout(); public void close_actionPerformed(ActionEvent e) { try { frame.setClosed(true); + } catch (Exception ex) + { } - catch (Exception ex) - {} } public void ok_actionPerformed() { - database.setEnabled(false); + databaseButt.setEnabled(false); + example.setEnabled(false); textArea.setEnabled(false); ok.setEnabled(false); close.setEnabled(false); @@ -185,22 +595,38 @@ 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"; } - 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)"; } @@ -210,380 +636,411 @@ extends JPanel implements Runnable resetDialog(); return; } + // TODO: Refactor to GUI independent code and write tests. + // indicate if successive sources should be merged into one alignment. + boolean addToLast = false; + List aresultq = new ArrayList(); + List presultTitle = new ArrayList(); + List presult = new ArrayList(); + List 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; - result = new StringBuffer(); - if (database.getSelectedItem().equals("Uniprot")) + FeatureSettingsModelI preferredFeatureColours = null; + while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0)) { - 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 (;si 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(); + try + { + // update status + guiWindow + .setProgressBar(MessageManager.formatMessage( + "status.fetching_sequence_queries_from", + new String[] { + Integer.valueOf(nqueries).toString(), + proxy.getDbName() }), Thread.currentThread() + .hashCode()); + if (proxy.getMaximumQueryCount() == 1) + { + /* + * proxy only handles one accession id at a time + */ + while (en.hasNext()) + { + String acc = en.next(); + if (!fetchSingleAccession(proxy, acc, aresultq, aresult)) + { + nextFetch.add(acc); } } - } else { - result.append("# no response for "+qry); } - } - if (seqs!=null && seqs.length>0) { - if (parseResult(new Alignment(seqs), null, null)!=null) + else { - result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment"); + /* + * proxy can fetch multiple accessions at one time + */ + fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch); } + } 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) + { + 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 if (database.getSelectedItem().equals("PDB")) - { - StringTokenizer qset = new StringTokenizer(textArea.getText(), ";"); - String query; - SequenceI[] seqs = null; - while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) + + // Stack results ready for opening in alignment windows + if (aresult != null && aresult.size() > 0) { - SequenceI[] seqparts = getPDBFile(query.toUpperCase()); - if (seqparts != null) + FeatureSettingsModelI proxyColourScheme = proxy + .getFeatureColourScheme(); + if (proxyColourScheme != null) + { + preferredFeatureColours = proxyColourScheme; + } + + AlignmentI ar = null; + if (proxy.isAlignmentSource()) { - if (seqs == null) + addToLast = false; + // new window for each result + while (aresult.size() > 0) { - seqs = seqparts; + presult.add(aresult.remove(0)); + presultTitle.add(aresultq.remove(0) + " " + + getDefaultRetrievalTitle()); } - else + } + else + { + String titl = null; + if (addToLast && presult.size() > 0) { - SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length]; - int i=0; - for (; i < seqs.length; i++) + 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) { - newseqs[i] = seqs[i]; - seqs[i] = null; + ar = aresult.remove(0); } - 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"); + addToLast = true; + presult.add(ar); + presultTitle.add(titl); } } + guiWindow.setProgressBar(MessageManager + .getString("status.finshed_querying"), Thread.currentThread() + .hashCode()); } - else if( database.getSelectedItem().equals("PFAM")) + guiWindow.setProgressBar( + (presult.size() > 0) ? MessageManager + .getString("status.parsing_results") : MessageManager + .getString("status.processing"), Thread.currentThread() + .hashCode()); + // process results + while (presult.size() > 0) { - try + parseResult(presult.remove(0), presultTitle.remove(0), null, + preferredFeatureColours); + } + // 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) { - 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) + if (l != sb.length()) { - parseResult( result.toString(), textArea.getText().toUpperCase() ); + sb.append("; "); } - - } - catch (java.io.IOException ex) - { - result = null; + if (lr - sb.length() > 40) + { + sb.append("\n"); + } + sb.append(s); } + showErrorMessage(sb.toString()); } - - if (result == null || result.length() == 0) - { - showErrorMessage("Error retrieving " + textArea.getText() - + " from " + database.getSelectedItem()); - } - resetDialog(); - return; } - void getUniprotFile(String id) + /** + * Tries to fetch one or more accession ids from the database proxy + * + * @param proxy + * @param accessions + * the queries to fetch + * @param aresultq + * a successful queries list to add to + * @param aresult + * a list of retrieved alignments to add to + * @param nextFetch + * failed queries are added to this list + * @throws Exception + */ + void fetchMultipleAccessions(DbSourceProxy proxy, + Iterator accessions, List aresultq, + List aresult, List nextFetch) + throws Exception { - EBIFetchClient ebi = new EBIFetchClient(); - File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null); - - DBRefFetcher dbref = new DBRefFetcher(); - Vector entries = dbref.getUniprotEntries(file); - - if (entries != null) + StringBuilder multiacc = new StringBuilder(); + List tosend = new ArrayList(); + while (accessions.hasNext()) { - //First, make the new sequences - Enumeration en = entries.elements(); - while (en.hasMoreElements()) + String nel = accessions.next(); + tosend.add(nel); + multiacc.append(nel); + if (accessions.hasNext()) { - 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"); - + multiacc.append(proxy.getAccessionSeparator()); } + } - //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++) + try + { + String query = multiacc.toString(); + AlignmentI rslt = proxy.getSequenceRecords(query); + if (rslt == null || rslt.getHeight() == 0) { - 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) + // no results - pass on all queries to next source + nextFetch.addAll(tosend); + } + else + { + aresultq.add(query); + aresult.add(rslt); + if (tosend.size() > 1) { - e = entry.getFeature().elements(); - while (e.hasMoreElements()) - { - SequenceFeature sf = (SequenceFeature) e.nextElement(); - sf.setFeatureGroup("Uniprot"); - al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); - } + checkResultForQueries(rslt, tosend, nextFetch, proxy); } } + } catch (OutOfMemoryError oome) + { + new OOMWarning("fetching " + multiacc + " from " + + database.getSelectedItem(), oome, this); } } - SequenceI[] getPDBFile(String id) + /** + * Query for a single accession id via the database proxy + * + * @param proxy + * @param accession + * @param aresultq + * a list of successful queries to add to + * @param aresult + * a list of retrieved alignments to add to + * @return true if the fetch was successful, else false + */ + boolean fetchSingleAccession(DbSourceProxy proxy, String accession, + List aresultq, List aresult) { - 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; - } + boolean success = false; try { - PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE); - for (int i = 0; i < pdbfile.chains.size(); i++) + if (aresult != null) { - if (chain == null || - ( (PDBChain) pdbfile.chains.elementAt(i)).id. - toUpperCase().equals(chain)) + try { - 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()); + // give the server a chance to breathe + Thread.sleep(5); + } catch (Exception e) + { + // } } - if (result.size() < 1) + AlignmentI indres = null; + try + { + indres = proxy.getSequenceRecords(accession); + } catch (OutOfMemoryError oome) { - throw new Exception("WsDBFetch for PDB id resulted in zero result size"); + new OOMWarning("fetching " + accession + " from " + + proxy.getDbName(), oome, this); } - } - 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++) + if (indres != null) + { + aresultq.add(accession); + aresult.add(indres); + success = true; + } + } catch (Exception e) { - results[i] = (SequenceI) result.elementAt(i); - result.setElementAt(null,i); + Cache.log.info( + "Error retrieving " + accession + + " from " + proxy.getDbName(), e); } - return results; + return success; } - Alignment parseResult(String result, String title) + + /** + * Checks which of the queries were successfully retrieved by searching the + * DBRefs of the retrieved sequences for a match. Any not found are added to + * the 'nextFetch' list. + * + * @param rslt + * @param queries + * @param nextFetch + * @param proxy + */ + void checkResultForQueries(AlignmentI rslt, List queries, + List nextFetch, DbSourceProxy proxy) { - String format = new IdentifyFile().Identify(result, "Paste"); - Alignment sequences = null; - if (FormatAdapter.isValidFormat(format)) + SequenceI[] rs = rslt.getSequencesArray(); + + for (String q : queries) { - sequences = null; - try + DBRefEntry dbr = new DBRefEntry(); + dbr.setSource(proxy.getDbSource()); + dbr.setVersion(null); + String accId = proxy.getAccessionIdFromQuery(q); + dbr.setAccessionId(accId); + boolean rfound = false; + for (int r = 0; r < rs.length; r++) { - sequences = new FormatAdapter().readFile(result.toString(), "Paste", - format); + if (rs[r] != null) + { + List found = DBRefUtils.searchRefs(rs[r].getDBRefs(), + accId); + if (!found.isEmpty()) + { + rfound = true; + break; + } + } } - catch (Exception ex) - {} - - if (sequences!=null) + if (!rfound) { - return parseResult(sequences, title, format); + nextFetch.add(q); } } - else - { - showErrorMessage("Error retrieving " + textArea.getText() - + " from " + database.getSelectedItem()); - } + } - 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(); } - Alignment parseResult(Alignment al, String title, String currentFileFormat) + AlignmentI parseResult(AlignmentI al, String title, + String currentFileFormat, + FeatureSettingsModelI preferredFeatureColours) { if (al != null && al.getHeight() > 0) { + if (title == null) + { + title = getDefaultRetrievalTitle(); + } if (alignFrame == null) { - AlignFrame af = new AlignFrame(al, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - if (currentFileFormat!=null) + AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + if (currentFileFormat != null) { - af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments? + af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT + // FORMAT FOR + // NON-FormatAdapter Sourced + // Alignments? } - if(title==null) + SequenceFeature[] sfs = null; + List alsqs; + synchronized (alsqs = al.getSequences()) { - title = "Retrieved from " + database.getSelectedItem(); + for (SequenceI sq : alsqs) + { + if ((sfs = sq.getSequenceFeatures()) != null) + { + if (sfs.length > 0) + { + af.setShowSeqFeatures(true); + break; + } + } + + } } - Desktop.addInternalFrame(af, - title, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + if (preferredFeatureColours != null) + { + af.getViewport().applyFeaturesStyle(preferredFeatureColours); + } + if (Cache.getDefault("HIDE_INTRONS", true)) + { + af.hideFeatureColumns(SequenceOntologyI.EXON, false); + } + if (newAlframes != null) + { + newAlframes.add(af); + } + 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 { - af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); + af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", + false)); + } catch (Exception ex) + { } - catch (Exception ex) - {} } 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; @@ -594,13 +1051,41 @@ 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); + JOptionPane.showInternalMessageDialog(Desktop.desktop, error, + MessageManager.getString("label.error_retrieving_data"), + JOptionPane.WARNING_MESSAGE); } }); } -} + public IProgressIndicator getProgressIndicator() + { + return progressIndicator; + } + + public void setProgressIndicator(IProgressIndicator progressIndicator) + { + this.progressIndicator = progressIndicator; + } + + /** + * Make this panel visible (after a selection has been made in the database + * chooser) + */ + void showPanel() + { + frame.setVisible(true); + } + + /** + * Hide this panel (on clicking the database button to open the database + * chooser) + */ + void hidePanel() + { + frame.setVisible(false); + } +}