From 0d27ff1200cf5bcc9e1d79a37c5932ba0f8931d4 Mon Sep 17 00:00:00 2001 From: BobHanson Date: Tue, 2 Jun 2020 14:11:10 -0500 Subject: [PATCH] JAL-3446 from JAL-3253-applet SequenceFetcher as AsyncSwingWorker - uses a javajs.async.SwingJSUtils.StateMachine - implements a subclass of javajs.async.AsyncSwingWorker, which itself subclasses SwingWorker - also required some temporary adjustments for not yet having yet handled ApplicationSingleton on this branch - added one Preferences final static - integrates several older methods that together were able to cycle through a list of items to fetch from a list of possible source "proxies" - allows either synchronous (testng) or asynchronous operation simply by setting the StateMachine's mainLoop timer (0 == synchronous). - allows JavaScript to display a progress monitor - allows Java to use a simple Java built in ProgressMonitor for a SwingWorker-like operation. (easily tested, but not implemented here). - for more details, see javajs.async.AsyncSwingWorker JavaDoc. --- src/jalview/fts/core/GFTSPanel.java | 4 +- src/jalview/fts/service/pdb/PDBFTSPanel.java | 4 +- .../fts/service/uniprot/UniprotFTSPanel.java | 4 +- src/jalview/gui/AlignFrame.java | 3 +- src/jalview/gui/Desktop.java | 14 + src/jalview/gui/Preferences.java | 4 + src/jalview/gui/SequenceFetcher.java | 600 +++++++++++++------- src/jalview/ws/DBRefFetcher.java | 2 +- src/jalview/ws/SequenceFetcher.java | 13 + test/jalview/io/CrossRef2xmlTests.java | 2 +- 10 files changed, 416 insertions(+), 234 deletions(-) diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java index 7ff0f75..e9fd33e 100644 --- a/src/jalview/fts/core/GFTSPanel.java +++ b/src/jalview/fts/core/GFTSPanel.java @@ -916,9 +916,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI public void transferToSequenceFetcher(String ids) { - seqFetcher.setQuery(ids); - Thread worker = new Thread(seqFetcher); - worker.start(); + seqFetcher.fetch(ids, true); } @Override diff --git a/src/jalview/fts/service/pdb/PDBFTSPanel.java b/src/jalview/fts/service/pdb/PDBFTSPanel.java index 2dd0f8c..7a2fe83 100644 --- a/src/jalview/fts/service/pdb/PDBFTSPanel.java +++ b/src/jalview/fts/service/pdb/PDBFTSPanel.java @@ -222,9 +222,7 @@ public class PDBFTSPanel extends GFTSPanel } String ids = selectedIds.toString(); - seqFetcher.setQuery(ids); - Thread worker = new Thread(seqFetcher); - worker.start(); + seqFetcher.fetch(ids, true); delayAndEnableActionButtons(); } diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java index 182e29b..2d7894f 100644 --- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java +++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java @@ -221,9 +221,7 @@ public class UniprotFTSPanel extends GFTSPanel } String ids = selectedIds.toString(); - seqFetcher.setQuery(ids); - Thread worker = new Thread(seqFetcher); - worker.start(); + seqFetcher.fetch(ids, true); delayAndEnableActionButtons(); } diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 29f6a2e..71fc831 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -5173,13 +5173,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher - .getSequenceFetcherSingleton(); javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { + final jalview.ws.SequenceFetcher sf = jalview.ws.SequenceFetcher.getInstance(); String[] dbclasses = sf.getNonAlignmentSources(); List otherdb; JMenu dfetch = new JMenu(); diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 1b85dd5..df76433 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -22,6 +22,7 @@ package jalview.gui; import java.awt.BorderLayout; import java.awt.Color; +import java.awt.Component; import java.awt.Dimension; import java.awt.FontMetrics; import java.awt.Graphics; @@ -3375,4 +3376,17 @@ public class Desktop extends jalview.jbgui.GDesktop return result; } + + /** + * BH just a placeholder until we get the singletons in place; for SequenceFetcher test + * + * @return + */ + + public static MyDesktopPane getDesktopPane() + { + Desktop desktop = Desktop.getInstance(); + // BH SwingJS TODO + return desktop == null ? null : desktop.desktop; + } } diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 55345e0..7d29e1e 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -173,10 +173,14 @@ public class Preferences extends GPreferences public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP"; + public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN"; + public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS"; public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION"; + public static final String SHOW_IDENTITY = "SHOW_IDENTITY"; + public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX"; public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP"; diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 8b5d3b7..ded241b 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -36,6 +36,7 @@ import jalview.util.Platform; import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; +import java.awt.Component; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -57,6 +58,8 @@ import javax.swing.JScrollPane; import javax.swing.JTextArea; import javax.swing.SwingConstants; +import javajs.async.AsyncSwingWorker; + /** * A panel where the use may choose a database source, and enter one or more * accessions, to retrieve entries from the database. @@ -64,9 +67,9 @@ import javax.swing.SwingConstants; * If the selected source is Uniprot or PDB, a free text search panel is opened * instead to perform the search and selection. */ -public class SequenceFetcher extends JPanel implements Runnable +@SuppressWarnings("serial") +public class SequenceFetcher extends JPanel { - private static jalview.ws.SequenceFetcher sfetch = null; JLabel exampleAccession; @@ -97,20 +100,6 @@ public class SequenceFetcher extends JPanel implements Runnable volatile boolean _isConstructing = false; /** - * Returns the shared instance of the SequenceFetcher client - * - * @return - */ - public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton() - { - if (sfetch == null) - { - sfetch = new jalview.ws.SequenceFetcher(); - } - return sfetch; - } - - /** * Constructor given a client to receive any status or progress messages * (currently either the Desktop, or an AlignFrame panel) * @@ -132,7 +121,7 @@ public class SequenceFetcher extends JPanel implements Runnable final String selectedDb, final String queryString) { this.progressIndicator = guiIndic; - getSequenceFetcherSingleton(); + this.guiWindow = progressIndicator; if (progressIndicator instanceof AlignFrame) @@ -145,8 +134,8 @@ public class SequenceFetcher extends JPanel implements Runnable frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, - Platform.isAMacAndNotJS() ? 240 : 180); + Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, + Platform.isAMacAndNotJS() ? 240 : 180); } private String getFrameTitle() @@ -164,7 +153,8 @@ public class SequenceFetcher extends JPanel implements Runnable database = new JComboBox<>(); database.setFont(JvSwingUtils.getLabelFont()); database.setPrototypeDisplayValue("ENSEMBLGENOMES "); - String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb(); + String[] sources = jalview.ws.SequenceFetcher.getInstance() + .getSupportedDb(); Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER); database.addItem(MessageManager.getString("action.select_ddbb")); for (String source : sources) @@ -315,7 +305,8 @@ public class SequenceFetcher extends JPanel implements Runnable { StringBuilder sb = new StringBuilder(); HashSet hs = new HashSet<>(); - for (DbSourceProxy dbs : sfetch.getSourceProxy(db)) + for (DbSourceProxy dbs : jalview.ws.SequenceFetcher.getInstance() + .getSourceProxy(db)) { String tq = dbs.getTestQuery(); if (hs.add(tq)) // not a duplicate source @@ -424,9 +415,9 @@ public class SequenceFetcher extends JPanel implements Runnable text = text.replace(",", ";"); } text = text.replaceAll("(\\s|[; ])+", ";"); - if (!t0.equals(text)) + if (!t0.equals(text)) { - textArea.setText(text); + textArea.setText(text); } if (text.isEmpty()) { @@ -436,25 +427,34 @@ public class SequenceFetcher extends JPanel implements Runnable resetDialog(); return; } - if (database.getSelectedIndex() == 0) - { - // todo i18n - showErrorMessage("Please choose a database"); - resetDialog(); - return; - } - exampleBtn.setEnabled(false); textArea.setEnabled(false); okBtn.setEnabled(false); closeBtn.setEnabled(false); backBtn.setEnabled(false); + fetch(null, true); + } - Thread worker = new Thread(this); - worker.start(); + public void fetch(String ids, boolean isAsync) + { + if (ids == null) + { + ids = textArea.getText(); + } + else + { + textArea.setText(ids); + } + Component parent = null; // or this + String title = null; // or some title for the progress monitor + int min = AsyncFetchTask.STATE_INIT; + int max = AsyncFetchTask.STATE_DONE; + int msDelay = (isAsync ? 5 : 0); + new AsyncFetchTask(ids, parent, title, msDelay, min, max).execute(); } - private void resetDialog() + + protected void resetDialog() { exampleBtn.setEnabled(true); textArea.setEnabled(true); @@ -463,176 +463,364 @@ public class SequenceFetcher extends JPanel implements Runnable backBtn.setEnabled(parentSearchPanel != null); } - @Override - public void run() + /** + * This asynchronous class allows for a single-threaded state machine + * SwingWorker to process a list of requests from multiple sources. + * + * A standard ProcessMonitor could be attached to this task, but it is + * currently not. + * + * @author hansonr + * + */ + private class AsyncFetchTask extends AsyncSwingWorker { - boolean addToLast = false; - List aresultq = new ArrayList<>(); - List presultTitle = new ArrayList<>(); - List presult = new ArrayList<>(); - List aresult = new ArrayList<>(); - List sources = sfetch - .getSourceProxy((String) database.getSelectedItem()); - Iterator proxies = sources.iterator(); - String[] qries = textArea.getText().trim().split(";"); - List nextFetch = Arrays.asList(qries); - Iterator en = Arrays.asList(new String[0]).iterator(); - int nqueries = qries.length; - - FeatureSettingsModelI preferredFeatureColours = null; - while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0)) - { - if (!en.hasNext() && nextFetch.size() > 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 + protected boolean addToLast = false; + + protected List aresultq = new ArrayList<>(); + + protected List presultTitle = new ArrayList<>(); + + protected List presult = new ArrayList<>(); + + protected List aresult = new ArrayList<>(); + + protected FeatureSettingsModelI preferredFeatureColours = null; + + protected List sources; + + protected Iterator sourceIterator; + + protected String[] fetchArray; + + protected List fetchList; + + protected Iterator fetchIterator; + + protected int fetchCount; + + protected DbSourceProxy source; + + protected String ids; + + protected long myID; + + protected boolean isAsync; + + protected Throwable taskError; + + public AsyncFetchTask(String ids, Component owner, String title, + int delayMillis, + int min, int max) + { + super(owner, title, delayMillis, min, max); + this.ids = ids; + isAsync = (delayMillis != 0); + myID = Thread.currentThread().getId(); + } + + @Override + public void initAsync() + { + sources = jalview.ws.SequenceFetcher.getInstance() + .getSourceProxy((String) database.getSelectedItem()); + sourceIterator = sources.iterator(); + fetchArray = ids.trim().split(";"); + fetchList = Arrays.asList(fetchArray); + } + + private final static int STATE_INIT = 0; + + private final static int STATE_NEXT_SOURCE = 10; + + private final static int STATE_FETCH_SINGLE = 30; + + private final static int STATE_FETCH_MULTIPLE = 40; + + private final static int STATE_PROCESS = 50; + + private final static int STATE_PARSE_RESULTS = 80; + + private final static int STATE_DONE = 100; + + protected static final int STATE_TASK_ERROR = 99; + + @Override + public int doInBackgroundAsync(int progress) + { + System.out.println("SequenceFetcher.AsyncFetchTask " + isAsync + " " + + progress + " " + + taskError); + switch (progress) { - // update status - guiWindow.setProgressBar(MessageManager.formatMessage( + case STATE_INIT: + case STATE_NEXT_SOURCE: + boolean doneFetching = (fetchIterator == null + || !fetchIterator.hasNext()); + boolean havePending = (fetchList.size() > 0); + if (!sourceIterator.hasNext() || doneFetching && !havePending) + { + showProgress((presult.size() > 0) + ? MessageManager.getString("status.parsing_results") + : MessageManager.getString("status.processing")); + return STATE_PARSE_RESULTS; + } + source = sourceIterator.next(); + if (doneFetching) + { + // if we are here, we must have some pending still + fetchCount = fetchList.size(); + fetchIterator = fetchList.iterator(); + // save the remaining queries in the original array + fetchArray = fetchList.toArray(new String[fetchCount]); + // and clear the + fetchList = new ArrayList<>(); + } + showProgress(MessageManager.formatMessage( "status.fetching_sequence_queries_from", new String[] - { Integer.valueOf(nqueries).toString(), - proxy.getDbName() }), - Thread.currentThread().hashCode()); - if (proxy.getMaximumQueryCount() == 1) + { Integer.valueOf(fetchCount).toString(), + source.getDbName() })); + return (source.getMaximumQueryCount() == 1 ? STATE_FETCH_SINGLE + : STATE_FETCH_MULTIPLE); + case STATE_FETCH_SINGLE: + if (fetchIterator.hasNext()) { - /* - * proxy only handles one accession id at a time - */ - while (en.hasNext()) + return runSubtask(new Runnable() { - String acc = en.next(); - if (!fetchSingleAccession(proxy, acc, aresultq, aresult)) + + @Override + public void run() { - nextFetch.add(acc); + // source only handles one accession id at a time + try + { + if (!isAsync) + { + // for CrossRef2xmlTest only; to "allow the server to breathe" + // (but we are doing that already when isAsync is true) + Thread.sleep(5); + } + String notFound = fetchSingleAccession(source, + fetchIterator.next(), aresultq, aresult); + if (notFound != null) + { + fetchList.add(notFound); + } + } catch (Throwable e) + { + taskError = e; + } } - } + }); } - else + return STATE_PROCESS; + case STATE_FETCH_MULTIPLE: + // proxy can fetch multiple accessions at one time + setProgressAsync(STATE_PROCESS); + return runSubtask(new Runnable() { - /* - * 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(); - } - // Stack results ready for opening in alignment windows - if (aresult != null && aresult.size() > 0) - { - FeatureSettingsModelI proxyColourScheme = proxy - .getFeatureColourScheme(); - if (proxyColourScheme != null) - { - preferredFeatureColours = proxyColourScheme; - } + @Override + public void run() + { + try + { + fetchMultipleAccessions(source, fetchIterator, aresultq, + aresult, fetchList); + } catch (Throwable e) + { + taskError = e; + } + } - AlignmentI ar = null; - if (proxy.isAlignmentSource()) + }); + case STATE_PROCESS: + // Stack results ready for opening in alignment windows + if (aresult != null && aresult.size() > 0) { - addToLast = false; - // new window for each result - while (aresult.size() > 0) + FeatureSettingsModelI proxyColourScheme = source + .getFeatureColourScheme(); + if (proxyColourScheme != null) { - presult.add(aresult.remove(0)); - presultTitle.add( - aresultq.remove(0) + " " + getDefaultRetrievalTitle()); + preferredFeatureColours = proxyColourScheme; } - } - else - { - String titl = null; - if (addToLast && presult.size() > 0) + + AlignmentI ar = null; + if (source.isAlignmentSource()) { - ar = presult.remove(presult.size() - 1); - titl = presultTitle.remove(presultTitle.size() - 1); + addToLast = false; + // new window for each result + while (aresult.size() > 0) + { + presult.add(aresult.remove(0)); + presultTitle.add(aresultq.remove(0) + " " + + getDefaultRetrievalTitle()); + } } - // concatenate all results in one window - while (aresult.size() > 0) + else { - if (ar == null) + String titl = null; + if (addToLast && presult.size() > 0) { - ar = aresult.remove(0); + ar = presult.remove(presult.size() - 1); + titl = presultTitle.remove(presultTitle.size() - 1); } - else + // concatenate all results in one window + while (aresult.size() > 0) { - ar.append(aresult.remove(0)); + if (ar == null) + { + ar = aresult.remove(0); + } + else + { + ar.append(aresult.remove(0)); + } } + addToLast = true; + presult.add(ar); + presultTitle.add(titl); } - addToLast = true; - presult.add(ar); - presultTitle.add(titl); } + showProgress(MessageManager.getString("status.finshed_querying")); + return STATE_NEXT_SOURCE; + case STATE_PARSE_RESULTS: + while (presult.size() > 0) + { + parseResult(presult.remove(0), presultTitle.remove(0), null, + preferredFeatureColours); + } + break; + case STATE_TASK_ERROR: + showProgress(null); + super.cancelAsync(); + return 0; // arbitrary; ignored } - guiWindow.setProgressBar( - MessageManager.getString("status.finshed_querying"), - Thread.currentThread().hashCode()); + return STATE_DONE; } - guiWindow - .setProgressBar( - (presult.size() > 0) - ? MessageManager - .getString("status.parsing_results") - : MessageManager.getString("status.processing"), - Thread.currentThread().hashCode()); - // process results - while (presult.size() > 0) - { - parseResult(presult.remove(0), presultTitle.remove(0), null, - preferredFeatureColours); + + protected void resume() + { + if (!isAsync) + { + return; + } + super.setPaused(false); + super.stateLoop(); } - // 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) + + private int runSubtask(Runnable subtask) + { + + Runnable r = new Runnable() { - if (l != sb.length()) + + @Override + public void run() { - sb.append("; "); + try + { + subtask.run(); + } catch (Throwable e) + { + taskError = e; + } + if (checkError(taskError)) + { + setProgressAsync(STATE_TASK_ERROR); + } + else + { + taskError = null; + } + if (isAsync) + { + resume(); + } } - if (lr - sb.length() > 40) + }; + + if (isAsync) + { + super.setPaused(true); + new Thread(r).start(); + return 0; // arbitrary return -- ignored because we are paused. + } + r.run(); + return super.getProgressAsync(); + } + + @Override + public void doneAsync() + { + showProgress(null); + if (fetchList.size() > 0) + { + StringBuffer sb = new StringBuffer(); + sb.append("Didn't retrieve the following " + + (fetchList.size() == 1 ? "query" + : fetchList.size() + " queries") + + ": \n"); + int l = sb.length(), lr = 0; + for (String s : fetchList) { - sb.append("\n"); + if (l != sb.length()) + { + sb.append("; "); + } + if (lr - sb.length() > 40) + { + sb.append("\n"); + } + sb.append(s); } - sb.append(s); + showErrorMessage(sb.toString()); } - showErrorMessage(sb.toString()); + resetDialog(); } - resetDialog(); + + /** + * + * @param e + * @return true if there was an error and we need to STOP + */ + protected boolean checkError(Throwable e) + { + if (e == null) + { + return false; + } + String problem = "retrieving " + ids + " from " + + database.getSelectedItem(); + if (e instanceof Exception) + { + showErrorMessage("Error " + problem); + System.err.println("Retrieval failed for source ='" + + database.getSelectedItem() + "' and query\n'" + + ids + "'\n"); + } + else if (e instanceof OutOfMemoryError) + { + showErrorMessage("Out of Memory when " + problem + + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n"); + // option here to return false and quit this, but that is not how + // original code works - BH + // return false; + } + else + { + showErrorMessage("Serious Error " + problem); + } + e.printStackTrace(); + return true; + } + + private void showProgress(String msg) + { + guiWindow.setProgressBar(msg, myID); + } + } /** @@ -700,48 +888,19 @@ public class SequenceFetcher extends JPanel implements Runnable * 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 + * @return null if the fetch was successful; the accession if not */ - boolean fetchSingleAccession(DbSourceProxy proxy, String accession, - List aresultq, List aresult) + String fetchSingleAccession(DbSourceProxy proxy, String accession, + List aresultq, List aresult) throws Throwable { - 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) + AlignmentI indres = proxy.getSequenceRecords(accession); + if (indres == null) { - Cache.log.info("Error retrieving " + accession + " from " - + proxy.getDbName(), e); + return accession; } - return success; + aresultq.add(accession); + aresult.add(indres); + return null; } /** @@ -761,12 +920,12 @@ public class SequenceFetcher extends JPanel implements Runnable for (String q : queries) { - // BH 2019.01.25 dbr is never used. -// DBRefEntry dbr = new DBRefEntry(); -// dbr.setSource(proxy.getDbSource()); -// dbr.setVersion(null); + // BH 2019.01.25 dbr is never used. + // DBRefEntry dbr = new DBRefEntry(); + // dbr.setSource(proxy.getDbSource()); + // dbr.setVersion(null); String accId = proxy.getAccessionIdFromQuery(q); -// dbr.setAccessionId(accId); + // dbr.setAccessionId(accId); boolean rfound = false; for (int r = 0, nr = rs.length; r < nr; r++) { @@ -835,7 +994,7 @@ public class SequenceFetcher extends JPanel implements Runnable { af.getViewport().applyFeaturesStyle(preferredFeatureColours); } - if (Cache.getDefault("HIDE_INTRONS", true)) + if (Cache.getDefault(Preferences.HIDE_INTRONS, true)) { af.hideFeatureColumns(SequenceOntologyI.EXON, false); } @@ -847,7 +1006,8 @@ public class SequenceFetcher extends JPanel implements Runnable try { - af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false)); + af.setMaximum( + Cache.getDefault(Preferences.SHOW_FULLSCREEN, false)); } catch (Exception ex) { } @@ -868,7 +1028,8 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, error, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + error, MessageManager.getString("label.error_retrieving_data"), JvOptionPane.WARNING_MESSAGE); } @@ -894,11 +1055,6 @@ public class SequenceFetcher extends JPanel implements Runnable frame.setVisible(false); } - public void setQuery(String ids) - { - textArea.setText(ids); - } - /** * Called to modify the search panel for embedding as an alternative tab of a * free text search panel. The database choice list is hidden (since the @@ -913,4 +1069,6 @@ public class SequenceFetcher extends JPanel implements Runnable backBtn.setVisible(true); parentSearchPanel = parentPanel; } + + } diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 7daa7b4..0290919 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -134,7 +134,7 @@ public class DBRefFetcher implements Runnable } this.dataset = ds; // TODO Jalview 2.5 lots of this code should be in the gui package! - sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(); + sfetcher = jalview.ws.SequenceFetcher.getInstance(); // set default behaviour for transferring excess sequence data to the // dataset trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true); diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java index a480176..0612530 100644 --- a/src/jalview/ws/SequenceFetcher.java +++ b/src/jalview/ws/SequenceFetcher.java @@ -90,4 +90,17 @@ public class SequenceFetcher extends ASequenceFetcher Collections.sort(src, String.CASE_INSENSITIVE_ORDER); return src.toArray(new String[src.size()]); } + + private static SequenceFetcher mockFetcher; + + /** + * used in jalview.gui.SequenceFetcher + * + * @return + */ + public static SequenceFetcher getInstance() + { + return (mockFetcher == null ? mockFetcher = new SequenceFetcher() : mockFetcher); + } + } diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index 3ca6ed8..120a4f7 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -186,7 +186,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase SequenceFetcher sf = new SequenceFetcher(Desktop.instance, forSource, forAccession); - sf.run(); + sf.fetch(null, false); AlignFrame[] afs = Desktop.getAlignFrames(); if (afs.length == 0) { -- 1.7.10.2