X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=8754fbb59cb3b15653d219a45684d65692ba92b4;hb=b483c2012e40cab4b38f650dc049c94efe7e27c2;hp=ab78ad322ec0a6d866b8110648f1fa70fedbcfe5;hpb=007af0c9001900071f6d8e9214143f79e10f4938;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index ab78ad3..8754fbb 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -26,12 +26,14 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.fts.core.GFTSPanel; import jalview.fts.service.pdb.PDBFTSPanel; import jalview.fts.service.uniprot.UniprotFTSPanel; +import jalview.io.FileFormatI; import jalview.io.gff.SequenceOntologyI; import jalview.util.DBRefUtils; import jalview.util.MessageManager; -import jalview.ws.dbsources.das.api.DasSourceRegistryI; +import jalview.util.Platform; import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; @@ -42,6 +44,7 @@ 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; @@ -49,7 +52,6 @@ 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; @@ -76,6 +78,8 @@ public class SequenceFetcher extends JPanel implements Runnable JButton close = new JButton(); + JButton back = new JButton(); + JPanel jPanel1 = new JPanel(); JTextArea textArea = new JTextArea(); @@ -106,16 +110,10 @@ public class SequenceFetcher extends JPanel implements Runnable 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; - int debounceTrap = 0; - public JTextArea getTextArea() { return textArea; @@ -136,11 +134,10 @@ public class SequenceFetcher extends JPanel implements Runnable { if (guiWindow != null) { - guiWindow - .setProgressBar( - MessageManager - .getString("status.waiting_sequence_database_fetchers_init"), - 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. @@ -157,19 +154,13 @@ public class SequenceFetcher extends JPanel implements Runnable } if (guiWindow != null) { - guiWindow - .setProgressBar( - MessageManager - .getString("status.waiting_sequence_database_fetchers_init"), - Thread.currentThread().hashCode()); + guiWindow.setProgressBar( + MessageManager.getString( + "status.waiting_sequence_database_fetchers_init"), + Thread.currentThread().hashCode()); } } - if (sfetch == null - || dasRegistry != Cache.getDasSourceRegistry() - || lastDasSourceRegistry != (Cache.getDasSourceRegistry() - .getDasRegistryURL() + Cache - .getDasSourceRegistry().getLocalSourceString()) - .hashCode()) + if (sfetch == null) { _initingFetcher = true; initingThread = Thread.currentThread(); @@ -178,20 +169,17 @@ public class SequenceFetcher extends JPanel implements Runnable */ if (guiWindow != null) { - guiWindow.setProgressBar(MessageManager - .getString("status.init_sequence_database_fetchers"), + guiWindow.setProgressBar( + MessageManager.getString( + "status.init_sequence_database_fetchers"), Thread.currentThread().hashCode()); } - dasRegistry = Cache.getDasSourceRegistry(); - dasRegistry.refreshSources(); jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher(); if (guiWindow != null) { guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); } - lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry - .getLocalSourceString()).hashCode(); sfetch = sf; _initingFetcher = false; initingThread = null; @@ -201,8 +189,19 @@ 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 @@ -214,7 +213,8 @@ public class SequenceFetcher extends JPanel implements Runnable { if (getSequenceFetcherSingleton(progressIndicator) != null) { - us.initGui(progressIndicator); + us.initGui(progressIndicator, selectedDb, queryString); + us._isConstructing = false; } else { @@ -223,14 +223,12 @@ public class SequenceFetcher extends JPanel implements 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); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString( + "warn.couldnt_create_sequence_fetcher_client"), + MessageManager.getString( + "label.couldnt_create_sequence_fetcher"), + JvOptionPane.ERROR_MESSAGE); } }); @@ -241,6 +239,32 @@ 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 { @@ -252,11 +276,58 @@ 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) @@ -267,6 +338,16 @@ 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(); @@ -274,23 +355,33 @@ 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); } } private String getFrameTitle() { - return ((alignFrame == null) ? MessageManager - .getString("label.new_sequence_fetcher") : MessageManager - .getString("label.additional_sequence_fetcher")); + return ((alignFrame == null) + ? MessageManager.getString("label.new_sequence_fetcher") + : MessageManager + .getString("label.additional_sequence_fetcher")); } + GFTSPanel parentFTSframe = null; + /** + * change the buttons so they fit with the FTS panel. + */ + public void embedWithFTSPanel(GFTSPanel toClose) + { + back.setVisible(true); + parentFTSframe = toClose; + } private void jbInit() throws Exception { this.setLayout(borderLayout2); @@ -305,8 +396,8 @@ public class SequenceFetcher extends JPanel implements Runnable replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER); replacePunctuation .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); - replacePunctuation.setText(MessageManager - .getString("label.replace_commas_semicolons")); + replacePunctuation.setText( + MessageManager.getString("label.replace_commas_semicolons")); ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { @@ -335,7 +426,7 @@ public class SequenceFetcher extends JPanel implements Runnable example_actionPerformed(); } }); - close.setText(MessageManager.getString("action.close")); + close.setText(MessageManager.getString("action.cancel")); close.addActionListener(new ActionListener() { @Override @@ -344,6 +435,17 @@ public class SequenceFetcher extends JPanel implements Runnable close_actionPerformed(e); } }); + back.setText(MessageManager.getString("action.back")); + back.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + parentFTSframe.btn_back_ActionPerformed(); + } + }); + // back not visible unless embedded + back.setVisible(false); textArea.setFont(JvSwingUtils.getLabelFont()); textArea.setLineWrap(true); textArea.addKeyListener(new KeyAdapter() @@ -359,29 +461,44 @@ public class SequenceFetcher extends JPanel implements Runnable }); jPanel3.setLayout(borderLayout1); borderLayout1.setVgap(5); - jPanel1.add(ok); + jPanel1.add(back); jPanel1.add(example); jPanel1.add(clear); + jPanel1.add(ok); 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 == null) + { + close_actionPerformed(null); + } + + showPanel(); - if (currentSelection.equalsIgnoreCase("pdb") - && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0))) + if ("pdb".equalsIgnoreCase(currentSelection)) { pdbSourceAction(); } - else if (currentSelection.equalsIgnoreCase("uniprot") - && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0))) + else if ("uniprot".equalsIgnoreCase(currentSelection)) { uniprotSourceAction(); } @@ -406,7 +523,6 @@ 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() @@ -422,6 +538,7 @@ public class SequenceFetcher extends JPanel implements Runnable new UniprotFTSPanel(this); frame.dispose(); } + private void otherSourceAction() { try @@ -431,17 +548,13 @@ public class SequenceFetcher extends JPanel implements Runnable + database.getSelectedSources().size() + " others)" : "")); String eq = database.getExampleQueries(); - dbeg.setText(MessageManager.formatMessage( - "label.example_query_param", new String[] { eq })); + dbeg.setText(MessageManager.formatMessage("label.example_query_param", + new String[] + { eq })); + // TODO this should be a property of the SequenceFetcher whether commas are and + // colons are allowed in the IDs... + 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) @@ -475,6 +588,10 @@ public class SequenceFetcher extends JPanel implements Runnable try { frame.setClosed(true); + if (parentFTSframe!=null) + { + parentFTSframe.btn_cancel_ActionPerformed(); + } } catch (Exception ex) { } @@ -487,7 +604,7 @@ public class SequenceFetcher extends JPanel implements Runnable textArea.setEnabled(false); ok.setEnabled(false); close.setEnabled(false); - + back.setEnabled(false); Thread worker = new Thread(this); worker.start(); } @@ -499,6 +616,7 @@ public class SequenceFetcher extends JPanel implements Runnable textArea.setEnabled(true); ok.setEnabled(true); close.setEnabled(true); + back.setEnabled(parentFTSframe != null); } @Override @@ -514,7 +632,7 @@ public class SequenceFetcher extends JPanel implements Runnable if (replacePunctuation.isEnabled() && replacePunctuation.isSelected()) { empty = new com.stevesoft.pat.Regex( - // replace commas and spaces with a semicolon + // replace commas and spaces with a semicolon "(\\s|[,; ])+", ";"); } else @@ -524,8 +642,8 @@ public class SequenceFetcher extends JPanel implements Runnable } textArea.setText(empty.replaceAll(textArea.getText())); // see if there's anthing to search with - if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea - .getText())) + 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)"; } @@ -538,160 +656,64 @@ public class SequenceFetcher extends JPanel implements Runnable // 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() - .split(";")); + List nextFetch = Arrays + .asList(qries = textArea.getText().split(";")); Iterator en = Arrays.asList(new String[0]).iterator(); int nqueries = qries.length; FeatureSettingsModelI preferredFeatureColours = null; - while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0)) + 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 - guiWindow - .setProgressBar(MessageManager.formatMessage( - "status.fetching_sequence_queries_from", - new String[] { - Integer.valueOf(nqueries).toString(), - proxy.getDbName() }), Thread.currentThread() - .hashCode()); - isAliSource = proxy.isAlignmentSource(); + 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 item = en.next(); - try + String acc = en.next(); + if (!fetchSingleAccession(proxy, acc, aresultq, aresult)) { - 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) - { - 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); - String accId = proxy.getAccessionIdFromQuery(q); - dbr.setAccessionId(accId); - boolean rfound = false; - for (int r = 0; r < rs.length; r++) - { - if (rs[r] != null) - { - found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId); - if (found != null && found.length > 0) - { - rfound = true; - rs[r] = null; - } - } - } - 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() - + " from " + database.getSelectedItem()); + showErrorMessage("Error retrieving " + textArea.getText() + " from " + + database.getSelectedItem()); // error // +="Couldn't retrieve sequences from "+database.getSelectedItem(); System.err.println("Retrieval failed for source ='" @@ -700,11 +722,8 @@ 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 " - + database.getSelectedItem() + + 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) @@ -713,6 +732,7 @@ 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) { @@ -724,15 +744,15 @@ public class SequenceFetcher extends JPanel implements Runnable } AlignmentI ar = null; - if (isAliSource) + if (proxy.isAlignmentSource()) { addToLast = false; // new window for each result while (aresult.size() > 0) { presult.add(aresult.remove(0)); - presultTitle.add(aresultq.remove(0) + " " - + getDefaultRetrievalTitle()); + presultTitle.add( + aresultq.remove(0) + " " + getDefaultRetrievalTitle()); } } else @@ -754,22 +774,23 @@ public class SequenceFetcher extends JPanel implements Runnable { ar.append(aresult.remove(0)); } - ; } addToLast = true; presult.add(ar); presultTitle.add(titl); } } - guiWindow.setProgressBar(MessageManager - .getString("status.finshed_querying"), Thread.currentThread() - .hashCode()); + guiWindow.setProgressBar( + MessageManager.getString("status.finshed_querying"), + Thread.currentThread().hashCode()); } - guiWindow.setProgressBar( - (presult.size() > 0) ? MessageManager - .getString("status.parsing_results") : MessageManager - .getString("status.processing"), Thread.currentThread() - .hashCode()); + guiWindow + .setProgressBar( + (presult.size() > 0) + ? MessageManager + .getString("status.parsing_results") + : MessageManager.getString("status.processing"), + Thread.currentThread().hashCode()); // process results while (presult.size() > 0) { @@ -778,14 +799,15 @@ public class SequenceFetcher extends JPanel implements Runnable } // 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() - + " queries") + ": \n"); + + (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()) { @@ -803,6 +825,158 @@ public class SequenceFetcher extends JPanel implements Runnable } /** + * 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 + { + 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 + { + String query = multiacc.toString(); + AlignmentI rslt = proxy.getSequenceRecords(query); + if (rslt == null || rslt.getHeight() == 0) + { + // 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); + } + } + + /** + * 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) + { + 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; + } + + /** + * 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); + } + } + } + + /** * * @return a standard title for any results retrieved using the currently * selected source and settings @@ -813,7 +987,7 @@ public class SequenceFetcher extends JPanel implements Runnable } AlignmentI parseResult(AlignmentI al, String title, - String currentFileFormat, + FileFormatI currentFileFormat, FeatureSettingsModelI preferredFeatureColours) { @@ -841,15 +1015,11 @@ public class SequenceFetcher extends JPanel implements Runnable { for (SequenceI sq : alsqs) { - if ((sfs = sq.getSequenceFeatures()) != null) + if (sq.getFeatures().hasFeatures()) { - if (sfs.length > 0) - { - af.setShowSeqFeatures(true); - break; - } + af.setShowSeqFeatures(true); + break; } - } } @@ -859,9 +1029,12 @@ public class SequenceFetcher extends JPanel implements Runnable } if (Cache.getDefault("HIDE_INTRONS", true)) { - hideIntronsIfPresent(af); + af.hideFeatureColumns(SequenceOntologyI.EXON, false); + } + if (newAlframes != null) + { + newAlframes.add(af); } - Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -870,8 +1043,7 @@ public class SequenceFetcher extends JPanel implements Runnable try { - af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", - false)); + af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (Exception ex) { } @@ -884,25 +1056,6 @@ public class SequenceFetcher extends JPanel implements Runnable return al; } - /** - * Hide columns not containing 'exon' features, provided there are exon - * features on the alignment - * - * @param af - */ - public void hideIntronsIfPresent(AlignFrame af) - { - boolean hasExons = af.avc.markColumnsContainingFeatures(false, false, - false, - SequenceOntologyI.EXON); - if (hasExons) - { - af.avc.markColumnsContainingFeatures(true, false, true, - SequenceOntologyI.EXON); - af.getViewport().hideSelectedColumns(); - } - } - void showErrorMessage(final String error) { resetDialog(); @@ -911,9 +1064,9 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, error, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, error, MessageManager.getString("label.error_retrieving_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -927,4 +1080,27 @@ 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); + } + + public void setDatabaseChooserVisible(boolean b) + { + databaseButt.setVisible(b); + } }