") + .append("

Version: ") + .append(Cache.getProperty("VERSION")).append("

") + .append("Built: ") + .append(Cache.getDefault("BUILD_DATE", "unknown")) + .append(" from ").append(Cache.getBuildDetailsForSplash()) + .append(""); - message.append("Version " - + jalview.bin.Cache.getProperty("VERSION") - + "; last updated: " - + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); - } - - if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") - .equals("Checking")) + String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking"); + if (latestVersion.equals("Checking")) { - message.append("
...Checking latest version...
"); + // JBP removed this message for 2.11: May be reinstated in future version + // message.append("
...Checking latest version...
"); } - else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") - .equals(jalview.bin.Cache.getProperty("VERSION"))) + else if (!latestVersion.equals(Cache.getProperty("VERSION"))) { boolean red = false; - if (jalview.bin.Cache.getProperty("VERSION").toLowerCase() + if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT) .indexOf("automated build") == -1) { red = true; @@@ -1795,9 -1612,9 +1795,9 @@@ MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE); } - setProgressBar(null, choice.hashCode()); + setProgressBar(null, chosenFile.hashCode()); } - }).start(); + }, "SaveJalviewProjectThread").start(); } } @@@ -2015,162 -1825,476 +2015,161 @@@ if (desktop != null) { AlignFrame[] frames = Desktop.getAlignFrames(); - - for (AlignFrame afr : frames) - { - if (sequenceSetId == null || afr.getViewport().getSequenceSetId() - .equals(sequenceSetId)) - { - if (afr.alignPanels != null) - { - for (AlignmentPanel ap : afr.alignPanels) - { - if (sequenceSetId == null - || sequenceSetId.equals(ap.av.getSequenceSetId())) - { - viewp.add(ap.av); - } - } - } - else - { - viewp.add(afr.getViewport()); - } - } - } - if (viewp.size() > 0) - { - return viewp.toArray(new AlignmentViewport[viewp.size()]); - } - } - return null; - } - - /** - * Explode the views in the given frame into separate AlignFrame - * - * @param af - */ - public static void explodeViews(AlignFrame af) - { - int size = af.alignPanels.size(); - if (size < 2) - { - return; - } - - for (int i = 0; i < size; i++) - { - AlignmentPanel ap = af.alignPanels.get(i); - AlignFrame newaf = new AlignFrame(ap); - - /* - * Restore the view's last exploded frame geometry if known. Multiple - * views from one exploded frame share and restore the same (frame) - * position and size. - */ - Rectangle geometry = ap.av.getExplodedGeometry(); - if (geometry != null) - { - newaf.setBounds(geometry); - } - - ap.av.setGatherViewsHere(false); - - addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - } - - af.alignPanels.clear(); - af.closeMenuItem_actionPerformed(true); - - } - - /** - * Gather expanded views (separate AlignFrame's) with the same sequence set - * identifier back in to this frame as additional views, and close the - * expanded views. Note the expanded frames may themselves have multiple - * views. We take the lot. - * - * @param source - */ - public void gatherViews(AlignFrame source) - { - source.viewport.setGatherViewsHere(true); - source.viewport.setExplodedGeometry(source.getBounds()); - JInternalFrame[] frames = desktop.getAllFrames(); - String viewId = source.viewport.getSequenceSetId(); - - for (int t = 0; t < frames.length; t++) - { - if (frames[t] instanceof AlignFrame && frames[t] != source) - { - AlignFrame af = (AlignFrame) frames[t]; - boolean gatherThis = false; - for (int a = 0; a < af.alignPanels.size(); a++) - { - AlignmentPanel ap = af.alignPanels.get(a); - if (viewId.equals(ap.av.getSequenceSetId())) - { - gatherThis = true; - ap.av.setGatherViewsHere(false); - ap.av.setExplodedGeometry(af.getBounds()); - source.addAlignmentPanel(ap, false); - } - } - - if (gatherThis) - { - af.alignPanels.clear(); - af.closeMenuItem_actionPerformed(true); - } - } - } - - } - - jalview.gui.VamsasApplication v_client = null; - - @Override - public void vamsasImport_actionPerformed(ActionEvent e) - { - if (v_client == null) - { - // Load and try to start a session. - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.open_saved_vamsas_session")); - chooser.setToolTipText(MessageManager.getString( - "label.select_vamsas_session_opened_as_new_vamsas_session")); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String fle = chooser.getSelectedFile().toString(); - if (!vamsasImport(chooser.getSelectedFile())) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.couldnt_import_as_vamsas_session", - new Object[] - { fle }), - MessageManager - .getString("label.vamsas_document_import_failed"), - JvOptionPane.ERROR_MESSAGE); - } - } - } - else - { - jalview.bin.Cache.log.error( - "Implementation error - load session from a running session is not supported."); - } - } - - /** - * import file into a new vamsas session (uses jalview.gui.VamsasApplication) - * - * @param file - * @return true if import was a success and a session was started. - */ - public boolean vamsasImport(URL url) - { - // TODO: create progress bar - if (v_client != null) - { - - jalview.bin.Cache.log.error( - "Implementation error - load session from a running session is not supported."); - return false; - } - - try - { - // copy the URL content to a temporary local file - // TODO: be a bit cleverer here with nio (?!) - File file = File.createTempFile("vdocfromurl", ".vdj"); - FileOutputStream fos = new FileOutputStream(file); - BufferedInputStream bis = new BufferedInputStream(url.openStream()); - byte[] buffer = new byte[2048]; - int ln; - while ((ln = bis.read(buffer)) > -1) - { - fos.write(buffer, 0, ln); - } - bis.close(); - fos.close(); - v_client = new jalview.gui.VamsasApplication(this, file, - url.toExternalForm()); - } catch (Exception ex) - { - jalview.bin.Cache.log.error( - "Failed to create new vamsas session from contents of URL " - + url, - ex); - return false; - } - setupVamsasConnectedGui(); - v_client.initial_update(); // TODO: thread ? - return v_client.inSession(); - } - - /** - * import file into a new vamsas session (uses jalview.gui.VamsasApplication) - * - * @param file - * @return true if import was a success and a session was started. - */ - public boolean vamsasImport(File file) - { - if (v_client != null) - { - - jalview.bin.Cache.log.error( - "Implementation error - load session from a running session is not supported."); - return false; - } - - setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); - try - { - v_client = new jalview.gui.VamsasApplication(this, file, null); - } catch (Exception ex) - { - setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); - jalview.bin.Cache.log.error( - "New vamsas session from existing session file failed:", ex); - return false; - } - setupVamsasConnectedGui(); - v_client.initial_update(); // TODO: thread ? - setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); - return v_client.inSession(); - } - - public boolean joinVamsasSession(String mysesid) - { - if (v_client != null) - { - throw new Error(MessageManager - .getString("error.try_join_vamsas_session_another")); - } - if (mysesid == null) - { - throw new Error( - MessageManager.getString("error.invalid_vamsas_session_id")); - } - v_client = new VamsasApplication(this, mysesid); - setupVamsasConnectedGui(); - v_client.initial_update(); - return (v_client.inSession()); - } - - @Override - public void vamsasStart_actionPerformed(ActionEvent e) - { - if (v_client == null) - { - // Start a session. - // we just start a default session for moment. - /* - * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - * getProperty("LAST_DIRECTORY")); - * - * chooser.setFileView(new JalviewFileView()); - * chooser.setDialogTitle("Load Vamsas file"); - * chooser.setToolTipText("Import"); - * - * int value = chooser.showOpenDialog(this); - * - * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new - * jalview.gui.VamsasApplication(this, chooser.getSelectedFile()); - */ - v_client = new VamsasApplication(this); - setupVamsasConnectedGui(); - v_client.initial_update(); // TODO: thread ? - } - else - { - // store current data in session. - v_client.push_update(); // TODO: thread - } - } - - protected void setupVamsasConnectedGui() - { - vamsasStart.setText(MessageManager.getString("label.session_update")); - vamsasSave.setVisible(true); - vamsasStop.setVisible(true); - vamsasImport.setVisible(false); // Document import to existing session is - // not possible for vamsas-client-1.0. - } - - protected void setupVamsasDisconnectedGui() - { - vamsasSave.setVisible(false); - vamsasStop.setVisible(false); - vamsasImport.setVisible(true); - vamsasStart - .setText(MessageManager.getString("label.new_vamsas_session")); - } - - @Override - public void vamsasStop_actionPerformed(ActionEvent e) - { - if (v_client != null) - { - v_client.end_session(); - v_client = null; - setupVamsasDisconnectedGui(); - } - } - - protected void buildVamsasStMenu() - { - if (v_client == null) - { - String[] sess = null; - try - { - sess = VamsasApplication.getSessionList(); - } catch (Exception e) + + for (AlignFrame afr : frames) { - jalview.bin.Cache.log.warn("Problem getting current sessions list.", - e); - sess = null; - } - if (sess != null) - { - jalview.bin.Cache.log.debug( - "Got current sessions list: " + sess.length + " entries."); - VamsasStMenu.removeAll(); - for (int i = 0; i < sess.length; i++) - { - JMenuItem sessit = new JMenuItem(); - sessit.setText(sess[i]); - sessit.setToolTipText(MessageManager - .formatMessage("label.connect_to_session", new Object[] - { sess[i] })); - final Desktop dsktp = this; - final String mysesid = sess[i]; - sessit.addActionListener(new ActionListener() + if (sequenceSetId == null || afr.getViewport().getSequenceSetId() + .equals(sequenceSetId)) + { + if (afr.alignPanels != null) { - - @Override - public void actionPerformed(ActionEvent e) + for (AlignmentPanel ap : afr.alignPanels) { - if (dsktp.v_client == null) + if (sequenceSetId == null + || sequenceSetId.equals(ap.av.getSequenceSetId())) { - Thread rthr = new Thread(new Runnable() - { - - @Override - public void run() - { - dsktp.v_client = new VamsasApplication(dsktp, mysesid); - dsktp.setupVamsasConnectedGui(); - dsktp.v_client.initial_update(); - } - - }, "VamsasSessionThread"); - rthr.start(); + viewp.add(ap.av); } - }; - }); - VamsasStMenu.add(sessit); + } + } + else + { + viewp.add(afr.getViewport()); + } } - // don't show an empty menu. - VamsasStMenu.setVisible(sess.length > 0); - } - else + if (viewp.size() > 0) { - jalview.bin.Cache.log.debug("No current vamsas sessions."); - VamsasStMenu.removeAll(); - VamsasStMenu.setVisible(false); + return viewp.toArray(new AlignmentViewport[viewp.size()]); } } - else - { - // Not interested in the content. Just hide ourselves. - VamsasStMenu.setVisible(false); - } + return null; } - @Override - public void vamsasSave_actionPerformed(ActionEvent e) + /** + * Explode the views in the given frame into separate AlignFrame + * + * @param af + */ + public static void explodeViews(AlignFrame af) { - if (v_client != null) + int size = af.alignPanels.size(); + if (size < 2) { - // TODO: VAMSAS DOCUMENT EXTENSION is VDJ - JalviewFileChooser chooser = new JalviewFileChooser("vdj", - "Vamsas Document"); + return; + } - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.save_vamsas_document_archive")); + // FIXME: ideally should use UI interface API + FeatureSettings viewFeatureSettings = (af.featureSettings != null + && af.featureSettings.isOpen()) ? af.featureSettings : null; + Rectangle fsBounds = af.getFeatureSettingsGeometry(); + for (int i = 0; i < size; i++) + { + AlignmentPanel ap = af.alignPanels.get(i); - int value = chooser.showSaveDialog(this); + AlignFrame newaf = new AlignFrame(ap); - if (value == JalviewFileChooser.APPROVE_OPTION) + // transfer reference for existing feature settings to new alignFrame + if (ap == af.alignPanel) { - java.io.File choice = chooser.getSelectedFile(); - JPanel progpanel = addProgressPanel(MessageManager - .formatMessage("label.saving_vamsas_doc", new Object[] - { choice.getName() })); - Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - String warnmsg = null; - String warnttl = null; - try + if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) { - v_client.vclient.storeDocument(choice); - } catch (Error ex) - { - warnttl = "Serious Problem saving Vamsas Document"; - warnmsg = ex.toString(); - jalview.bin.Cache.log - .error("Error Whilst saving document to " + choice, ex); + newaf.featureSettings = viewFeatureSettings; + } + newaf.setFeatureSettingsGeometry(fsBounds); + } - } catch (Exception ex) - { - warnttl = "Problem saving Vamsas Document."; - warnmsg = ex.toString(); - jalview.bin.Cache.log.warn( - "Exception Whilst saving document to " + choice, ex); + /* + * Restore the view's last exploded frame geometry if known. Multiple views from + * one exploded frame share and restore the same (frame) position and size. + */ + Rectangle geometry = ap.av.getExplodedGeometry(); + if (geometry != null) + { + newaf.setBounds(geometry); + } - } - removeProgressPanel(progpanel); - if (warnmsg != null) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + ap.av.setGatherViewsHere(false); - warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); - } + addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + // and materialise a new feature settings dialog instance for the new + // alignframe + // (closes the old as if 'OK' was pressed) + if (ap == af.alignPanel && newaf.featureSettings != null + && newaf.featureSettings.isOpen() + && af.alignPanel.getAlignViewport().isShowSequenceFeatures()) + { + newaf.showFeatureSettingsUI(); } } - } - JPanel vamUpdate = null; + af.featureSettings = null; + af.alignPanels.clear(); + af.closeMenuItem_actionPerformed(true); + + } /** - * hide vamsas user gui bits when a vamsas document event is being handled. + * Gather expanded views (separate AlignFrame's) with the same sequence set + * identifier back in to this frame as additional views, and close the + * expanded views. Note the expanded frames may themselves have multiple + * views. We take the lot. * - * @param b - * true to hide gui, false to reveal gui + * @param source */ - public void setVamsasUpdate(boolean b) + public void gatherViews(AlignFrame source) { - Cache.log.debug("Setting gui for Vamsas update " - + (b ? "in progress" : "finished")); - - if (vamUpdate != null) + source.viewport.setGatherViewsHere(true); + source.viewport.setExplodedGeometry(source.getBounds()); + JInternalFrame[] frames = desktop.getAllFrames(); + String viewId = source.viewport.getSequenceSetId(); + for (int t = 0; t < frames.length; t++) { - this.removeProgressPanel(vamUpdate); + if (frames[t] instanceof AlignFrame && frames[t] != source) + { + AlignFrame af = (AlignFrame) frames[t]; + boolean gatherThis = false; + for (int a = 0; a < af.alignPanels.size(); a++) + { + AlignmentPanel ap = af.alignPanels.get(a); + if (viewId.equals(ap.av.getSequenceSetId())) + { + gatherThis = true; + ap.av.setGatherViewsHere(false); + ap.av.setExplodedGeometry(af.getBounds()); + source.addAlignmentPanel(ap, false); + } + } + + if (gatherThis) + { + if (af.featureSettings != null && af.featureSettings.isOpen()) + { + if (source.featureSettings == null) + { + // preserve the feature settings geometry for this frame + source.featureSettings = af.featureSettings; + source.setFeatureSettingsGeometry( + af.getFeatureSettingsGeometry()); + } + else + { + // close it and forget + af.featureSettings.close(); + } + } + af.alignPanels.clear(); + af.closeMenuItem_actionPerformed(true); + } + } } - if (b) + + // refresh the feature setting UI for the source frame if it exists + if (source.featureSettings != null && source.featureSettings.isOpen()) { - vamUpdate = this.addProgressPanel( - MessageManager.getString("label.updating_vamsas_session")); + source.showFeatureSettingsUI(); } - - vamsasStart.setVisible(!b); - vamsasStop.setVisible(!b); - vamsasSave.setVisible(!b); } public JInternalFrame[] getAllFrames() @@@ -2754,11 -2850,10 +2753,11 @@@ } // JAL-940 - disabled JWS1 service configuration - always start discoverer // until we phase out completely - (t0 = new Thread(discoverer)).start(); + (t0 = new Thread(discoverer, "DiscovererThread")).start(); } - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + if (ignore_SHOW_JWS2_SERVICES_preference + || Cache.getDefault("SHOW_JWS2_SERVICES", true)) { t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() .startDiscoverer(changeSupport); diff --cc src/jalview/gui/StructureViewerBase.java index ec5579c,aa07b7c..474b63c --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@@ -401,9 -350,9 +401,9 @@@ public abstract class StructureViewerBa } } // and call ourselves again. - addStructure(pdbentry, seqs, chains, align, alignFrame); + addStructure(pdbentry, seqs, chains, alignFrame); } - }).start(); + }, "Adding3DStructureQueueThread").start(); return; } } @@@ -413,7 -362,8 +413,7 @@@ { seqs }, new String[][] { chains }); addingStructures = true; _started = false; - worker = new Thread(this); - alignAddedStructures = align; + worker = new Thread(this, "Adding3DStructureThread"); worker.start(); return; } diff --cc src/jalview/gui/TreePanel.java index d735402,e8f78d8..042147f --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@@ -20,18 -20,9 +20,12 @@@ */ package jalview.gui; +import java.util.Locale; + import jalview.analysis.AlignmentSorter; - import jalview.analysis.AverageDistanceTree; - import jalview.analysis.NJTree; - import jalview.analysis.TreeBuilder; import jalview.analysis.TreeModel; - import jalview.analysis.scoremodels.ScoreModels; - import jalview.api.analysis.ScoreModelI; - import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.Alignment; @@@ -86,9 -74,7 +78,9 @@@ public class TreePanel extends GTreePan String treeTitle; // if tree loaded + SimilarityParamsI similarityParams; + - private TreeCanvas treeCanvas; + TreeCanvas treeCanvas; TreeModel tree; @@@ -129,45 -125,20 +131,21 @@@ public AlignmentViewport getViewPort() { - return treeCanvas.av; + // @Mungo - Why don't we return our own viewport ??? + return getTreeCanvas().getViewport(); } - void initTreePanel(AlignmentPanel ap, String type, String modelName, - NewickFile newTree, AlignmentView inputData) + /** + * Initialize a tree panel based on a calculated tree + * + * @param ap + * @param tree + */ + void initTreePanel(AlignmentPanel ap, TreeModel tree) { + buildTreeCanvas(ap); - av = ap.av; - this.treeType = type; - this.scoreModelName = modelName; - - treeCanvas = new TreeCanvas(this, ap, scrollPane); - scrollPane.setViewportView(treeCanvas); - - PaintRefresher.Register(this, ap.av.getSequenceSetId()); - - buildAssociatedViewMenu(); - - final PropertyChangeListener listener = addAlignmentListener(); - - /* - * remove listener when window is closed, so that this - * panel can be garbage collected - */ - addInternalFrameListener(new InternalFrameAdapter() - { - @Override - public void internalFrameClosed(InternalFrameEvent evt) - { - if (av != null) - { - av.removePropertyChangeListener(listener); - } - releaseReferences(); - } - }); - - TreeLoader tl = new TreeLoader(newTree, inputData); + TreeLoader tl = new TreeLoader(null, null); tl.start(); } @@@ -319,18 -304,16 +312,13 @@@ public void buildTreeCanvas(AlignmentPa { originalSeqData.setVisible(false); } - - - } - else - { - ScoreModelI sm = ScoreModels.getInstance().getScoreModel( - scoreModelName, treeCanvas.getAssociatedPanel()); - TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) - ? new NJTree(av, sm, similarityParams) - : new AverageDistanceTree(av, sm, similarityParams); - tree = new TreeModel(njtree); - showDistances(true); - } + showTree(tree); + } + + public void showTree(TreeModel tree) + { tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); treeCanvas.setTree(tree); @@@ -784,67 -866,25 +774,75 @@@ { return treeTitle; } + else + { + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager + .getString("label.tree_calc_" + treeType.toLowerCase()); - /* - * short score model name (long description can be too long) - */ - String smn = substitutionMatrix; - - /* - * put them together as Using - */ - final String ttl = MessageManager - .formatMessage("label.treecalc_title", treecalcnm, smn); + /* + * i18n description of Neighbour Joining or Average Distance method + */ + String treecalcnm = MessageManager.getString( + "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT)); + + /* + * short score model name (long description can be too long) + */ + String smn = scoreModelName; + + /* + * put them together as Using + */ + final String ttl = MessageManager.formatMessage("label.calc_title", + treecalcnm, smn); - return ttl; + return ttl; + } } + + /** + * Builds an EPS image and writes it to the specified file. + * + * @param outFile + * @param textOption + * true for Text character rendering, false for Lineart + */ + protected void writeEpsFile(File outFile, boolean textOption) + { + try + { + int width = treeCanvas.getWidth(); + int height = treeCanvas.getHeight(); + + FileOutputStream out = new FileOutputStream(outFile); + EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, + height); + pg.setAccurateTextMode(!textOption); + treeCanvas.draw(pg, width, height); + + pg.flush(); + pg.close(); + } catch (Exception ex) + { + System.err.println("Error writing tree as EPS"); + ex.printStackTrace(); + } + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; + } } diff --cc src/jalview/gui/VamsasApplication.java index 8a8ba8d,f855474..df63be1 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@@ -319,13 -320,13 +319,13 @@@ public class VamsasApplication implemen @Override public void run() { - Cache.log.info("Jalview updating to the Vamsas Session."); + Console.info("Jalview updating to the Vamsas Session."); dealWithDocumentUpdate(true); - Cache.log.info("Jalview finished updating to the Vamsas Session."); + Console.info("Jalview finished updating to the Vamsas Session."); } - }); + }, "UpdateVamsasThread"); udthread.start(); } diff --cc src/jalview/gui/WebserviceInfo.java index ee1b473,be812b5..034cbad --- a/src/jalview/gui/WebserviceInfo.java +++ b/src/jalview/gui/WebserviceInfo.java @@@ -346,27 -342,26 +346,27 @@@ public class WebserviceInfo extends GWe } AnimatedPanel ap = new AnimatedPanel(); - titlePanel.add(ap, BorderLayout.CENTER); + ap.setPreferredSize(new Dimension(60, 60)); + titlePanel.add(ap, BorderLayout.WEST); + titlePanel.add(titleText, BorderLayout.CENTER); + setStatus(currentStatus); - Thread thread = new Thread(ap); + Thread thread = new Thread(ap, "AnimatedPanelThread"); thread.start(); final WebserviceInfo thisinfo = this; - frame.addInternalFrameListener( - new javax.swing.event.InternalFrameAdapter() - { - @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - // System.out.println("Shutting down webservice client"); - WSClientI service = thisinfo.getthisService(); - if (service != null && service.isCancellable()) - { - service.cancelJob(); - } - }; - }); + frame.addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent evt) + { + // System.out.println("Shutting down webservice client"); + WSClientI service = thisinfo.getthisService(); + if (service != null && service.isCancellable()) + { + service.cancelJob(); + } + } + }); frame.validate(); } diff --cc src/jalview/io/FileLoader.java index 4016e71,241b833..fec0b3a --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@@ -208,8 -183,19 +208,7 @@@ public class FileLoader implements Runn */ protected AlignFrame _LoadFileWaitTillLoaded() { - Thread loader = new Thread(this, "LoadFileWithWaitingThread"); - loader.start(); - - while (loader.isAlive()) - { - try - { - Thread.sleep(500); - } catch (Exception ex) - { - } - } - + this.run(); - return alignFrame; } diff --cc src/jalview/io/NewickFile.java index 4a30d73,7444b5f..a283691 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@@ -470,9 -477,9 +470,9 @@@ public class NewickFile extends FilePar { try { - bootstrap = (new Integer(nbootstrap.stringMatched(1))) + bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1))) .intValue(); - HasBootstrap = true; + hasBootstrap = true; } catch (Exception e) { Error = ErrorStringrange(Error, "Can't parse bootstrap value", diff --cc src/jalview/jbgui/GAlignFrame.java index 71b6b9e,9b0c6a8..4d2850b --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@@ -1791,12 -1810,8 +1893,12 @@@ public class GAlignFrame extends JInter fileMenu.add(exportImageMenu); fileMenu.add(exportFeatures); fileMenu.add(exportAnnotations); - fileMenu.add(loadTreeMenuItem); + fileMenu.add(loadTreeMenu); fileMenu.add(associatedData); + if (!Platform.isJS()) + { + fileMenu.add(loadVcf); + } fileMenu.addSeparator(); fileMenu.add(closeMenuItem); @@@ -1949,12 -1955,40 +2051,44 @@@ // JAL-574 // selectMenu.addSeparator(); // selectMenu.add(listenToViewSelections); + + + } + + protected void loadTreeOfLife_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void loadTreeFam_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void loadTreePfam_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void loadTreeBase_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + + } + + protected void loadTreeBaseStudy_actionPerformed(ActionEvent e) + { + // TODO Auto-generated method stub + } + protected void loadVcf_actionPerformed() + { + } + /** * Constructs the entries on the Colour menu (but does not add them to the * menu). diff --cc src/jalview/math/Matrix.java index b22bf4e,5c264a8..b5a2b33 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@@ -973,53 -996,10 +973,59 @@@ public class Matrix implements Matrix } } + @Override + public void setD(double[] v) + { + d = v; + } + + @Override + public void setE(double[] v) + { + e = v; + } + + public double getTotal() + { + double d = 0d; + for (int i = 0; i < this.height(); i++) + { + for (int j = 0; j < this.width(); j++) + { + d += value[i][j]; + } + } + return d; + } + + /** + * {@inheritDoc} + */ + @Override + public boolean equals(MatrixI m2, double delta) + { + if (m2 == null || this.height() != m2.height() + || this.width() != m2.width()) + { + return false; + } + for (int i = 0; i < this.height(); i++) + { + for (int j = 0; j < this.width(); j++) + { + double diff = this.getValue(i, j) - m2.getValue(i, j); + if (Math.abs(diff) > delta) + { + return false; + } + } + } + return true; + } + + @Override + public double[][] getValues() + { + return value; + } } diff --cc src/jalview/math/MatrixI.java index e98007e,840e93b..4fe31ea --- a/src/jalview/math/MatrixI.java +++ b/src/jalview/math/MatrixI.java @@@ -68,48 -64,20 +68,56 @@@ public interface Matrix double[] getRow(int i); /** + * Answers a new matrix with a copy of the values in this one + * + * @return + */ + MatrixI copy(); + + /** + * Answers all values present in the Matrix ordered by row,column + * + * @return the double array containing the values ordered in {row values} per + * column + */ + double[][] getValues(); + - - MatrixI copy(); - ++ /** + * Returns a new matrix which is the transpose of this one + * + * @return + */ MatrixI transpose(); + /** + * Returns a new matrix which is the result of premultiplying this matrix by + * the supplied argument. If this of size AxB (A rows and B columns), and the + * argument is CxA (C rows and A columns), the result is of size CxB. + * + * @param in + * + * @return + * @throws IllegalArgumentException + * if the number of columns in the pre-multiplier is not equal to + * the number of rows in the multiplicand (this) + */ MatrixI preMultiply(MatrixI m); + /** + * Returns a new matrix which is the result of postmultiplying this matrix by + * the supplied argument. If this of size AxB (A rows and B columns), and the + * argument is BxC (B rows and C columns), the result is of size AxC. + *
+ * This method simply returns the result of in.preMultiply(this) + * + * @param in + * + * @return + * @throws IllegalArgumentException + * if the number of rows in the post-multiplier is not equal to the + * number of columns in the multiplicand (this) + * @see #preMultiply(Matrix) + */ MatrixI postMultiply(MatrixI m); double[] getD(); diff --cc src/jalview/util/MappingUtils.java index 25cb810,78a833e..05fc1c6 --- a/src/jalview/util/MappingUtils.java +++ b/src/jalview/util/MappingUtils.java @@@ -1027,86 -991,22 +1027,103 @@@ public final class MappingUtil } } + /** + * Converts a list of {@code start-end} ranges to a single array of + * {@code start1, end1, start2, ... } ranges + * + * @param ranges + * @return + */ + public static int[] rangeListToArray(List ranges) + { + int rangeCount = ranges.size(); + int[] result = new int[rangeCount * 2]; + int j = 0; + for (int i = 0; i < rangeCount; i++) + { + int[] range = ranges.get(i); + result[j++] = range[0]; + result[j++] = range[1]; + } + return result; + } + + /* + * Returns the maximal start-end positions in the given (ordered) list of + * ranges which is overlapped by the given begin-end range, or null if there + * is no overlap. + * + *
+ * Examples: + * if ranges is {[4, 8], [10, 12], [16, 19]} + * then + * findOverlap(ranges, 1, 20) == [4, 19] + * findOverlap(ranges, 6, 11) == [6, 11] + * findOverlap(ranges, 9, 15) == [10, 12] + * findOverlap(ranges, 13, 15) == null + *
+ * + * @param ranges + * @param begin + * @param end + * @return + */ + protected static int[] findOverlap(List ranges, final int begin, + final int end) + { + boolean foundStart = false; + int from = 0; + int to = 0; + /* + * traverse the ranges to find the first position (if any) >= begin, + * and the last position (if any) <= end + */ + for (int[] range : ranges) + { + if (!foundStart) + { + if (range[0] >= begin) + { + /* + * first range that starts with, or follows, begin + */ + foundStart = true; + from = Math.max(range[0], begin); + } + else if (range[1] >= begin) + { + /* + * first range that contains begin + */ + foundStart = true; + from = begin; + } + } + + if (range[0] <= end) + { + to = Math.min(end, range[1]); + } + } + + return foundStart && to >= from ? new int[] { from, to } : null; + } ++ + public static Map putWithDuplicationCheck(Map map, K key, + V value) + { + if (!map.containsKey(key)) + { + map.put(key, value); + } + else + { + jalview.bin.Cache.log.warn( + "Attempt to add duplicate entry detected for map with key: " + + key.toString() + " and value: " + value.toString()); + } + + return map; - + } } diff --cc src/jalview/ws/DBRefFetcher.java index d8858a9,2b7c6df..eb66016 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@@ -814,25 -824,20 +814,27 @@@ public class DBRefFetcher implements Ru */ private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray) { - Vector nseq = new Vector<>(); - for (int i = 0; sequencesArray != null - && i < sequencesArray.length; i++) + int n; + if (sequencesArray == null || (n = sequencesArray.length) == 0) + { - nseq.addElement(sequencesArray[i]); - DBRefEntry[] dbr = sequencesArray[i].getDBRefs(); + return sequencesArray; ++ } + ArrayList nseq = new ArrayList<>(); + for (int i = 0; i < n; i++) + { + nseq.add(sequencesArray[i]); + List dbr = sequencesArray[i].getDBRefs(); Mapping map = null; - for (int r = 0; (dbr != null) && r < dbr.length; r++) + if (dbr != null) { - if ((map = dbr[r].getMap()) != null) + for (int r = 0, rn = dbr.size(); r < rn; r++) { - if (map.getTo() != null && !nseq.contains(map.getTo())) + if ((map = dbr.get(r).getMap()) != null) { - nseq.addElement(map.getTo()); + if (map.getTo() != null && !nseq.contains(map.getTo())) + { + nseq.add(map.getTo()); + } } } } diff --cc src/jalview/ws/jws2/Jws2Discoverer.java index b6b4b2e,fe303f8..7bf5a97 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@@ -457,9 -457,9 +457,8 @@@ public class Jws2Discoverer implements sv.action, sv); changeSupport.firePropertyChange("services", new Vector(), services); - } - }).start(); - + }; + }, "LoadPreferredServiceThread").start(); - } }); } diff --cc utils/eclipse/org.eclipse.jdt.core.jalview.prefs index 4b7c545,0000000..d3f77b1 mode 100644,000000..100644 --- a/utils/eclipse/org.eclipse.jdt.core.jalview.prefs +++ b/utils/eclipse/org.eclipse.jdt.core.jalview.prefs @@@ -1,298 -1,0 +1,316 @@@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate +org.eclipse.jdt.core.compiler.codegen.targetPlatform=11 +org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve +org.eclipse.jdt.core.compiler.compliance=11 +org.eclipse.jdt.core.compiler.debug.lineNumber=generate +org.eclipse.jdt.core.compiler.debug.localVariable=generate +org.eclipse.jdt.core.compiler.debug.sourceFile=generate +org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.compiler.problem.enumIdentifier=error +org.eclipse.jdt.core.compiler.source=11 ++org.eclipse.jdt.core.formatter.align_fields_grouping_blank_lines=2147483647 +org.eclipse.jdt.core.formatter.align_type_members_on_columns=false +org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16 +org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=52 +org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=16 +org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call=16 +org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation=16 +org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression=16 +org.eclipse.jdt.core.formatter.alignment_for_assignment=0 +org.eclipse.jdt.core.formatter.alignment_for_binary_expression=16 +org.eclipse.jdt.core.formatter.alignment_for_compact_if=16 +org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80 +org.eclipse.jdt.core.formatter.alignment_for_enum_constants=16 +org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16 ++org.eclipse.jdt.core.formatter.alignment_for_expressions_in_for_loop_header=0 +org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0 +org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16 ++org.eclipse.jdt.core.formatter.alignment_for_parameterized_type_references=0 +org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16 +org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16 +org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80 +org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16 +org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16 +org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=16 +org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16 +org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16 +org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16 ++org.eclipse.jdt.core.formatter.alignment_for_type_arguments=0 ++org.eclipse.jdt.core.formatter.alignment_for_type_parameters=0 +org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16 +org.eclipse.jdt.core.formatter.blank_lines_after_imports=1 +org.eclipse.jdt.core.formatter.blank_lines_after_package=1 +org.eclipse.jdt.core.formatter.blank_lines_before_field=1 +org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration=0 +org.eclipse.jdt.core.formatter.blank_lines_before_imports=1 +org.eclipse.jdt.core.formatter.blank_lines_before_member_type=1 +org.eclipse.jdt.core.formatter.blank_lines_before_method=1 +org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=1 +org.eclipse.jdt.core.formatter.blank_lines_before_package=0 +org.eclipse.jdt.core.formatter.blank_lines_between_import_groups=1 +org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations=1 +org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration=next_line +org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration=next_line +org.eclipse.jdt.core.formatter.brace_position_for_array_initializer=next_line_on_wrap +org.eclipse.jdt.core.formatter.brace_position_for_block=next_line +org.eclipse.jdt.core.formatter.brace_position_for_block_in_case=next_line +org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration=next_line +org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=next_line +org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration=next_line +org.eclipse.jdt.core.formatter.brace_position_for_lambda_body=end_of_line +org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=next_line +org.eclipse.jdt.core.formatter.brace_position_for_switch=next_line +org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=next_line +org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false +org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false ++org.eclipse.jdt.core.formatter.comment.count_line_length_from_starting_position=false +org.eclipse.jdt.core.formatter.comment.format_block_comments=false +org.eclipse.jdt.core.formatter.comment.format_header=false +org.eclipse.jdt.core.formatter.comment.format_html=true +org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true +org.eclipse.jdt.core.formatter.comment.format_line_comments=true +org.eclipse.jdt.core.formatter.comment.format_source_code=true +org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true +org.eclipse.jdt.core.formatter.comment.indent_root_tags=true +org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert +org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert +org.eclipse.jdt.core.formatter.comment.line_length=80 +org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true +org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true +org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false +org.eclipse.jdt.core.formatter.compact_else_if=true +org.eclipse.jdt.core.formatter.continuation_indentation=4 +org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer=2 +org.eclipse.jdt.core.formatter.disabling_tag=@formatter\:off +org.eclipse.jdt.core.formatter.enabling_tag=@formatter\:on +org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line=false +org.eclipse.jdt.core.formatter.format_line_comment_starting_on_first_column=true +org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header=true +org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header=true +org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header=true +org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header=true 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+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert 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++org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment=common_lines ++org.eclipse.jdt.core.formatter.parentheses_positions_in_if_while_statement=common_lines ++org.eclipse.jdt.core.formatter.parentheses_positions_in_lambda_declaration=common_lines ++org.eclipse.jdt.core.formatter.parentheses_positions_in_method_delcaration=common_lines ++org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation=common_lines ++org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement=common_lines ++org.eclipse.jdt.core.formatter.parentheses_positions_in_try_clause=common_lines +org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true +org.eclipse.jdt.core.formatter.tabulation.char=space +org.eclipse.jdt.core.formatter.tabulation.size=2 +org.eclipse.jdt.core.formatter.use_on_off_tags=true +org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false ++org.eclipse.jdt.core.formatter.wrap_before_assignment_operator=false 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