X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=e05230bdb71f1e223acf5d7b80e05f9c73cee643;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=434029326c7860d4a076b47896b566bc4385e984;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 4340293..e05230b 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -28,6 +28,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; 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; @@ -51,7 +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; @@ -136,11 +136,10 @@ 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. @@ -157,18 +156,17 @@ 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() + if (sfetch == null || dasRegistry != Cache.getDasSourceRegistry() || lastDasSourceRegistry != (Cache.getDasSourceRegistry() - .getDasRegistryURL() + Cache.getDasSourceRegistry() - .getLocalSourceString()).hashCode()) + .getDasRegistryURL() + + Cache.getDasSourceRegistry().getLocalSourceString()) + .hashCode()) { _initingFetcher = true; initingThread = Thread.currentThread(); @@ -177,8 +175,9 @@ 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(); @@ -189,8 +188,8 @@ public class SequenceFetcher extends JPanel implements Runnable { guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); } - lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry - .getLocalSourceString()).hashCode(); + lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + + dasRegistry.getLocalSourceString()).hashCode(); sfetch = sf; _initingFetcher = false; initingThread = null; @@ -234,14 +233,12 @@ 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); } }); @@ -311,14 +308,15 @@ public class SequenceFetcher extends JPanel implements Runnable if (sourcep.getTier() == 0) { database.selection = Arrays - .asList(new DbSourceProxy[] { sourcep }); + .asList(new DbSourceProxy[] + { sourcep }); break; } } if (database.selection == null || database.selection.size() == 0) { - System.err.println("Ignoring fetch parameter db='" + selectedDb - + "'"); + System.err.println( + "Ignoring fetch parameter db='" + selectedDb + "'"); return false; } textArea.setText(queryString); @@ -379,9 +377,10 @@ public class SequenceFetcher extends JPanel implements Runnable 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")); } private void jbInit() throws Exception @@ -398,8 +397,8 @@ 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() { @@ -538,8 +537,9 @@ 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 })); boolean enablePunct = !(eq != null && eq.indexOf(",") > -1); for (DbSourceProxy dbs : database.getSelectedSources()) { @@ -621,7 +621,7 @@ 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 @@ -631,8 +631,8 @@ 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)"; } @@ -652,8 +652,8 @@ public class SequenceFetcher extends JPanel implements Runnable 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; @@ -673,13 +673,11 @@ public class SequenceFetcher extends JPanel implements Runnable try { // update status - guiWindow - .setProgressBar(MessageManager.formatMessage( - "status.fetching_sequence_queries_from", - new String[] { - Integer.valueOf(nqueries).toString(), - proxy.getDbName() }), Thread.currentThread() - .hashCode()); + guiWindow.setProgressBar(MessageManager.formatMessage( + "status.fetching_sequence_queries_from", new String[] + { Integer.valueOf(nqueries).toString(), + proxy.getDbName() }), + Thread.currentThread().hashCode()); if (proxy.getMaximumQueryCount() == 1) { /* @@ -703,8 +701,8 @@ public class SequenceFetcher extends JPanel implements Runnable } } 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 ='" @@ -714,9 +712,7 @@ public class SequenceFetcher extends JPanel implements Runnable } catch (OutOfMemoryError e) { 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) @@ -744,8 +740,8 @@ public class SequenceFetcher extends JPanel implements Runnable while (aresult.size() > 0) { presult.add(aresult.remove(0)); - presultTitle.add(aresultq.remove(0) + " " - + getDefaultRetrievalTitle()); + presultTitle.add( + aresultq.remove(0) + " " + getDefaultRetrievalTitle()); } } else @@ -773,15 +769,17 @@ public class SequenceFetcher extends JPanel implements Runnable 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) { @@ -794,8 +792,9 @@ public class SequenceFetcher extends JPanel implements Runnable { 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) { @@ -830,8 +829,7 @@ public class SequenceFetcher extends JPanel implements Runnable */ void fetchMultipleAccessions(DbSourceProxy proxy, Iterator accessions, List aresultq, - List aresult, List nextFetch) - throws Exception + List aresult, List nextFetch) throws Exception { StringBuilder multiacc = new StringBuilder(); List tosend = new ArrayList(); @@ -906,8 +904,9 @@ public class SequenceFetcher extends JPanel implements Runnable indres = proxy.getSequenceRecords(accession); } catch (OutOfMemoryError oome) { - new OOMWarning("fetching " + accession + " from " - + proxy.getDbName(), oome, this); + new OOMWarning( + "fetching " + accession + " from " + proxy.getDbName(), + oome, this); } if (indres != null) { @@ -917,9 +916,8 @@ public class SequenceFetcher extends JPanel implements Runnable } } catch (Exception e) { - Cache.log.info( - "Error retrieving " + accession + " from " - + proxy.getDbName(), e); + Cache.log.info("Error retrieving " + accession + " from " + + proxy.getDbName(), e); } return success; } @@ -978,7 +976,7 @@ public class SequenceFetcher extends JPanel implements Runnable } AlignmentI parseResult(AlignmentI al, String title, - String currentFileFormat, + FileFormatI currentFileFormat, FeatureSettingsModelI preferredFeatureColours) { @@ -1006,15 +1004,11 @@ 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; } - } } @@ -1059,9 +1053,9 @@ 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); } }); }