X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=9e5bbff6372b80145a92a6b7ee94b2855cf77904;hb=a40bbc57a85658544e2e5d7cc2a7596b762566dc;hp=70c8355bd9f46d3990d6156d0656e2b2e12269c0;hpb=0c5e8f8ba81b913c63b60d7670d66aca661ea4f5;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 70c8355..9e5bbff 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,16 +20,21 @@ */ package jalview.gui; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; +import jalview.io.JSONFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; +import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; import jalview.structure.StructureSelectionManager; import jalview.util.ImageMaker; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.ParamManager; import java.awt.BorderLayout; @@ -69,6 +74,7 @@ import java.lang.reflect.Constructor; import java.net.URL; import java.util.ArrayList; import java.util.Hashtable; +import java.util.List; import java.util.StringTokenizer; import java.util.Vector; import java.util.concurrent.ExecutorService; @@ -162,6 +168,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements static final int yOffset = 30; + private static final int THREE = 3; + + private static AlignFrame currentAlignFrame; + public static jalview.ws.jws1.Discoverer discoverer; public static Object[] jalviewClipboard; @@ -330,8 +340,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements + jalview.bin.Cache.getProperty("VERSION") + "\n" + "Jalview Installation: " + jalview.bin.Cache.getDefault("INSTALLATION", "unknown") - + "\n" - + "Build Date: " + + "\n" + "Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n" + "Java version: " + System.getProperty("java.version") + "\n" + System.getProperty("os.arch") + " " @@ -432,9 +441,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements { ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault( Preferences.ADD_TEMPFACT_ANN, true)); - ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true)); - ssm.setSecStructServices(jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, - true)); + ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault( + Preferences.STRUCT_FROM_PDB, true)); + ssm.setSecStructServices(jalview.bin.Cache.getDefault( + Preferences.USE_RNAVIEW, true)); } else { @@ -480,7 +490,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void run() { long instance = System.currentTimeMillis(); - Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), instance); + Desktop.instance.setProgressBar( + MessageManager.getString("status.refreshing_news"), + instance); jvnews.refreshNews(); Desktop.instance.setProgressBar(null, instance); jvnews.showNews(); @@ -648,7 +660,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements addInternalFrame(frame, title, true, w, h, true); } - /** * Add an internal frame to the Jalview desktop * @@ -1014,6 +1025,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements { new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format); + viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled()); + AlignFrame af = viewport.getAlignPanel().alignFrame; + if (af != null) + { + af.changeColour(JSONFile.getColourScheme()); + af.setMenusForViewport(); + } } else { @@ -1087,7 +1105,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (format.equals("URL NOT FOUND")) { JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.couldnt_locate", new String[]{url}), MessageManager.getString("label.url_not_found"), + MessageManager.formatMessage("label.couldnt_locate", + new Object[] + { url }), MessageManager + .getString("label.url_not_found"), JOptionPane.WARNING_MESSAGE); return; @@ -1190,8 +1211,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (shortv) { message.append("

Version: " - + jalview.bin.Cache.getProperty("VERSION") - + "

"); + + jalview.bin.Cache.getProperty("VERSION") + ""); message.append("Last Updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + ""); @@ -1237,8 +1257,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } message.append("
Authors: " + jalview.bin.Cache - .getDefault( - "AUTHORFNAMES", + .getDefault("AUTHORFNAMES", "The Jalview Authors (See AUTHORS file for current list)") + "

Development managed by The Barton Group, University of Dundee, Scotland, UK.
" + "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list" @@ -1363,7 +1382,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return; } - AlignViewport source = null, target = null; + AlignmentViewport source = null, target = null; if (frames[0] instanceof AlignFrame) { source = ((AlignFrame) frames[0]).getCurrentView(); @@ -1475,8 +1494,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void run() { - setProgressBar(MessageManager.formatMessage("label.saving_jalview_project", new String[]{choice.getName()}), - choice.hashCode()); + setProgressBar(MessageManager.formatMessage( + "label.saving_jalview_project", new Object[] + { choice.getName() }), choice.hashCode()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); // TODO catch and handle errors for savestate @@ -1493,10 +1513,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.log.error( "Problems whilst trying to save to " + choice.getName(), ex); - JOptionPane.showMessageDialog( - me, - MessageManager.formatMessage("label.error_whilst_saving_current_state_to", new String[]{ choice.getName()}), - MessageManager.getString("label.couldnt_save_project"), + JOptionPane.showMessageDialog(me, MessageManager.formatMessage( + "label.error_whilst_saving_current_state_to", + new Object[] + { choice.getName() }), MessageManager + .getString("label.couldnt_save_project"), JOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); @@ -1564,13 +1585,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements final File selectedFile = chooser.getSelectedFile(); setProjectFile(selectedFile); final String choice = selectedFile.getAbsolutePath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + selectedFile.getParent()); new Thread(new Runnable() { public void run() { - setProgressBar(MessageManager.formatMessage("label.loading_jalview_project", new String[]{choice}), - choice.hashCode()); + setProgressBar(MessageManager.formatMessage( + "label.loading_jalview_project", new Object[] + { choice }), choice.hashCode()); try { new Jalview2XML().loadJalviewAlign(choice); @@ -1581,9 +1604,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.error("Problems whilst loading project from " + choice, ex); - JOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.error_whilst_loading_project_from", new String[]{choice}), - MessageManager.getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE); + JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + .formatMessage( + "label.error_whilst_loading_project_from", + new Object[] + { choice }), MessageManager + .getString("label.couldnt_load_project"), + JOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } @@ -1604,7 +1631,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (fileLoadingCount == 0) { - fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new String[]{fileName}))); + fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage( + "label.loading_file", new Object[] + { fileName }))); } fileLoadingCount++; } @@ -1670,38 +1699,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements public static int getViewCount(String alignmentId) { - AlignViewport[] aps = getViewports(alignmentId); + AlignmentViewport[] aps = getViewports(alignmentId); return (aps == null) ? 0 : aps.length; } /** * * @param alignmentId + * - if null, all sets are returned * @return all AlignmentPanels concerning the alignmentId sequence set */ public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { - int count = 0; if (Desktop.desktop == null) { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode return null; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - ArrayList aps = new ArrayList(); - for (int t = 0; t < frames.length; t++) + List aps = new ArrayList(); + AlignFrame[] frames = getAlignFrames(); + if (frames == null) { - if (frames[t] instanceof AlignFrame) + return null; + } + for (AlignFrame af : frames) + { + for (AlignmentPanel ap : af.alignPanels) { - AlignFrame af = (AlignFrame) frames[t]; - for (int a = 0; a < af.alignPanels.size(); a++) + if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId())) { - if (alignmentId.equals(((AlignmentPanel) af.alignPanels - .elementAt(a)).av.getSequenceSetId())) - { - aps.add(af.alignPanels.elementAt(a)); - } + aps.add(ap); } } } @@ -1709,11 +1737,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - AlignmentPanel[] vap = new AlignmentPanel[aps.size()]; - for (int t = 0; t < vap.length; t++) - { - vap[t] = (AlignmentPanel) aps.get(t); - } + AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]); return vap; } @@ -1721,52 +1745,51 @@ public class Desktop extends jalview.jbgui.GDesktop implements * get all the viewports on an alignment. * * @param sequenceSetId - * unique alignment id + * unique alignment id (may be null - all viewports returned in that + * case) * @return all viewports on the alignment bound to sequenceSetId */ - public static AlignViewport[] getViewports(String sequenceSetId) + public static AlignmentViewport[] getViewports(String sequenceSetId) { - Vector viewp = new Vector(); + List viewp = new ArrayList(); if (desktop != null) { - javax.swing.JInternalFrame[] frames = instance.getAllFrames(); + AlignFrame[] frames = Desktop.getAlignFrames(); - for (int t = 0; t < frames.length; t++) + for (AlignFrame afr : frames) { - if (frames[t] instanceof AlignFrame) + if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) { - AlignFrame afr = ((AlignFrame) frames[t]); - if (afr.getViewport().getSequenceSetId().equals(sequenceSetId)) + if (afr.alignPanels != null) { - if (afr.alignPanels != null) + for (AlignmentPanel ap : afr.alignPanels) { - for (int a = 0; a < afr.alignPanels.size(); a++) + if (sequenceSetId == null + || sequenceSetId.equals(ap.av.getSequenceSetId())) { - if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels - .elementAt(a)).av.getSequenceSetId())) - { - viewp.addElement(((AlignmentPanel) afr.alignPanels - .elementAt(a)).av); - } + viewp.add(ap.av); } } - else - { - viewp.addElement(((AlignFrame) frames[t]).getViewport()); - } + } + else + { + viewp.add(afr.getViewport()); } } } if (viewp.size() > 0) { - AlignViewport[] vp = new AlignViewport[viewp.size()]; - viewp.copyInto(vp); - return vp; + return viewp.toArray(new AlignmentViewport[viewp.size()]); } } return null; } + /** + * Explode the views in the given frame into separate AlignFrame + * + * @param af + */ public void explodeViews(AlignFrame af) { int size = af.alignPanels.size(); @@ -1777,15 +1800,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (int i = 0; i < size; i++) { - AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i); + AlignmentPanel ap = af.alignPanels.get(i); AlignFrame newaf = new AlignFrame(ap); - if (ap.av.explodedPosition != null - && !ap.av.explodedPosition.equals(af.getBounds())) + + /* + * 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(ap.av.explodedPosition); + newaf.setBounds(geometry); } - ap.av.gatherViewsHere = false; + ap.av.setGatherViewsHere(false); addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -1796,10 +1825,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements } + /** + * 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.gatherViewsHere = true; - source.viewport.explodedPosition = source.getBounds(); + source.viewport.setGatherViewsHere(true); + source.viewport.setExplodedGeometry(source.getBounds()); JInternalFrame[] frames = desktop.getAllFrames(); String viewId = source.viewport.getSequenceSetId(); @@ -1811,12 +1848,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements boolean gatherThis = false; for (int a = 0; a < af.alignPanels.size(); a++) { - AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a); + AlignmentPanel ap = af.alignPanels.get(a); if (viewId.equals(ap.av.getSequenceSetId())) { gatherThis = true; - ap.av.gatherViewsHere = false; - ap.av.explodedPosition = af.getBounds(); + ap.av.setGatherViewsHere(false); + ap.av.setExplodedGeometry(af.getBounds()); source.addAlignmentPanel(ap, false); } } @@ -1842,7 +1879,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.open_saved_vamsas_session")); + chooser.setDialogTitle(MessageManager + .getString("label.open_saved_vamsas_session")); chooser.setToolTipText(MessageManager .getString("label.select_vamsas_session_opened_as_new_vamsas_session")); @@ -1858,7 +1896,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Desktop.desktop, MessageManager.formatMessage( "label.couldnt_import_as_vamsas_session", - new String[] + new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), @@ -1935,23 +1973,26 @@ public class Desktop extends jalview.jbgui.GDesktop implements return false; } - setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{file.getName()}), - file.hashCode()); + 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 String[]{file.getName()}), - file.hashCode()); + 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 String[]{file.getName()}), - file.hashCode()); + setProgressBar(MessageManager.formatMessage( + "status.importing_vamsas_session_from", new Object[] + { file.getName() }), file.hashCode()); return v_client.inSession(); } @@ -1959,11 +2000,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (v_client != null) { - throw new Error(MessageManager.getString("error.try_join_vamsas_session_another")); + throw new Error( + MessageManager + .getString("error.try_join_vamsas_session_another")); } if (mysesid == null) { - throw new Error(MessageManager.getString("error.invalid_vamsas_session_id")); + throw new Error( + MessageManager.getString("error.invalid_vamsas_session_id")); } v_client = new VamsasApplication(this, mysesid); setupVamsasConnectedGui(); @@ -2053,7 +2097,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); sessit.setToolTipText(MessageManager.formatMessage( - "label.connect_to_session", new String[] + "label.connect_to_session", new Object[] { sess[i] })); final Desktop dsktp = this; final String mysesid = sess[i]; @@ -2110,14 +2154,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements { "Vamsas Document" }, "Vamsas Document"); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_vamsas_document_archive")); + chooser.setDialogTitle(MessageManager + .getString("label.save_vamsas_document_archive")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { java.io.File choice = chooser.getSelectedFile(); - JPanel progpanel = addProgressPanel(MessageManager.formatMessage("label.saving_vamsas_doc", new String[]{choice.getName()})); + JPanel progpanel = addProgressPanel(MessageManager.formatMessage( + "label.saving_vamsas_doc", new Object[] + { choice.getName() })); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; @@ -2169,7 +2216,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } if (b) { - vamUpdate = this.addProgressPanel(MessageManager.getString("label.updating_vamsas_session")); + vamUpdate = this.addProgressPanel(MessageManager + .getString("label.updating_vamsas_session")); } vamsasStart.setVisible(!b); vamsasStop.setVisible(!b); @@ -2204,6 +2252,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements public class MyDesktopPane extends JDesktopPane implements Runnable { + private static final float ONE_MB = 1048576f; + boolean showMemoryUsage = false; Runtime runtime; @@ -2243,9 +2293,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { try { - maxMemory = runtime.maxMemory() / 1048576f; - allocatedMemory = runtime.totalMemory() / 1048576f; - freeMemory = runtime.freeMemory() / 1048576f; + maxMemory = runtime.maxMemory() / ONE_MB; + allocatedMemory = runtime.totalMemory() / ONE_MB; + freeMemory = runtime.freeMemory() / ONE_MB; totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); percentUsage = (totalFreeMemory / maxMemory) * 100; @@ -2279,7 +2329,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { g.drawString(MessageManager.formatMessage( "label.memory_stats", - new String[] + new Object[] { df.format(totalFreeMemory), df.format(maxMemory), df.format(percentUsage) }), 10, getHeight() - fm.getHeight()); @@ -2319,8 +2369,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Accessor method to quickly get all the AlignmentFrames loaded. + * + * @return an array of AlignFrame, or null if none found */ - public static AlignFrame[] getAlignframes() + public static AlignFrame[] getAlignFrames() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -2328,35 +2380,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - Vector avp = new Vector(); - try + List avp = new ArrayList(); + // REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) { - // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + if (frames[i] instanceof AlignFrame) { - if (frames[i] instanceof AlignFrame) + avp.add((AlignFrame) frames[i]); + } + else if (frames[i] instanceof SplitFrame) + { + /* + * Also check for a split frame containing an AlignFrame + */ + GSplitFrame sf = (GSplitFrame) frames[i]; + if (sf.getTopFrame() instanceof AlignFrame) + { + avp.add((AlignFrame) sf.getTopFrame()); + } + if (sf.getBottomFrame() instanceof AlignFrame) { - AlignFrame af = (AlignFrame) frames[i]; - avp.addElement(af); + avp.add((AlignFrame) sf.getBottomFrame()); } } - } catch (Exception ex) - { - ex.printStackTrace(); } if (avp.size() == 0) { return null; } - AlignFrame afs[] = new AlignFrame[avp.size()]; - for (int i = 0, j = avp.size(); i < j; i++) - { - afs[i] = (AlignFrame) avp.elementAt(i); - } - avp.clear(); + AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]); return afs; } + /** + * Returns an array of any AppJmol frames in the Desktop (or null if none). + * + * @return + */ public GStructureViewer[] getJmols() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -2365,32 +2425,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - Vector avp = new Vector(); - try + List avp = new ArrayList(); + // REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) { - // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + if (frames[i] instanceof AppJmol) { - if (frames[i] instanceof AppJmol) - { - GStructureViewer af = (GStructureViewer) frames[i]; - avp.addElement(af); - } + GStructureViewer af = (GStructureViewer) frames[i]; + avp.add(af); } - } catch (Exception ex) - { - ex.printStackTrace(); } if (avp.size() == 0) { return null; } - GStructureViewer afs[] = new GStructureViewer[avp.size()]; - for (int i = 0, j = avp.size(); i < j; i++) - { - afs[i] = (GStructureViewer) avp.elementAt(i); - } - avp.clear(); + GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]); return afs; } @@ -2402,31 +2451,31 @@ public class Desktop extends jalview.jbgui.GDesktop implements // use reflection to avoid creating compilation dependency. if (!jalview.bin.Cache.groovyJarsPresent()) { - throw new Error(MessageManager.getString("error.implementation_error_cannot_create_groovyshell")); + throw new Error( + MessageManager + .getString("error.implementation_error_cannot_create_groovyshell")); } try { - Class gcClass = Desktop.class.getClassLoader().loadClass( + Class gcClass = Desktop.class.getClassLoader().loadClass( "groovy.ui.Console"); - Constructor gccons = gcClass.getConstructor(null); + Constructor gccons = gcClass.getConstructor(); java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class }); - java.lang.reflect.Method run = gcClass.getMethod("run", null); - Object gc = gccons.newInstance(null); + java.lang.reflect.Method run = gcClass.getMethod("run"); + Object gc = gccons.newInstance(); setvar.invoke(gc, new Object[] { "Jalview", this }); - run.invoke(gc, null); + run.invoke(gc); } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, + JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.couldnt_create_groovy_shell"), - MessageManager.getString("label.groovy_support_failed"), - JOptionPane.ERROR_MESSAGE); + MessageManager.getString("label.couldnt_create_groovy_shell"), + MessageManager.getString("label.groovy_support_failed"), + JOptionPane.ERROR_MESSAGE); } } @@ -2476,7 +2525,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { - throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); + throw new Error( + MessageManager + .getString("error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = progressBars.get(new Long(id)); @@ -2491,7 +2542,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); + us.setProgressBar(MessageManager.formatMessage( + "label.cancelled_params", new Object[] + { ((JLabel) progressPanel.getComponent(0)).getText() }), + id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -2513,20 +2567,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * This will return the first AlignFrame viewing AlignViewport av. It will - * break if there are more than one AlignFrames viewing a particular av. This + * This will return the first AlignFrame holding the given viewport instance. It + * will break if there are more than one AlignFrames viewing a particular av. * - * @param av - * @return alignFrame for av + * @param viewport + * @return alignFrame for viewport */ - public static AlignFrame getAlignFrameFor(AlignViewport av) + public static AlignFrame getAlignFrameFor(AlignViewportI viewport) { if (desktop != null) { - AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId()); + AlignmentPanel[] aps = getAlignmentPanels(viewport + .getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { - if (aps[panel] != null && aps[panel].av == av) + if (aps[panel] != null && aps[panel].av == viewport) { return aps[panel].alignFrame; } @@ -2753,17 +2808,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progress != null) { - progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new String[]{url}), this.hashCode()); + progress.setProgressBar(MessageManager.formatMessage( + "status.opening_params", new Object[] + { url }), this.hashCode()); } jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager.getString("label.web_browser_not_found_unix"), - MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager + .getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -2878,6 +2934,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements dialogPause = false; block.release(); } + @Override protected void snapShotWindow_actionPerformed(ActionEvent e) { @@ -2887,14 +2944,155 @@ public class Desktop extends jalview.jbgui.GDesktop implements "View of Desktop", getWidth(), getHeight(), of = new File( "Jalview_snapshot" + System.currentTimeMillis() + ".eps"), "View of desktop"); - try { + try + { paintAll(im.getGraphics()); im.writeImage(); } catch (Exception q) { - Cache.log.error("Couldn't write snapshot to "+of.getAbsolutePath(),q); + Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(), + q); + return; + } + Cache.log.info("Successfully written snapshot to file " + + of.getAbsolutePath()); + } + + /** + * Explode the views in the given frame into separate AlignFrame windows. + * + * @param sf + */ + public void explodeViews(SplitFrame sf) + { + AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame(); + AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame(); + List topPanels = oldTopFrame + .getAlignPanels(); + List bottomPanels = oldBottomFrame + .getAlignPanels(); + int viewCount = topPanels.size(); + if (viewCount < 2) + { return; } - Cache.log.info("Successfully written snapshot to file "+of.getAbsolutePath()); + + /* + * Processing in reverse order works, forwards order leaves the first panels + * not visible. I don't know why! + */ + for (int i = viewCount - 1; i >= 0; i--) + { + /* + * Make new top and bottom frames. These take over the respective + * AlignmentPanel objects, including their AlignmentViewports, so the + * cdna/protein relationships between the viewports is carried over to the + * new split frames. + */ + AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i); + AlignFrame newTopFrame = new AlignFrame(topPanel); + newTopFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT)); + newTopFrame.setVisible(true); + AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i); + AlignFrame newBottomFrame = new AlignFrame(bottomPanel); + newBottomFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT)); + newBottomFrame.setVisible(true); + topPanel.av.setGatherViewsHere(false); + bottomPanel.av.setGatherViewsHere(false); + JInternalFrame splitFrame = new SplitFrame(newTopFrame, + newBottomFrame); + // either panel may hold previous exploded frame geometry + Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) + .getExplodedGeometry(); + if (geometry != null) + { + splitFrame.setBounds(geometry); + } + Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); + } + + /* + * Clear references to the panels (now relocated in the new SplitFrames) + * before closing the old SplitFrame. + */ + topPanels.clear(); + bottomPanels.clear(); + sf.close(); } + + /** + * Gather expanded split frames, sharing the same pairs of sequence set ids, + * back into the given SplitFrame as additional views. Note that the gathered + * frames may themselves have multiple views. + * + * @param source + */ + public void gatherViews(GSplitFrame source) + { + AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); + AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); + myTopFrame.viewport.setExplodedGeometry(source.getBounds()); + myBottomFrame.viewport.setExplodedGeometry(source.getBounds()); + myTopFrame.viewport.setGatherViewsHere(true); + myBottomFrame.viewport.setGatherViewsHere(true); + String topViewId = myTopFrame.viewport.getSequenceSetId(); + String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); + + JInternalFrame[] frames = desktop.getAllFrames(); + for (JInternalFrame frame : frames) + { + if (frame instanceof SplitFrame && frame != source) + { + SplitFrame sf = (SplitFrame) frame; + AlignFrame topFrame = (AlignFrame) sf.getTopFrame(); + AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame(); + boolean gatherThis = false; + for (int a = 0; a < topFrame.alignPanels.size(); a++) + { + AlignmentPanel topPanel = topFrame.alignPanels.get(a); + AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a); + if (topViewId.equals(topPanel.av.getSequenceSetId()) + && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) + { + gatherThis = true; + topPanel.av.setGatherViewsHere(false); + bottomPanel.av.setGatherViewsHere(false); + // both panels refer to the same split frame geometry + Rectangle position = sf.getBounds(); + topPanel.av.setExplodedGeometry(position); + bottomPanel.av.setExplodedGeometry(position); + myTopFrame.addAlignmentPanel(topPanel, false); + myBottomFrame.addAlignmentPanel(bottomPanel, false); + } + } + + if (gatherThis) + { + topFrame.getAlignPanels().clear(); + bottomFrame.getAlignPanels().clear(); + sf.close(); + } + } + } + + /* + * The dust settles...give focus to the tab we did this from. + */ + myTopFrame.setDisplayedView(myTopFrame.alignPanel); + + } + + public static AlignFrame getCurrentAlignFrame() + { + return currentAlignFrame; + } + + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + Desktop.currentAlignFrame = currentAlignFrame; + } + + }