X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=434029326c7860d4a076b47896b566bc4385e984;hp=f8d3734dcee1eccc9ecbf8824ff3736ea56dc9da;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hpb=a90e2fe3cc3b779521a81cf8de410936f3a777c1 diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index f8d3734..4340293 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -20,15 +20,18 @@ */ package jalview.gui; +import jalview.api.FeatureSettingsModelI; +import jalview.bin.Cache; 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.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; @@ -40,6 +43,7 @@ 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; @@ -54,8 +58,6 @@ 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 { JLabel dbeg = new JLabel(); @@ -114,7 +116,10 @@ public class SequenceFetcher extends JPanel implements Runnable private static Thread initingThread = null; - int debounceTrap = 0; + public JTextArea getTextArea() + { + return textArea; + } /** * Blocking method that initialises and returns the shared instance of the @@ -160,11 +165,10 @@ public class SequenceFetcher extends JPanel implements Runnable } } if (sfetch == null - || dasRegistry != jalview.bin.Cache.getDasSourceRegistry() - || lastDasSourceRegistry != (jalview.bin.Cache - .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache - .getDasSourceRegistry().getLocalSourceString()) - .hashCode()) + || dasRegistry != Cache.getDasSourceRegistry() + || lastDasSourceRegistry != (Cache.getDasSourceRegistry() + .getDasRegistryURL() + Cache.getDasSourceRegistry() + .getLocalSourceString()).hashCode()) { _initingFetcher = true; initingThread = Thread.currentThread(); @@ -177,7 +181,7 @@ public class SequenceFetcher extends JPanel implements Runnable .getString("status.init_sequence_database_fetchers"), Thread.currentThread().hashCode()); } - dasRegistry = jalview.bin.Cache.getDasSourceRegistry(); + dasRegistry = Cache.getDasSourceRegistry(); dasRegistry.refreshSources(); jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher(); @@ -196,8 +200,19 @@ public class SequenceFetcher extends JPanel implements Runnable private IProgressIndicator progressIndicator; + private volatile boolean _isConstructing = false; + + private List 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 @@ -209,7 +224,8 @@ public class SequenceFetcher extends JPanel implements Runnable { if (getSequenceFetcherSingleton(progressIndicator) != null) { - us.initGui(progressIndicator); + us.initGui(progressIndicator, selectedDb, queryString); + us._isConstructing = false; } else { @@ -236,6 +252,32 @@ public class SequenceFetcher extends JPanel implements Runnable 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 { @@ -247,11 +289,57 @@ public class SequenceFetcher extends JPanel implements Runnable }; /** + * 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 + { + 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; + } + return true; + } + + /** * called by thread spawned by constructor * * @param guiWindow + * @param queryString + * @param selectedDb */ - private void initGui(IProgressIndicator guiWindow) + private void initGui(IProgressIndicator guiWindow, String selectedDb, + String queryString) { this.guiWindow = guiWindow; if (guiWindow instanceof AlignFrame) @@ -262,6 +350,16 @@ public class SequenceFetcher extends JPanel implements Runnable 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(); @@ -269,13 +367,13 @@ public class SequenceFetcher extends JPanel implements Runnable frame = new JInternalFrame(); frame.setContentPane(this); - if (new jalview.util.Platform().isAMac()) + if (Platform.isAMac()) { - Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240); + Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240); } else { - Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180); + Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180); } } @@ -358,26 +456,46 @@ public class SequenceFetcher extends JPanel implements Runnable jPanel1.add(example); jPanel1.add(clear); jPanel1.add(close); - jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER); jPanel2.setLayout(borderLayout3); - databaseButt = database.getDatabaseSelectorButton(); + 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) { - debounceTrap++; String currentSelection = database.getSelectedItem(); - if (!currentSelection.equalsIgnoreCase("pdb")) + if (currentSelection == null) { - otherSourceAction(); + close_actionPerformed(null); } - if (currentSelection.equalsIgnoreCase("pdb") - && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0))) + + showPanel(); + + if ("pdb".equalsIgnoreCase(currentSelection)) { pdbSourceAction(); } + else if ("uniprot".equalsIgnoreCase(currentSelection)) + { + uniprotSourceAction(); + } + else + { + otherSourceAction(); + } database.action = -1; } }); @@ -395,13 +513,19 @@ public class SequenceFetcher extends JPanel implements Runnable 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 PDBSearchPanel(this); + new PDBFTSPanel(this); + frame.dispose(); + } + + private void uniprotSourceAction() + { + databaseButt.setText(database.getSelectedItem()); + new UniprotFTSPanel(this); frame.dispose(); } @@ -518,30 +642,34 @@ public class SequenceFetcher 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; - ArrayList aresultq = new ArrayList(), presultTitle = new ArrayList(); - ArrayList presult = new ArrayList(), aresult = new ArrayList(); + 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() + 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)) + + FeatureSettingsModelI preferredFeatureColours = null; + while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0)) { - if (!en.hasNext() && nextfetch.size() > 0) + if (!en.hasNext() && nextFetch.size() > 0) { - en = nextfetch.iterator(); - nqueries = nextfetch.size(); + en = nextFetch.iterator(); + nqueries = nextFetch.size(); // save the remaining queries in the original array - qries = nextfetch.toArray(new String[nqueries]); - nextfetch = new ArrayList(); + qries = nextFetch.toArray(new String[nqueries]); + nextFetch = new ArrayList(); } DbSourceProxy proxy = proxies.next(); - boolean isAliSource = false; try { // update status @@ -552,136 +680,27 @@ public class SequenceFetcher extends JPanel implements Runnable Integer.valueOf(nqueries).toString(), proxy.getDbName() }), Thread.currentThread() .hashCode()); - isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB); - if (proxy.getAccessionSeparator() == null) + if (proxy.getMaximumQueryCount() == 1) { + /* + * proxy only handles one accession id at a time + */ while (en.hasNext()) { - 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 - { - 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) + String acc = en.next(); + if (!fetchSingleAccession(proxy, acc, aresultq, aresult)) { - jalview.bin.Cache.log.info("Error retrieving " + item - + " from " + proxy.getDbName(), e); - nextfetch.add(item); + nextFetch.add(acc); } } } 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()) - { - multiacc.append(proxy.getAccessionSeparator()); - } - } - try - { - AlignmentI rslt; - SequenceI[] rs; - List nores = new ArrayList(); - rslt = proxy.getSequenceRecords(multiacc.toString()); - if (rslt == null || rslt.getHeight() == 0) - { - // no results - pass on all queries to next source - nextfetch.addAll(tosend); - } - 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) - { - 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 (OutOfMemoryError oome) - { - new OOMWarning("fetching " + multiacc + " from " - + database.getSelectedItem(), oome, this); - } + /* + * proxy can fetch multiple accessions at one time + */ + fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch); } - } catch (Exception e) { showErrorMessage("Error retrieving " + textArea.getText() @@ -694,7 +713,6 @@ public class SequenceFetcher extends JPanel implements Runnable e.printStackTrace(); } catch (OutOfMemoryError e) { - // resets dialog box - so we don't use OOMwarning here. showErrorMessage("Out of Memory when retrieving " + textArea.getText() + " from " @@ -707,11 +725,19 @@ public class SequenceFetcher extends JPanel implements Runnable + " from " + database.getSelectedItem()); e.printStackTrace(); } + // Stack results ready for opening in alignment windows if (aresult != null && aresult.size() > 0) { + FeatureSettingsModelI proxyColourScheme = proxy + .getFeatureColourScheme(); + if (proxyColourScheme != null) + { + preferredFeatureColours = proxyColourScheme; + } + AlignmentI ar = null; - if (isAliSource) + if (proxy.isAlignmentSource()) { addToLast = false; // new window for each result @@ -741,7 +767,6 @@ public class SequenceFetcher extends JPanel implements Runnable { ar.append(aresult.remove(0)); } - ; } addToLast = true; presult.add(ar); @@ -760,18 +785,19 @@ public class SequenceFetcher extends JPanel implements Runnable // process results while (presult.size() > 0) { - parseResult(presult.remove(0), presultTitle.remove(0), null); + 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) + if (nextFetch.size() > 0) { StringBuffer sb = new StringBuffer(); sb.append("Didn't retrieve the following " - + (nextfetch.size() == 1 ? "query" : nextfetch.size() + + (nextFetch.size() == 1 ? "query" : nextFetch.size() + " queries") + ": \n"); int l = sb.length(), lr = 0; - for (String s : nextfetch) + for (String s : nextFetch) { if (l != sb.length()) { @@ -788,33 +814,157 @@ public class SequenceFetcher extends JPanel implements Runnable resetDialog(); } - AlignmentI parseResult(String result, String title) + /** + * 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 { - String format = new IdentifyFile().Identify(result, "Paste"); - AlignmentI sequences = null; - if (FormatAdapter.isValidFormat(format)) + StringBuilder multiacc = new StringBuilder(); + List tosend = new ArrayList(); + while (accessions.hasNext()) { - sequences = null; - try - { - sequences = new FormatAdapter().readFile(result.toString(), - "Paste", format); - } catch (Exception ex) + String nel = accessions.next(); + tosend.add(nel); + multiacc.append(nel); + if (accessions.hasNext()) { + multiacc.append(proxy.getAccessionSeparator()); } + } - if (sequences != null) + try + { + String query = multiacc.toString(); + AlignmentI rslt = proxy.getSequenceRecords(query); + if (rslt == null || rslt.getHeight() == 0) { - return parseResult(sequences, title, format); + // no results - pass on all queries to next source + nextFetch.addAll(tosend); } + else + { + aresultq.add(query); + aresult.add(rslt); + if (tosend.size() > 1) + { + checkResultForQueries(rslt, tosend, nextFetch, proxy); + } + } + } catch (OutOfMemoryError oome) + { + new OOMWarning("fetching " + multiacc + " from " + + database.getSelectedItem(), oome, this); } - else + } + + /** + * 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) + { + boolean success = false; + try { - showErrorMessage("Error retrieving " + textArea.getText() + " from " - + database.getSelectedItem()); + if (aresult != null) + { + try + { + // give the server a chance to breathe + Thread.sleep(5); + } catch (Exception e) + { + // + } + } + + AlignmentI indres = null; + try + { + indres = proxy.getSequenceRecords(accession); + } catch (OutOfMemoryError oome) + { + new OOMWarning("fetching " + accession + " from " + + proxy.getDbName(), oome, this); + } + if (indres != null) + { + aresultq.add(accession); + aresult.add(indres); + success = true; + } + } catch (Exception e) + { + Cache.log.info( + "Error retrieving " + accession + " from " + + proxy.getDbName(), e); } + return success; + } - return null; + /** + * 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) + { + SequenceI[] rs = rslt.getSequencesArray(); + + for (String q : queries) + { + 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++) + { + if (rs[r] != null) + { + List found = DBRefUtils.searchRefs(rs[r].getDBRefs(), + accId); + if (!found.isEmpty()) + { + rfound = true; + break; + } + } + } + if (!rfound) + { + nextFetch.add(q); + } + } } /** @@ -828,7 +978,8 @@ public class SequenceFetcher extends JPanel implements Runnable } AlignmentI parseResult(AlignmentI al, String title, - String currentFileFormat) + String currentFileFormat, + FeatureSettingsModelI preferredFeatureColours) { if (al != null && al.getHeight() > 0) @@ -866,6 +1017,19 @@ public class SequenceFetcher extends JPanel implements Runnable } } + + 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); @@ -874,8 +1038,7 @@ public class SequenceFetcher extends JPanel implements Runnable try { - af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", - false)); + af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (Exception ex) { } @@ -912,4 +1075,22 @@ public class SequenceFetcher extends JPanel implements Runnable { 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); + } }