X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=afe6754f913391ce94597aef803d020763cd3980;hb=ba7cba06e47fd8f46aafb04c5f2b33718db4f320;hp=a97375756c895bf6bc0fc98b04ccf3bbf4fc3b10;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index a973757..afe6754 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; @@ -54,8 +57,6 @@ 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 +115,10 @@ 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 @@ -160,9 +164,9 @@ public class SequenceFetcher extends JPanel implements Runnable } } if (sfetch == null - || dasRegistry != jalview.bin.Cache.getDasSourceRegistry() - || lastDasSourceRegistry != (jalview.bin.Cache - .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache + || dasRegistry != Cache.getDasSourceRegistry() + || lastDasSourceRegistry != (Cache.getDasSourceRegistry() + .getDasRegistryURL() + Cache .getDasSourceRegistry().getLocalSourceString()) .hashCode()) { @@ -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(); @@ -269,13 +273,13 @@ 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 +362,46 @@ 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; } }); @@ -396,15 +420,25 @@ public class SequenceFetcher extends JPanel implements Runnable this.add(jPanel2, java.awt.BorderLayout.NORTH); jScrollPane1.getViewport().add(textArea); + /* + * open the database tree + */ + database.waitForInput(); } 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(); + } private void otherSourceAction() { try @@ -518,30 +552,34 @@ 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 +590,27 @@ 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 +623,6 @@ 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 +635,19 @@ 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 +677,6 @@ public class SequenceFetcher extends JPanel implements Runnable { ar.append(aresult.remove(0)); } - ; } addToLast = true; presult.add(ar); @@ -760,18 +695,19 @@ 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 +724,157 @@ 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()) + { + String nel = accessions.next(); + tosend.add(nel); + multiacc.append(nel); + if (accessions.hasNext()) + { + multiacc.append(proxy.getAccessionSeparator()); + } + } + + try { - sequences = null; - try + String query = multiacc.toString(); + AlignmentI rslt = proxy.getSequenceRecords(query); + if (rslt == null || rslt.getHeight() == 0) { - sequences = new FormatAdapter().readFile(result.toString(), - "Paste", format); - } catch (Exception ex) + // 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); + } + } - if (sequences != null) + /** + * 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 + { + if (aresult != null) { - return parseResult(sequences, title, format); + try + { + // give the server a chance to breathe + Thread.sleep(5); + } catch (Exception e) + { + // + } } - } - else + + 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) { - showErrorMessage("Error retrieving " + textArea.getText() + " from " - + database.getSelectedItem()); + 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 +888,8 @@ 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 +927,16 @@ 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); + } + Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -874,7 +945,7 @@ public class SequenceFetcher extends JPanel implements Runnable try { - af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", + af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (Exception ex) { @@ -912,4 +983,22 @@ 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); + } }