X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=fb3bbc02f4de6983436e778f402433f22c6ecb82;hb=b3fb6325a8bc315c5c938faf10ffd2e73d965f16;hp=26051954cf5354a615331bc9557ac046fa44ec54;hpb=952d6b6fecfb976c0c113f013ed2b8980af3d190;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 2605195..fb3bbc0 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -102,8 +102,13 @@ import org.stackoverflowusers.file.WindowsShortcut; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.bin.Jalview; +import jalview.datamodel.Alignment; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; import jalview.gui.ImageExporter.ImageWriterI; import jalview.gui.QuitHandler.QResponse; import jalview.io.BackupFiles; @@ -197,6 +202,8 @@ public class Desktop extends jalview.jbgui.GDesktop { DRAG_MODE = b ? JDesktopPane.LIVE_DRAG_MODE : JDesktopPane.OUTLINE_DRAG_MODE; + if (desktop != null) + desktop.setDragMode(DRAG_MODE); } private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); @@ -428,7 +435,11 @@ public class Desktop extends jalview.jbgui.GDesktop { if (LaunchUtils.getJavaVersion() >= 11) { - jalview.bin.Console.info( + /* + * Send this message to stderr as the warning that follows (due to + * reflection) also goes to stderr. + */ + System.err.println( "Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that."); } try @@ -500,11 +511,15 @@ public class Desktop extends jalview.jbgui.GDesktop // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised desktop.setDesktopManager(new MyDesktopManager( - (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() - : Platform.isAMacAndNotJS() - ? new AquaInternalFrameManager( - desktop.getDesktopManager()) - : desktop.getDesktopManager()))); + Platform.isJS() ? desktop.getDesktopManager() + : new DefaultDesktopManager())); + /* + (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() + : Platform.isAMacAndNotJS() + ? new AquaInternalFrameManager( + desktop.getDesktopManager()) + : desktop.getDesktopManager()))); + */ Rectangle dims = getLastKnownDimensions(""); if (dims != null) @@ -792,26 +807,64 @@ public class Desktop extends jalview.jbgui.GDesktop public void paste() { - try + // quick patch for JAL-4150 - needs some more work and test coverage + // TODO - unify below and AlignFrame.paste() + // TODO - write tests and fix AlignFrame.paste() which doesn't track if + // clipboard has come from a different alignment window than the one where + // paste has been called! JAL-4151 + + if (Desktop.jalviewClipboard != null) { - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - Transferable contents = c.getContents(this); + // The clipboard was filled from within Jalview, we must use the + // sequences + // And dataset from the copied alignment + SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; + // be doubly sure that we create *new* sequence objects. + SequenceI[] sequences = new SequenceI[newseq.length]; + for (int i = 0; i < newseq.length; i++) + { + sequences[i] = new Sequence(newseq[i]); + } + Alignment alignment = new Alignment(sequences); + // dataset is inherited + alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); + AlignFrame af = new AlignFrame(alignment, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + String newtitle = new String("Copied sequences"); + + if (Desktop.jalviewClipboard[2] != null) + { + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); + } - if (contents != null) + Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + + } + else + { + try { - String file = (String) contents - .getTransferData(DataFlavor.stringFlavor); + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + Transferable contents = c.getContents(this); + + if (contents != null) + { + String file = (String) contents + .getTransferData(DataFlavor.stringFlavor); - FileFormatI format = new IdentifyFile().identify(file, - DataSourceType.PASTE); + FileFormatI format = new IdentifyFile().identify(file, + DataSourceType.PASTE); - new FileLoader().LoadFile(file, DataSourceType.PASTE, format); + new FileLoader().LoadFile(file, DataSourceType.PASTE, format); + } + } catch (Exception ex) + { + System.out.println( + "Unable to paste alignment from system clipboard:\n" + ex); } - } catch (Exception ex) - { - System.out.println( - "Unable to paste alignment from system clipboard:\n" + ex); } } @@ -1373,7 +1426,17 @@ public class Desktop extends jalview.jbgui.GDesktop if (jvnews != null) { storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); + } + + // Frames should all close automatically. Keeping external + // viewers open should already be decided by user. + closeAll_actionPerformed(null); + // check for aborted quit + if (QuitHandler.quitCancelled()) + { + jalview.bin.Console.debug("Desktop aborting quit"); + return null; } if (dialogExecutor != null) @@ -1381,8 +1444,6 @@ public class Desktop extends jalview.jbgui.GDesktop dialogExecutor.shutdownNow(); } - closeAll_actionPerformed(null); - if (groovyConsole != null) { // suppress a possible repeat prompt to save script @@ -1421,7 +1482,7 @@ public class Desktop extends jalview.jbgui.GDesktop // this will run the shutdownHook but QuitHandler.getQuitResponse() should // not run a second time if gotQuitResponse flag has been set (i.e. user // confirmed quit of some kind). - System.exit(0); + Jalview.exit("Desktop exiting.", 0); } private void storeLastKnownDimensions(String string, Rectangle jc) @@ -1567,6 +1628,22 @@ public class Desktop extends jalview.jbgui.GDesktop } } + public int structureViewersStillRunningCount() + { + int count = 0; + JInternalFrame[] frames = desktop.getAllFrames(); + for (int i = 0; i < frames.length; i++) + { + if (frames[i] != null + && frames[i] instanceof JalviewStructureDisplayI) + { + if (((JalviewStructureDisplayI) frames[i]).stillRunning()) + count++; + } + } + return count; + } + @Override public void raiseRelated_actionPerformed(ActionEvent e) { @@ -1830,7 +1907,7 @@ public class Desktop extends jalview.jbgui.GDesktop saveState_actionPerformed(true); } - private void setProjectFile(File choice) + protected void setProjectFile(File choice) { this.projectFile = choice; } @@ -2968,7 +3045,7 @@ public class Desktop extends jalview.jbgui.GDesktop /** * single thread that handles display of dialogs to user. */ - ExecutorService dialogExecutor = Executors.newSingleThreadExecutor(); + ExecutorService dialogExecutor = Executors.newFixedThreadPool(3); /** * flag indicating if dialogExecutor should try to acquire a permit