X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2849d6b5aa8216ece73cb94b97693b99f0c75e07;hb=96d1dabfb3cf7a879ef9f1b3bfce3d2fe8c46954;hp=71f8c7d80fb8c2b073a9a9b0a5fdd7892e802df2;hpb=01bf99892a24279c17fc18c19de0d1661f1faff2;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 71f8c7d..2849d6b 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,9 +20,18 @@ */ package jalview.gui; +import java.util.Locale; + +import java.io.IOException; +import java.util.HashSet; +import java.util.Set; + +import javax.swing.JFileChooser; +import javax.swing.JOptionPane; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; +import java.awt.Dimension; import java.awt.Rectangle; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; @@ -45,6 +54,7 @@ import java.awt.event.KeyEvent; import java.awt.event.MouseEvent; import java.awt.print.PageFormat; import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileWriter; @@ -54,6 +64,8 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; import java.util.List; import java.util.Vector; @@ -72,6 +84,7 @@ import javax.swing.SwingUtilities; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import ext.vamsas.ServiceHandle; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; @@ -90,6 +103,7 @@ import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.bin.Jalview; import jalview.commands.CommandI; import jalview.commands.EditCommand; @@ -150,6 +164,7 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; +import jalview.util.HttpUtils; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; @@ -167,7 +182,12 @@ import jalview.ws.params.ArgumentI; import jalview.ws.params.ParamDatastoreI; import jalview.ws.params.WsParamSetI; import jalview.ws.seqfetcher.DbSourceProxy; -import jalview.ws.slivkaws.SlivkaWSDiscoverer; +import jalview.ws2.client.api.WebServiceDiscovererI; +import jalview.ws2.client.ebi.JobDispatcherWSDiscoverer; +import jalview.ws2.client.jpred4.JPred4WSDiscoverer; +import jalview.ws2.client.slivka.SlivkaWSDiscoverer; +import jalview.ws2.gui.WebServicesMenuManager; + import java.io.IOException; import java.util.HashSet; import java.util.Set; @@ -175,6 +195,64 @@ import java.util.Set; import javax.swing.JFileChooser; import javax.swing.JOptionPane; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JComponent; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + +import ext.vamsas.ServiceHandle; + /** * DOCUMENT ME! * @@ -186,6 +264,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener, ServiceChangeListener { + + public static int frameCount; public static final int DEFAULT_WIDTH = 700; public static final int DEFAULT_HEIGHT = 500; @@ -216,6 +296,9 @@ public class AlignFrame extends GAlignFrame */ File fileObject; + private int id; + + private DataSourceType protocol ; /** * Creates a new AlignFrame object with specific width and height. * @@ -310,6 +393,7 @@ public class AlignFrame extends GAlignFrame public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, int height, String sequenceSetId, String viewId) { + id = (++frameCount); setSize(width, height); if (al.getDataset() == null) @@ -319,9 +403,9 @@ public class AlignFrame extends GAlignFrame viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); - alignPanel = new AlignmentPanel(this, viewport); - - addAlignmentPanel(alignPanel, true); + // JalviewJS needs to distinguish a new panel from an old one in init() + // alignPanel = new AlignmentPanel(this, viewport); + // addAlignmentPanel(alignPanel, true); init(); } @@ -341,8 +425,8 @@ public class AlignFrame extends GAlignFrame { viewport.hideSequence(hiddenSeqs); } - alignPanel = new AlignmentPanel(this, viewport); - addAlignmentPanel(alignPanel, true); + // alignPanel = new AlignmentPanel(this, viewport); + // addAlignmentPanel(alignPanel, true); init(); } @@ -358,7 +442,7 @@ public class AlignFrame extends GAlignFrame { viewport = ap.av; alignPanel = ap; - addAlignmentPanel(ap, false); + // addAlignmentPanel(ap, false); init(); } @@ -368,11 +452,34 @@ public class AlignFrame extends GAlignFrame */ void init() { + boolean newPanel = (alignPanel == null); + viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + if (newPanel) + { + if (Platform.isJS()) + { + // need to set this up front if NOANNOTATION is + // used in conjunction with SHOWOVERVIEW. + + // I have not determined if this is appropriate for + // Jalview/Java, as it means we are setting this flag + // for all subsequent AlignFrames. For now, at least, + // I am setting it to be JalviewJS-only. + + boolean showAnnotation = Jalview.getInstance().getShowAnnotation(); + viewport.setShowAnnotation(showAnnotation); + } + alignPanel = new AlignmentPanel(this, viewport); + } + addAlignmentPanel(alignPanel, newPanel); // setBackground(Color.white); // BH 2019 if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); + // JalviewJS options + statusPanel.setVisible(Jalview.getInstance().getShowStatus()); + alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar()); } avc = new jalview.controller.AlignViewController(this, viewport, @@ -387,7 +494,7 @@ public class AlignFrame extends GAlignFrame // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + String sortby = Cache.getDefault(Preferences.SORT_ALIGNMENT, "No sort"); if (sortby.equals("Id")) @@ -399,8 +506,10 @@ public class AlignFrame extends GAlignFrame sortPairwiseMenuItem_actionPerformed(null); } - this.alignPanel.av - .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + // BH see above + // + // this.alignPanel.av + // .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); @@ -415,12 +524,12 @@ public class AlignFrame extends GAlignFrame }); buildColourMenu(); - if (Desktop.desktop != null) + if (Desktop.getDesktopPane() != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + addServiceListeners(); if (!Platform.isJS()) { - addServiceListeners(); } setGUINucleotide(); } @@ -430,14 +539,14 @@ public class AlignFrame extends GAlignFrame wrapMenuItem_actionPerformed(null); } - if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) + if (Cache.getDefault(Preferences.SHOW_OVERVIEW, false)) { this.overviewMenuItem_actionPerformed(null); } addKeyListener(); - final List selviews = new ArrayList<>(); + final List selviews = new ArrayList<>(); final List origview = new ArrayList<>(); final String menuLabel = MessageManager .getString("label.copy_format_from"); @@ -505,10 +614,10 @@ public class AlignFrame extends GAlignFrame } } }); - if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) .indexOf("devel") > -1 - || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() - .indexOf("test") > -1) + || Cache.getDefault("VERSION", "DEVELOPMENT") + .toLowerCase(Locale.ROOT).indexOf("test") > -1) { formatMenu.add(vsel); } @@ -532,6 +641,7 @@ public class AlignFrame extends GAlignFrame * @param format * format of file */ + @Deprecated public void setFileName(String file, FileFormatI format) { fileName = file; @@ -540,6 +650,22 @@ public class AlignFrame extends GAlignFrame } /** + * + * @param fileName + * @param file from SwingJS; may contain bytes -- for reload + * @param protocol from SwingJS; may be RELATIVE_URL + * @param format + */ + public void setFile(String fileName, File file, DataSourceType protocol, FileFormatI format) + { + this.fileName = fileName; + this.fileObject = file; + this.protocol = protocol; + setFileFormat(format); + reload.setEnabled(true); + } + + /** * JavaScript will have this, maybe others. More dependable than a file name * and maintains a reference to the actual bytes loaded. * @@ -574,8 +700,9 @@ public class AlignFrame extends GAlignFrame switch (evt.getKeyCode()) { - case 27: // escape key - deselectAllSequenceMenuItem_actionPerformed(null); + case KeyEvent.VK_ESCAPE: // escape key + // alignPanel.deselectAllSequences(); + alignPanel.deselectAllSequences(); break; @@ -586,7 +713,7 @@ public class AlignFrame extends GAlignFrame } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); } break; @@ -597,7 +724,7 @@ public class AlignFrame extends GAlignFrame } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown()); } break; @@ -610,7 +737,7 @@ public class AlignFrame extends GAlignFrame } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -622,7 +749,7 @@ public class AlignFrame extends GAlignFrame } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; @@ -758,16 +885,14 @@ public class AlignFrame extends GAlignFrame case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } break; } @@ -813,10 +938,13 @@ public class AlignFrame extends GAlignFrame { ap.av.getAlignment().padGaps(); } - ap.av.updateConservation(ap); - ap.av.updateConsensus(ap); - ap.av.updateStrucConsensus(ap); - ap.av.initInformationWorker(ap); + if (Jalview.getInstance().getStartCalculations()) + { + ap.av.updateConservation(ap); + ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); + } } } @@ -842,32 +970,68 @@ public class AlignFrame extends GAlignFrame buildWebServicesMenu(); } + private WebServiceDiscovererI.ServicesChangeListener slivkaServiceChangeListener = + (discoverer, services) -> { + // run when slivka services change + var menu = AlignFrame.this.slivkaMenu; + menu.setServices(discoverer); + menu.setInProgress(discoverer.isRunning()); + menu.setNoServices(services.isEmpty() && discoverer.isDone()); + }; + + private WebServiceDiscovererI.ServicesChangeListener ebiServiceChangeListener = + (discoverer, services) -> { + // run when ebi services change + var menu = AlignFrame.this.ebiMenu; + menu.setServices(discoverer); + menu.setInProgress(discoverer.isRunning()); + menu.setNoServices(services.isEmpty() && discoverer.isDone()); + }; + + private WebServiceDiscovererI.ServicesChangeListener jpred4ServiceChangeListener = + (discoverer, services) -> { + // run when jpred4 services change + var menu = AlignFrame.this.jpred4Menu; + menu.setServices(discoverer); + menu.setInProgress(discoverer.isRunning()); + menu.setNoServices(services.isEmpty() && discoverer.isDone()); + }; + /* Set up intrinsic listeners for dynamically generated GUI bits. */ private void addServiceListeners() { if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - WSDiscovererI discoverer = SlivkaWSDiscoverer.getInstance(); - discoverer.addServiceChangeListener(this); + WebServiceDiscovererI discoverer = SlivkaWSDiscoverer.getInstance(); + discoverer.addServicesChangeListener(slivkaServiceChangeListener); + } + if (Cache.getDefault("SHOW_EBI_SERVICES", true)) + { + JobDispatcherWSDiscoverer.getInstance().addServicesChangeListener(ebiServiceChangeListener); + } + if (Cache.getDefault("SHOW_JPRED4_SERVICES", true)) + { + JPred4WSDiscoverer.getInstance().addServicesChangeListener(jpred4ServiceChangeListener); } if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - WSDiscovererI discoverer = Jws2Discoverer.getDiscoverer(); + WSDiscovererI discoverer = Jws2Discoverer.getInstance(); discoverer.addServiceChangeListener(this); } // legacy event listener for compatibility with jws1 PropertyChangeListener legacyListener = (changeEvent) -> { buildWebServicesMenu(); }; - Desktop.instance.addJalviewPropertyChangeListener("services",legacyListener); + Desktop.getInstance().addJalviewPropertyChangeListener("services",legacyListener); addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameClosed(InternalFrameEvent e) { System.out.println("deregistering discoverer listener"); - SlivkaWSDiscoverer.getInstance().removeServiceChangeListener(AlignFrame.this); - Jws2Discoverer.getDiscoverer().removeServiceChangeListener(AlignFrame.this); - Desktop.instance.removeJalviewPropertyChangeListener("services", legacyListener); + SlivkaWSDiscoverer.getInstance().removeServicesChangeListener(slivkaServiceChangeListener); + JPred4WSDiscoverer.getInstance().removeServicesChangeListener(jpred4ServiceChangeListener); + Jws2Discoverer.getInstance().removeServiceChangeListener(AlignFrame.this); + Desktop.getInstance().removeJalviewPropertyChangeListener("services", legacyListener); closeMenuItem_actionPerformed(true); } }); @@ -932,13 +1096,8 @@ public class AlignFrame extends GAlignFrame scaleLeft.setVisible(av.getWrapAlignment()); scaleRight.setVisible(av.getWrapAlignment()); annotationPanelMenuItem.setState(av.isShowAnnotation()); - /* - * Show/hide annotations only enabled if annotation panel is shown - */ - showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); - hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); - showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); - hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); + // Show/hide annotations only enabled if annotation panel is shown + syncAnnotationMenuItems(av.isShowAnnotation()); viewBoxesMenuItem.setSelected(av.getShowBoxes()); viewTextMenuItem.setSelected(av.getShowText()); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); @@ -959,7 +1118,8 @@ public class AlignFrame extends GAlignFrame applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); showDbRefsMenuitem.setSelected(av.isShowDBRefs()); - autoCalculate.setSelected(av.autoCalculateConsensus); + autoCalculate + .setSelected(av.getAutoCalculateConsensusAndConservation()); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); @@ -991,6 +1151,18 @@ public class AlignFrame extends GAlignFrame { progressBar.setProgressBar(message, id); } + + @Override + public void addProgressBar(long id, String message) + { + progressBar.addProgressBar(id, message); + } + + @Override + public void removeProgressBar(long id) + { + progressBar.removeProgressBar(id); + } @Override public void registerHandler(final long id, @@ -1025,7 +1197,7 @@ public class AlignFrame extends GAlignFrame */ public String getVersion() { - return jalview.bin.Cache.getProperty("VERSION"); + return Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() @@ -1042,7 +1214,7 @@ public class AlignFrame extends GAlignFrame @Override public void addFromFile_actionPerformed(ActionEvent e) { - Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); + Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport); } @Override @@ -1064,16 +1236,18 @@ public class AlignFrame extends GAlignFrame { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMBuild(this, args2)).start(); + } + }); + } + else + { + new Thread(new HMMBuild(this, args)).start(); } - new Thread(new HMMBuild(this, args)).start(); } @Override @@ -1095,16 +1269,18 @@ public class AlignFrame extends GAlignFrame { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMAlign(this, args2)).start(); + } + }); + } + else + { + new Thread(new HMMAlign(this, args)).start(); } - new Thread(new HMMAlign(this, args)).start(); } @Override @@ -1126,17 +1302,20 @@ public class AlignFrame extends GAlignFrame { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMSearch(this, args2)).start(); + alignPanel.repaint(); + } + }); + } + else + { + new Thread(new HMMSearch(this, args)).start(); + alignPanel.repaint(); } - new Thread(new HMMSearch(this, args)).start(); - alignPanel.repaint(); } @Override @@ -1155,18 +1334,20 @@ public class AlignFrame extends GAlignFrame { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new JackHMMER(this, args2)).start(); + alignPanel.repaint(); + } + }); + } + else + { + new Thread(new JackHMMER(this, args)).start(); + alignPanel.repaint(); } - new Thread(new JackHMMER(this, args)).start(); - alignPanel.repaint(); - } /** @@ -1299,104 +1480,98 @@ public class AlignFrame extends GAlignFrame @Override public void reload_actionPerformed(ActionEvent e) { - if (fileName != null) + if (fileName == null && fileObject == null) { - // TODO: JAL-1108 - ensure all associated frames are closed regardless of - // originating file's format - // TODO: work out how to recover feature settings for correct view(s) when - // file is reloaded. - if (FileFormat.Jalview.equals(currentFileFormat)) + return; + } + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. + if (FileFormat.Jalview.equals(currentFileFormat)) + { + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); + for (int i = 0; i < frames.length; i++) { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - for (int i = 0; i < frames.length; i++) + if (frames[i] instanceof AlignFrame && frames[i] != this + && ((AlignFrame) frames[i]).fileName != null + && ((AlignFrame) frames[i]).fileName.equals(fileName)) { - if (frames[i] instanceof AlignFrame && frames[i] != this - && ((AlignFrame) frames[i]).fileName != null - && ((AlignFrame) frames[i]).fileName.equals(fileName)) + try + { + frames[i].setSelected(true); + Desktop.getInstance().closeAssociatedWindows(); + } catch (java.beans.PropertyVetoException ex) { - try - { - frames[i].setSelected(true); - Desktop.instance.closeAssociatedWindows(); - } catch (java.beans.PropertyVetoException ex) - { - } } - } - Desktop.instance.closeAssociatedWindows(); - FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } - else - { - Rectangle bounds = this.getBounds(); + Desktop.getInstance().closeAssociatedWindows(); - FileLoader loader = new FileLoader(); + FileLoader loader = new FileLoader(); + loader.LoadFile(viewport, (fileObject == null ? fileName : fileObject), protocol, currentFileFormat); + } + else + { + Rectangle bounds = this.getBounds(); - AlignFrame newframe = null; + FileLoader loader = new FileLoader(); - if (fileObject == null) - { + AlignFrame newframe = null; - DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE); - newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, - currentFileFormat); - } - else - { - newframe = loader.LoadFileWaitTillLoaded(fileObject, - DataSourceType.FILE, currentFileFormat); - } + if (fileObject == null) + { + newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, + currentFileFormat); + } + else + { + newframe = loader.LoadFileWaitTillLoaded(fileObject, + DataSourceType.FILE, currentFileFormat); + } - newframe.setBounds(bounds); - if (featureSettings != null && featureSettings.isShowing()) + newframe.setBounds(bounds); + if (featureSettings != null && featureSettings.isShowing()) + { + final Rectangle fspos = featureSettings.frame.getBounds(); + // TODO: need a 'show feature settings' function that takes bounds - + // need to refactor Desktop.addFrame + newframe.featureSettings_actionPerformed(null); + final FeatureSettings nfs = newframe.featureSettings; + SwingUtilities.invokeLater(new Runnable() { - final Rectangle fspos = featureSettings.frame.getBounds(); - // TODO: need a 'show feature settings' function that takes bounds - - // need to refactor Desktop.addFrame - newframe.featureSettings_actionPerformed(null); - final FeatureSettings nfs = newframe.featureSettings; - SwingUtilities.invokeLater(new Runnable() + @Override + public void run() { - @Override - public void run() - { - nfs.frame.setBounds(fspos); - } - }); - this.featureSettings.close(); - this.featureSettings = null; - } - this.closeMenuItem_actionPerformed(true); + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; } + this.closeMenuItem_actionPerformed(true); } } @Override public void addFromText_actionPerformed(ActionEvent e) { - Desktop.instance + Desktop.getInstance() .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel()); } @Override public void addFromURL_actionPerformed(ActionEvent e) { - Desktop.instance.inputURLMenuItem_actionPerformed(viewport); + Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport); } @Override public void save_actionPerformed(ActionEvent e) { if (fileName == null || (currentFileFormat == null) - || fileName.startsWith("http")) + || HttpUtils.startsWithHttpOrHttps(fileName)) { saveAs_actionPerformed(); } @@ -1433,7 +1608,7 @@ public class AlignFrame extends GAlignFrame // todo is this (2005) test now obsolete - value is never null? while (currentFileFormat == null) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("label.select_file_format_before_saving"), MessageManager.getString("label.file_format_not_specified"), @@ -1469,11 +1644,20 @@ public class AlignFrame extends GAlignFrame if (!lastSaveSuccessful) { - JvOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", new Object[] - { lastFilenameSaved }), - MessageManager.getString("label.error_saving_file"), - JvOptionPane.WARNING_MESSAGE); + if (!Platform.isHeadless()) + { + JvOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { lastFilenameSaved }), + MessageManager.getString("label.error_saving_file"), + JvOptionPane.WARNING_MESSAGE); + } + else + { + Console.error(MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { lastFilenameSaved })); + } } else { @@ -1550,32 +1734,65 @@ public class AlignFrame extends GAlignFrame { // create backupfiles object and get new temp filename destination boolean doBackup = BackupFiles.getEnabled(); - BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null; + BackupFiles backupfiles = null; + if (doBackup) + { + Console.trace( + "ALIGNFRAME making backupfiles object for " + file); + backupfiles = new BackupFiles(file); + } try { String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; + Console.trace("ALIGNFRAME setting PrintWriter"); PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + if (backupfiles != null) + { + Console.trace("ALIGNFRAME about to write to temp file " + + backupfiles.getTempFilePath()); + } + out.print(output); + Console.trace("ALIGNFRAME about to close file"); out.close(); + Console.trace("ALIGNFRAME closed file"); AlignFrame.this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { fileName, format.getName() })); lastSaveSuccessful = true; + } catch (IOException e) + { + lastSaveSuccessful = false; + Console.error( + "ALIGNFRAME Something happened writing the temp file"); + Console.error(e.getMessage()); + Console.debug(Cache.getStackTraceString(e)); } catch (Exception ex) { lastSaveSuccessful = false; - ex.printStackTrace(); + Console.error( + "ALIGNFRAME Something unexpected happened writing the temp file"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } if (doBackup) { backupfiles.setWriteSuccess(lastSaveSuccessful); + Console.debug("ALIGNFRAME writing temp file was " + + (lastSaveSuccessful ? "" : "NOT ") + "successful"); // do the backup file roll and rename the temp file to actual file + Console.trace( + "ALIGNFRAME about to rollBackupsAndRenameTempFile"); lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); + Console.debug( + "ALIGNFRAME performed rollBackupsAndRenameTempFile " + + (lastSaveSuccessful ? "" : "un") + + "successfully"); } } } @@ -1677,6 +1894,7 @@ public class AlignFrame extends GAlignFrame bjs.exportHTML(null); } + // ?? public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1756,7 +1974,7 @@ public class AlignFrame extends GAlignFrame throws IOException, InterruptedException { final JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); String tooltip = MessageManager .getString("label.load_jalview_annotations"); @@ -1768,7 +1986,7 @@ public class AlignFrame extends GAlignFrame public void run() { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); } }); @@ -1955,7 +2173,7 @@ public class AlignFrame extends GAlignFrame { if (originalSource != viewport) { - Cache.log.warn( + Console.warn( "Implementation worry: mismatch of viewport origin for undo"); } originalSource.updateHiddenColumns(); @@ -1964,8 +2182,7 @@ public class AlignFrame extends GAlignFrame // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.getAlignment().getSequences()); + originalSource.notifyAlignment(); } } @@ -1995,7 +2212,7 @@ public class AlignFrame extends GAlignFrame if (originalSource != viewport) { - Cache.log.warn( + Console.warn( "Implementation worry: mismatch of viewport origin for redo"); } originalSource.updateHiddenColumns(); @@ -2004,8 +2221,7 @@ public class AlignFrame extends GAlignFrame // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.getAlignment().getSequences()); + originalSource.notifyAlignment(); } } @@ -2052,10 +2268,11 @@ public class AlignFrame extends GAlignFrame } /** - * DOCUMENT ME! + * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection + * or the sequence under cursor in keyboard mode * * @param up - * DOCUMENT ME! + * or down (if !up) */ public void moveSelectedSequences(boolean up) { @@ -2063,8 +2280,25 @@ public class AlignFrame extends GAlignFrame if (sg == null) { + if (viewport.cursorMode) + { + sg = new SequenceGroup(); + sg.addSequence(viewport.getAlignment().getSequenceAt( + alignPanel.getSeqPanel().seqCanvas.cursorY), false); + } + else + { + return; + } + } + + if (sg.getSize() < 1) + { return; } + + // TODO: JAL-3733 - add an event to the undo buffer for this ! + viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true, false); @@ -2203,16 +2437,17 @@ public class AlignFrame extends GAlignFrame StringSelection ss = new StringSelection(output); + Desktop d = Desktop.getInstance(); try { - jalview.gui.Desktop.internalCopy = true; + d.internalCopy = true; // Its really worth setting the clipboard contents // to empty before setting the large StringSelection!! Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(""), null); Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, - Desktop.instance); + d); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); @@ -2232,7 +2467,7 @@ public class AlignFrame extends GAlignFrame hiddenCutoff, hiddenOffset); } - Desktop.jalviewClipboard = new Object[] { seqs, + d.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; setStatus(MessageManager.formatMessage( "label.copied_sequences_to_clipboard", new Object[] @@ -2312,12 +2547,14 @@ public class AlignFrame extends GAlignFrame boolean annotationAdded = false; AlignmentI alignment = null; - if (Desktop.jalviewClipboard != null) + Desktop d = Desktop.getInstance(); + + if (d.jalviewClipboard != null) { // The clipboard was filled from within Jalview, we must use the // sequences // And dataset from the copied alignment - SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; + SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0]; // be doubly sure that we create *new* sequence objects. sequences = new SequenceI[newseq.length]; for (int i = 0; i < newseq.length; i++) @@ -2342,10 +2579,10 @@ public class AlignFrame extends GAlignFrame if (newAlignment) { - if (Desktop.jalviewClipboard != null) + if (d.jalviewClipboard != null) { // dataset is inherited - alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); + alignment.setDataset((Alignment) d.jalviewClipboard[1]); } else { @@ -2361,8 +2598,8 @@ public class AlignFrame extends GAlignFrame alignment = viewport.getAlignment(); alwidth = alignment.getWidth() + 1; // decide if we need to import sequences from an existing dataset - boolean importDs = Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[1] != alignment.getDataset(); + boolean importDs = d.jalviewClipboard != null + && d.jalviewClipboard[1] != alignment.getDataset(); // importDs==true instructs us to copy over new dataset sequences from // an existing alignment Vector newDs = (importDs) ? new Vector<>() : null; // used to @@ -2543,8 +2780,7 @@ public class AlignFrame extends GAlignFrame } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, - alignment.getSequences()); + viewport.notifyAlignment(); if (alignPanels != null) { for (AlignmentPanel ap : alignPanels) @@ -2564,10 +2800,9 @@ public class AlignFrame extends GAlignFrame DEFAULT_HEIGHT); String newtitle = new String("Copied sequences"); - if (Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[2] != null) + if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null) { - HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } @@ -2606,6 +2841,7 @@ public class AlignFrame extends GAlignFrame System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } + } @Override @@ -2619,10 +2855,10 @@ public class AlignFrame extends GAlignFrame DEFAULT_HEIGHT); String newtitle = new String("Flanking alignment"); - if (Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[2] != null) + Desktop d = Desktop.getInstance(); + if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null) { - HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } @@ -2699,8 +2935,7 @@ public class AlignFrame extends GAlignFrame viewport.sendSelection(); viewport.getAlignment().deleteGroup(sg); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); if (viewport.getAlignment().getHeight() < 1) { try @@ -2709,6 +2944,8 @@ public class AlignFrame extends GAlignFrame } catch (Exception ex) { } + } else { + updateAll(null); } } }; @@ -2722,7 +2959,8 @@ public class AlignFrame extends GAlignFrame + 1) == viewport.getAlignment().getWidth()) ? true : false; if (wholeHeight && wholeWidth) { - JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop); + JvOptionPane dialog = JvOptionPane + .newOptionDialog(Desktop.getDesktopPane()); dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION Object[] options = new Object[] { MessageManager.getString("action.ok"), @@ -2749,10 +2987,26 @@ public class AlignFrame extends GAlignFrame { if (avc.deleteGroups()) { - PaintRefresher.Refresh(this, viewport.getSequenceSetId()); - alignPanel.updateAnnotation(); + updateAll(viewport.getSequenceSetId()); + } + } + + private void updateAll(String id) + { + if (id == null) + { + // this will force a non-fast repaint of both the IdPanel and SeqPanel + alignPanel.getIdPanel().getIdCanvas().setNoFastPaint(); + alignPanel.getSeqPanel().seqCanvas.setNoFastPaint(); + alignPanel.repaint(); + } + else + { + // original version + PaintRefresher.Refresh(this, id); alignPanel.paintAlignment(true, true); } + alignPanel.updateAnnotation(); } /** @@ -2764,18 +3018,7 @@ public class AlignFrame extends GAlignFrame @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - SequenceGroup sg = new SequenceGroup( - viewport.getAlignment().getSequences()); - - sg.setEndRes(viewport.getAlignment().getWidth() - 1); - viewport.setSelectionGroup(sg); - viewport.isSelectionGroupChanged(true); - viewport.sendSelection(); - // JAL-2034 - should delegate to - // alignPanel to decide if overview needs - // updating. - alignPanel.paintAlignment(false, false); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + alignPanel.selectAllSequences(); } /** @@ -2787,21 +3030,7 @@ public class AlignFrame extends GAlignFrame @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - if (viewport.cursorMode) - { - alignPanel.getSeqPanel().keyboardNo1 = null; - alignPanel.getSeqPanel().keyboardNo2 = null; - } - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.getIdPanel().getIdCanvas().searchResults = null; - // JAL-2034 - should delegate to - // alignPanel to decide if overview needs - // updating. - alignPanel.paintAlignment(false, false); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); - viewport.sendSelection(); + alignPanel.deselectAllSequences(); } /** @@ -2817,7 +3046,7 @@ public class AlignFrame extends GAlignFrame if (sg == null) { - selectAllSequenceMenuItem_actionPerformed(null); + alignPanel.selectAllSequences(); return; } @@ -2907,8 +3136,8 @@ public class AlignFrame extends GAlignFrame column, viewport.getAlignment()); } - setStatus(MessageManager - .formatMessage("label.removed_columns", new String[] + setStatus(MessageManager.formatMessage("label.removed_columns", + new String[] { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); @@ -2922,8 +3151,7 @@ public class AlignFrame extends GAlignFrame } } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } } @@ -2957,8 +3185,8 @@ public class AlignFrame extends GAlignFrame addHistoryItem(removeGapCols); - setStatus(MessageManager - .formatMessage("label.removed_empty_columns", new Object[] + setStatus(MessageManager.formatMessage("label.removed_empty_columns", + new Object[] { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue @@ -2972,8 +3200,7 @@ public class AlignFrame extends GAlignFrame // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); ranges.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } @@ -3011,8 +3238,7 @@ public class AlignFrame extends GAlignFrame viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } @@ -3026,20 +3252,18 @@ public class AlignFrame extends GAlignFrame public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } /** - * DOCUMENT ME! + * Opens a Finder dialog * * @param e - * DOCUMENT ME! */ @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(); + new Finder(alignPanel, false, null); } /** @@ -3080,8 +3304,8 @@ public class AlignFrame extends GAlignFrame if (viewport.getViewName() == null) { - viewport.setViewName(MessageManager - .getString("label.view_name_original")); + viewport.setViewName( + MessageManager.getString("label.view_name_original")); } /* @@ -3198,7 +3422,7 @@ public class AlignFrame extends GAlignFrame @Override public void gatherViews_actionPerformed(ActionEvent e) { - Desktop.instance.gatherViews(this); + Desktop.getInstance().gatherViews(this); } /** @@ -3583,11 +3807,26 @@ public class AlignFrame extends GAlignFrame { final boolean setVisible = annotationPanelMenuItem.isSelected(); viewport.setShowAnnotation(setVisible); - this.showAllSeqAnnotations.setEnabled(setVisible); - this.hideAllSeqAnnotations.setEnabled(setVisible); - this.showAllAlAnnotations.setEnabled(setVisible); - this.hideAllAlAnnotations.setEnabled(setVisible); + syncAnnotationMenuItems(setVisible); alignPanel.updateLayout(); + repaint(); + SwingUtilities.invokeLater(new Runnable() { + + @Override + public void run() + { + alignPanel.updateScrollBarsFromRanges(); + } + + }); + } + + private void syncAnnotationMenuItems(boolean setVisible) + { + showAllSeqAnnotations.setEnabled(setVisible); + hideAllSeqAnnotations.setEnabled(setVisible); + showAllAlAnnotations.setEnabled(setVisible); + hideAllAlAnnotations.setEnabled(setVisible); } @Override @@ -3650,12 +3889,34 @@ public class AlignFrame extends GAlignFrame } JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel); + // BH 2019.07.26 we allow for an embedded + // undecorated overview with defined size + frame.setName(Platform.getAppID("overview")); + // + Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1); + if (dim != null && dim.width == 0) + { + dim = null; // hidden, not embedded + } + OverviewPanel overview = new OverviewPanel(alignPanel, dim); frame.setContentPane(overview); + if (dim == null) + { + dim = new Dimension(); + // was frame.getSize(), but that is 0,0 at this point; + } + else + { + // we are imbedding, and so we have an undecorated frame + // and we can set the the frame dimensions accordingly. + } + // allowing for unresizable option using, style="resize:none" + boolean resizable = (Platform.getEmbeddedAttribute(frame, + "resize") != "none"); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.overview_params", new Object[] - { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), - true, true); + { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width, + dim.height, resizable, Desktop.FRAME_ALLOW_ANY_SIZE); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener( @@ -3913,7 +4174,6 @@ public class AlignFrame extends GAlignFrame alignPanel.paintAlignment(true, false); } - /** * DOCUMENT ME! * @@ -3957,11 +4217,11 @@ public class AlignFrame extends GAlignFrame @Override public void autoCalculate_actionPerformed(ActionEvent e) { - viewport.autoCalculateConsensus = autoCalculate.isSelected(); - if (viewport.autoCalculateConsensus) + viewport.setAutoCalculateConsensusAndConservation( + autoCalculate.isSelected()); + if (viewport.getAutoCalculateConsensusAndConservation()) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.notifyAlignment(); } } @@ -4004,7 +4264,7 @@ public class AlignFrame extends GAlignFrame { if (_s.getLength() < sg.getEndRes()) { - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager.getString( "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), MessageManager.getString( @@ -4036,7 +4296,8 @@ public class AlignFrame extends GAlignFrame frameTitle += this.title; - Desktop.addInternalFrame(tp, frameTitle, 600, 500); + Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height); } /** @@ -4153,6 +4414,18 @@ public class AlignFrame extends GAlignFrame } /** + * Enable (or, if desired, make visible) the By Tree + * submenu only if it has at least one element (or will have). + * + */ + @Override + protected void enableSortMenuOptions() + { + List treePanels = getTreePanels(); + sortByTreeMenu.setEnabled(!treePanels.isEmpty()); + } + + /** * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a * TreePanel with an appropriate jalview.analysis.AlignmentSorter * call. Listeners are added to remove the menu item when the treePanel is @@ -4164,24 +4437,7 @@ public class AlignFrame extends GAlignFrame { sortByTreeMenu.removeAll(); - List comps = PaintRefresher.components - .get(viewport.getSequenceSetId()); - List treePanels = new ArrayList<>(); - for (Component comp : comps) - { - if (comp instanceof TreePanel) - { - treePanels.add((TreePanel) comp); - } - } - - if (treePanels.size() < 1) - { - sortByTreeMenu.setVisible(false); - return; - } - - sortByTreeMenu.setVisible(true); + List treePanels = getTreePanels(); for (final TreePanel tp : treePanels) { @@ -4201,6 +4457,20 @@ public class AlignFrame extends GAlignFrame } } + private List getTreePanels() + { + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); + List treePanels = new ArrayList<>(); + for (Component comp : comps) + { + if (comp instanceof TreePanel) + { + treePanels.add((TreePanel) comp); + } + } + return treePanels; + } public boolean sortBy(AlignmentOrder alorder, String undoname) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -4302,7 +4572,7 @@ public class AlignFrame extends GAlignFrame { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.select_newick_like_tree_file")); @@ -4324,7 +4594,8 @@ public class AlignFrame extends GAlignFrame viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); } catch (Exception ex) { - JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), + ex.getMessage(), MessageManager .getString("label.problem_reading_tree_file"), JvOptionPane.WARNING_MESSAGE); @@ -4332,7 +4603,7 @@ public class AlignFrame extends GAlignFrame } if (fin != null && fin.hasWarningMessage()) { - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), fin.getWarningMessage(), MessageManager.getString( "label.possible_problem_with_tree_file"), @@ -4387,14 +4658,24 @@ public class AlignFrame extends GAlignFrame { tp = new TreePanel(alignPanel, nf, treeTitle, input); - tp.setSize(w, h); + Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1); + if (dim == null) + { + dim = new Dimension(w, h); + } + else + { + // no offset, either + x = 0; + } + tp.setSize(dim.width, dim.height); if (x > 0 && y > 0) { tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, treeTitle, w, h); + Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height); } } catch (Exception ex) { @@ -4404,37 +4685,64 @@ public class AlignFrame extends GAlignFrame return tp; } + private WebServicesMenuManager slivkaMenu = new WebServicesMenuManager("slivka", this); + private WebServicesMenuManager ebiMenu = new WebServicesMenuManager("job dispatcher", this); + private WebServicesMenuManager jpred4Menu = new WebServicesMenuManager("jpred4", this); + /** * Schedule the web services menu rebuild to the event dispatch thread. */ public void buildWebServicesMenu() { SwingUtilities.invokeLater(() -> { + Console.info("Rebuiling WS menu"); webService.removeAll(); if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { + Console.info("Building web service menu for slivka"); SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance(); - JMenu submenu = new JMenu("Slivka"); - buildWebServicesMenu(discoverer, submenu); - webService.add(submenu); + slivkaMenu.setServices(discoverer); + slivkaMenu.setInProgress(discoverer.isRunning()); + slivkaMenu.setNoServices(discoverer.isDone() && !discoverer.hasServices()); + webService.add(slivkaMenu.getMenu()); + } + if (Cache.getDefault("SHOW_EBI_SERVICES", true)) + { + Console.info("Building web services menu for jobs dispatcher"); + JobDispatcherWSDiscoverer discoverer = JobDispatcherWSDiscoverer.getInstance(); + ebiMenu.setServices(discoverer); + ebiMenu.setInProgress(discoverer.isRunning()); + ebiMenu.setNoServices(discoverer.isDone() && !discoverer.hasServices()); + webService.add(ebiMenu.getMenu()); + } + if (Cache.getDefault("SHOW_JPRED4_SERVICES", true)) + { + Console.info("Building web services menu for jpred4"); + JPred4WSDiscoverer discoverer = JPred4WSDiscoverer.getInstance(); + jpred4Menu.setServices(discoverer); + jpred4Menu.setInProgress(discoverer.isRunning()); + jpred4Menu.setNoServices(discoverer.isDone() && !discoverer.hasServices()); + webService.add(jpred4Menu.getMenu()); } if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer(); + WSDiscovererI jws2servs = Jws2Discoverer.getInstance(); JMenu submenu = new JMenu("JABAWS"); buildLegacyWebServicesMenu(submenu); buildWebServicesMenu(jws2servs, submenu); webService.add(submenu); } + build_urlServiceMenu(webService); + build_fetchdbmenu(webService); }); } private void buildLegacyWebServicesMenu(JMenu menu) { JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); - if (Discoverer.services != null && Discoverer.services.size() > 0) + if (Discoverer.getServices() != null && Discoverer.getServices().size() > 0) { - var secstrpred = Discoverer.services.get("SecStrPred"); + var secstrpred = Discoverer.getServices().get("SecStrPred"); if (secstrpred != null) { for (ext.vamsas.ServiceHandle sh : secstrpred) @@ -4461,7 +4769,8 @@ public class AlignFrame extends GAlignFrame if (discoverer.hasServices()) { PreferredServiceRegistry.getRegistry().populateWSMenuEntry( - discoverer.getServices(), null, menu, this, null); + discoverer.getServices(), sv -> buildWebServicesMenu(), menu, + this, null); } if (discoverer.isRunning()) { @@ -4490,7 +4799,7 @@ public class AlignFrame extends GAlignFrame * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { * - * @Override public void actionPerformed(ActionEvent e) { + * public void actionPerformed(ActionEvent e) { * jalview.datamodel.AlignmentView * .testSelectionViews(af.viewport.getAlignment(), * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } @@ -4559,7 +4868,7 @@ public class AlignFrame extends GAlignFrame showProducts.setEnabled(showp); } catch (Exception e) { - Cache.log.warn( + Console.warn( "canShowProducts threw an exception - please report to help@jalview.org", e); return false; @@ -4600,15 +4909,15 @@ public class AlignFrame extends GAlignFrame al = dna.translateCdna(codeTable); } catch (Exception ex) { - jalview.bin.Cache.log.error( - "Exception during translation. Please report this !", ex); + Console.error("Exception during translation. Please report this !", + ex); final String msg = MessageManager.getString( "label.error_when_translating_sequences_submit_bug_report"); final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("label.translation_failed"); - JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JvOptionPane.ERROR_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, + errorTitle, JvOptionPane.ERROR_MESSAGE); return; } if (al == null || al.getHeight() == 0) @@ -4617,8 +4926,8 @@ public class AlignFrame extends GAlignFrame "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); final String errorTitle = MessageManager .getString("label.translation_failed"); - JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JvOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, + errorTitle, JvOptionPane.WARNING_MESSAGE); } else { @@ -4631,7 +4940,7 @@ public class AlignFrame extends GAlignFrame if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); - viewport.openSplitFrame(af, new Alignment(seqs)); + AlignViewport.openSplitFrame(this, af, new Alignment(seqs)); } else { @@ -4664,7 +4973,7 @@ public class AlignFrame extends GAlignFrame { // BH 2018 return avc.parseFeaturesFile(file, sourceType, - Cache.getDefault("RELAXEDSEQIDMATCHING", false)); + Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false)); } @@ -4710,187 +5019,191 @@ public class AlignFrame extends GAlignFrame evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - final AlignFrame thisaf = this; final List files = new ArrayList<>(); List protocols = new ArrayList<>(); try { Desktop.transferFromDropTarget(files, protocols, evt, t); + if (files.size() > 0) + { + new Thread(new Runnable() + { + + @Override + public void run() + { + loadDroppedFiles(files, protocols, evt, t); + } + }).start(); + } } catch (Exception e) { e.printStackTrace(); } - if (files != null) + } + + protected void loadDroppedFiles(List files, + List protocols, DropTargetDropEvent evt, + Transferable t) + { + try { - new Thread(new Runnable() + // check to see if any of these files have names matching sequences + // in + // the alignment + SequenceIdMatcher idm = new SequenceIdMatcher( + viewport.getAlignment().getSequencesArray()); + /** + * Object[] { String,SequenceI} + */ + ArrayList filesmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); + for (int i = 0; i < files.size(); i++) { - @Override - public void run() + // BH 2018 + Object fileObj = files.get(i); + String fileName = fileObj.toString(); + String pdbfn = ""; + DataSourceType protocol = (fileObj instanceof File + ? DataSourceType.FILE + : FormatAdapter.checkProtocol(fileName)); + if (protocol == DataSourceType.FILE) { - try + File file; + if (fileObj instanceof File) { - // check to see if any of these files have names matching sequences - // in - // the alignment - SequenceIdMatcher idm = new SequenceIdMatcher( - viewport.getAlignment().getSequencesArray()); - /** - * Object[] { String,SequenceI} - */ - ArrayList filesmatched = new ArrayList<>(); - ArrayList filesnotmatched = new ArrayList<>(); - for (int i = 0; i < files.size(); i++) + file = (File) fileObj; + Platform.cacheFileData(file); + } + else + { + file = new File(fileName); + } + pdbfn = file.getName(); + } + else if (protocol == DataSourceType.URL) + { + URL url = new URL(fileName); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) + { + do { - // BH 2018 - Object file = files.get(i); - String fileName = file.toString(); - String pdbfn = ""; - DataSourceType protocol = (file instanceof File - ? DataSourceType.FILE - : FormatAdapter.checkProtocol(fileName)); - if (protocol == DataSourceType.FILE) - { - File fl; - if (file instanceof File) - { - fl = (File) file; - Platform.cacheFileData(fl); - } - else - { - fl = new File(fileName); - } - pdbfn = fl.getName(); - } - else if (protocol == DataSourceType.URL) - { - URL url = new URL(fileName); - pdbfn = url.getFile(); - } - if (pdbfn.length() > 0) - { - // attempt to find a match in the alignment - SequenceI[] mtch = idm.findAllIdMatches(pdbfn); - int l = 0, c = pdbfn.indexOf("."); - while (mtch == null && c != -1) - { - do - { - l = c; - } while ((c = pdbfn.indexOf(".", l)) > l); - if (l > -1) - { - pdbfn = pdbfn.substring(0, l); - } - mtch = idm.findAllIdMatches(pdbfn); - } - if (mtch != null) - { - FileFormatI type; - try - { - type = new IdentifyFile().identify(file, protocol); - } catch (Exception ex) - { - type = null; - } - if (type != null && type.isStructureFile()) - { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; - } - } - // File wasn't named like one of the sequences or wasn't a PDB - // file. - filesnotmatched.add(file); - } + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); } - int assocfiles = 0; - if (filesmatched.size() > 0) + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + FileFormatI type; + try { - boolean autoAssociate = Cache - .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); - if (!autoAssociate) - { - String msg = MessageManager.formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] - { Integer.valueOf(filesmatched.size()) - .toString() }); - String ttl = MessageManager.getString( - "label.automatically_associate_structure_files_by_name"); - int choice = JvOptionPane.showConfirmDialog(thisaf, msg, - ttl, JvOptionPane.YES_NO_OPTION); - autoAssociate = choice == JvOptionPane.YES_OPTION; - } - if (autoAssociate) - { - for (Object[] fm : filesmatched) - { - // try and associate - // TODO: may want to set a standard ID naming formalism for - // associating PDB files which have no IDs. - for (SequenceI toassoc : (SequenceI[]) fm[2]) - { - PDBEntry pe = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(fm[0].toString(), - (DataSourceType) fm[1], toassoc, false, - Desktop.instance); - if (pe != null) - { - System.err.println("Associated file : " - + (fm[0].toString()) + " with " - + toassoc.getDisplayId(true)); - assocfiles++; - } - } - // TODO: do we need to update overview ? only if features are - // shown I guess - alignPanel.paintAlignment(true, false); - } - } - else - { - /* - * add declined structures as sequences - */ - for (Object[] o : filesmatched) - { - filesnotmatched.add(o[0]); - } - } + type = new IdentifyFile().identify(fileObj, protocol); + } catch (Exception ex) + { + type = null; } - if (filesnotmatched.size() > 0) + if (type != null && type.isStructureFile()) { - if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) - || JvOptionPane.showConfirmDialog(thisaf, - "" + MessageManager.formatMessage( - "label.ignore_unmatched_dropped_files_info", - new Object[] - { Integer.valueOf( - filesnotmatched.size()) - .toString() }) - + "", - MessageManager.getString( - "label.ignore_unmatched_dropped_files"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) - { - return; - } - for (Object fn : filesnotmatched) + filesmatched.add(new Object[] { fileObj, protocol, mtch }); + continue; + } + } + // File wasn't named like one of the sequences or wasn't a PDB + // file. + filesnotmatched.add(fileObj); + } + } + int assocfiles = 0; + if (filesmatched.size() > 0) + { + boolean autoAssociate = Cache + .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false); + if (!autoAssociate) + { + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()).toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(this, msg, ttl, + JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) + { + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc : (SequenceI[]) fm[2]) + { + PDBEntry pe = AssociatePdbFileWithSeq.associatePdbWithSeq( + fm[0].toString(), (DataSourceType) fm[1], toassoc, + false); + if (pe != null) { - loadJalviewDataFile(fn, null, null, null); + System.err.println("Associated file : " + (fm[0].toString()) + + " with " + toassoc.getDisplayId(true)); + assocfiles++; } } - } catch (Exception ex) + // TODO: do we need to update overview ? only if features are + // shown I guess + alignPanel.paintAlignment(true, false); + } + } + else + { + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) { - ex.printStackTrace(); + filesnotmatched.add(o[0]); } } - }).start(); + } + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 && (Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) + || JvOptionPane.showConfirmDialog(this, + "" + MessageManager.formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] + { Integer.valueOf(filesnotmatched.size()) + .toString() }) + + "", + MessageManager.getString( + "label.ignore_unmatched_dropped_files"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) + { + return; + } + for (Object fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + + } + } catch (Exception ex) + { + ex.printStackTrace(); } } @@ -4949,7 +5262,7 @@ public class AlignFrame extends GAlignFrame { // some problem - if no warning its probable that the ID matching // process didn't work - JvOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), tcf.getWarningMessage() == null ? MessageManager.getString( "label.check_file_matches_sequence_ids_alignment") @@ -4965,7 +5278,7 @@ public class AlignFrame extends GAlignFrame } } catch (Exception x) { - Cache.log.debug( + Console.debug( "Exception when processing data source as T-COFFEE score file", x); tcf = null; @@ -5022,10 +5335,8 @@ public class AlignFrame extends GAlignFrame } if (isAnnotation) { - alignPanel.adjustAnnotationHeight(); - viewport.updateSequenceIdColours(); - buildSortByAnnotationScoresMenu(); - alignPanel.paintAlignment(true, true); + + updateForAnnotations(); } } catch (Exception ex) { @@ -5049,7 +5360,47 @@ public class AlignFrame extends GAlignFrame + (format != null ? "(parsing as '" + format + "' file)" : ""), - oom, Desktop.desktop); + oom, Desktop.getDesktopPane()); + } + } + + /** + * Do all updates necessary after an annotation file such as jnet. Also called + * from Jalview.loadAppletParams for "annotations", "jnetFile" + */ + + public void updateForAnnotations() + { + alignPanel.adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); + buildSortByAnnotationScoresMenu(); + alignPanel.paintAlignment(true, true); + } + + /** + * Change the display state for the given feature groups -- Added by BH from + * JalviewLite + * + * @param groups + * list of group strings + * @param state + * visible or invisible + */ + + public void setFeatureGroupState(String[] groups, boolean state) + { + jalview.api.FeatureRenderer fr = null; + viewport.setShowSequenceFeatures(true); + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + + fr.setGroupVisibility(Arrays.asList(groups), state); + alignPanel.getSeqPanel().seqCanvas.repaint(); + if (alignPanel.overviewPanel != null) + { + alignPanel.overviewPanel.updateOverviewImage(); + } } } @@ -5301,13 +5652,16 @@ public class AlignFrame extends GAlignFrame @Override public void run() { - final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher - .getSequenceFetcherSingleton(); + // ?? + // final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher + // .getSequenceFetcherSingleton(); javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { + jalview.ws.SequenceFetcher sf = jalview.ws.SequenceFetcher + .getInstance(); String[] dbclasses = sf.getNonAlignmentSources(); List otherdb; JMenu dfetch = new JMenu(); @@ -5331,9 +5685,8 @@ public class AlignFrame extends GAlignFrame } if (otherdb.size() == 1) { - final DbSourceProxy[] dassource = otherdb - .toArray(new DbSourceProxy[0]); DbSourceProxy src = otherdb.get(0); + DbSourceProxy[] dassource = new DbSourceProxy[] { src }; fetchr = new JMenuItem(src.getDbSource()); fetchr.addActionListener(new ActionListener() { @@ -5534,9 +5887,8 @@ public class AlignFrame extends GAlignFrame @Override protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { - AlignmentI al = viewport.getAlignment(); - al.justify(false); - viewport.firePropertyChange("alignment", null, al); + viewport.getAlignment().justify(false); + viewport.notifyAlignment(); } /** @@ -5545,9 +5897,8 @@ public class AlignFrame extends GAlignFrame @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { - AlignmentI al = viewport.getAlignment(); - al.justify(true); - viewport.firePropertyChange("alignment", null, al); + viewport.getAlignment().justify(true); + viewport.notifyAlignment(); } @Override @@ -5884,7 +6235,7 @@ public class AlignFrame extends GAlignFrame } catch (Exception ex) { System.err.println((ex.toString())); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.couldnt_run_groovy_script"), MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE); @@ -5978,7 +6329,6 @@ public class AlignFrame extends GAlignFrame { hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); } - @Override protected void loadVcf_actionPerformed() { @@ -6016,41 +6366,108 @@ public class AlignFrame extends GAlignFrame { return lastFeatureSettingsBounds; } -} -class PrintThread extends Thread -{ - AlignmentPanel ap; + public void scrollTo(int row, int column) + { + alignPanel.getSeqPanel().scrollTo(row, column); + } - public PrintThread(AlignmentPanel ap) + public void scrollToRow(int row) { - this.ap = ap; + alignPanel.getSeqPanel().scrollToRow(row); } - static PageFormat pf; + public void scrollToColumn(int column) + { + alignPanel.getSeqPanel().scrollToColumn(column); + } - @Override - public void run() + /** + * BH 2019 from JalviewLite + * + * get sequence feature groups that are hidden or shown + * + * @param visible + * true is visible + * @return list + */ + + public String[] getFeatureGroupsOfState(boolean visible) { - PrinterJob printJob = PrinterJob.getPrinterJob(); + jalview.api.FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + List gps = fr.getGroups(visible); + String[] _gps = gps.toArray(new String[gps.size()]); + return _gps; + } + return null; + } - if (pf != null) + /** + * + * @return list of feature groups on the view + */ + + public String[] getFeatureGroups() + { + jalview.api.FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) { - printJob.setPrintable(ap, pf); + List gps = fr.getFeatureGroups(); + String[] _gps = gps.toArray(new String[gps.size()]); + return _gps; } - else + return null; + } + + public void select(SequenceGroup sel, ColumnSelection csel, + HiddenColumns hidden) + { + alignPanel.getSeqPanel().selection(sel, csel, hidden, null); + } + + public int getID() + { + return id; + } + + static class PrintThread extends Thread + { + AlignmentPanel ap; + + public PrintThread(AlignmentPanel ap) { - printJob.setPrintable(ap); + this.ap = ap; } - if (printJob.printDialog()) + static PageFormat pf; + + @Override + public void run() { - try + PrinterJob printJob = PrinterJob.getPrinterJob(); + + if (pf != null) + { + printJob.setPrintable(ap, pf); + } + else { - printJob.print(); - } catch (Exception PrintException) + printJob.setPrintable(ap); + } + + if (printJob.printDialog()) { - PrintException.printStackTrace(); + try + { + printJob.print(); + } catch (Exception PrintException) + { + PrintException.printStackTrace(); + } } } }