X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=bfd700f0c069971aa2737d87a9b8a580817d40dd;hb=a27b3832ad1bbe70548bcc53301446c75d02672a;hp=dbc99c0dd13d73b405d402b662afabdd230fb2fe;hpb=9b943e6d79fd92f78a61916a6f6eb047ba0a9755;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index dbc99c0..bfd700f 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -64,7 +64,6 @@ import java.util.List; import java.util.ListIterator; import java.util.Locale; import java.util.Vector; -import java.util.concurrent.Callable; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; @@ -105,6 +104,10 @@ 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; @@ -118,6 +121,7 @@ import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; +import jalview.io.exceptions.ImageOutputException; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; import jalview.project.Jalview2XML; @@ -431,9 +435,14 @@ 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."); } + final String awtAppClassName = "awtAppClassName"; try { Toolkit xToolkit = Toolkit.getDefaultToolkit(); @@ -441,10 +450,10 @@ public class Desktop extends jalview.jbgui.GDesktop Field awtAppClassNameField = null; if (Arrays.stream(declaredFields) - .anyMatch(f -> f.getName().equals("awtAppClassName"))) + .anyMatch(f -> f.getName().equals(awtAppClassName))) { awtAppClassNameField = xToolkit.getClass() - .getDeclaredField("awtAppClassName"); + .getDeclaredField(awtAppClassName); } String title = ChannelProperties.getProperty("app_name"); @@ -455,11 +464,12 @@ public class Desktop extends jalview.jbgui.GDesktop } else { - jalview.bin.Console.debug("XToolkit: awtAppClassName not found"); + jalview.bin.Console + .debug("XToolkit: " + awtAppClassName + " not found"); } } catch (Exception e) { - jalview.bin.Console.debug("Error setting awtAppClassName"); + jalview.bin.Console.debug("Error setting " + awtAppClassName); jalview.bin.Console.trace(Cache.getStackTraceString(e)); } } @@ -503,11 +513,15 @@ 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) @@ -795,26 +809,64 @@ 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 (contents != null) + if (Desktop.jalviewClipboard[2] != null) { - String file = (String) contents - .getTransferData(DataFlavor.stringFlavor); + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); + } - FileFormatI format = new IdentifyFile().identify(file, - DataSourceType.PASTE); + Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + + } + else + { + try + { + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + Transferable contents = c.getContents(this); + + if (contents != null) + { + String file = (String) contents + .getTransferData(DataFlavor.stringFlavor); - new FileLoader().LoadFile(file, DataSourceType.PASTE, format); + FileFormatI format = new IdentifyFile().identify(file, + DataSourceType.PASTE); + 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); } } @@ -1212,7 +1264,6 @@ public class Desktop extends jalview.jbgui.GDesktop new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, format); - return null; }); chooser.showOpenDialog(this); } @@ -1268,7 +1319,7 @@ public class Desktop extends jalview.jbgui.GDesktop Object[] options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; - Callable action = () -> { + Runnable action = () -> { @SuppressWarnings("unchecked") String url = (history instanceof JTextField ? ((JTextField) history).getText() @@ -1307,8 +1358,7 @@ public class Desktop extends jalview.jbgui.GDesktop JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE); - - return null; // Void + return; } if (viewport != null) @@ -1321,7 +1371,6 @@ public class Desktop extends jalview.jbgui.GDesktop new FileLoader().LoadFile(url, DataSourceType.URL, format); } } - return null; // Void }; String dialogOption = MessageManager .getString("label.input_alignment_from_url"); @@ -1360,7 +1409,7 @@ public class Desktop extends jalview.jbgui.GDesktop public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag) { - final Callable doDesktopQuit = () -> { + final Runnable doDesktopQuit = () -> { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); @@ -1386,7 +1435,7 @@ public class Desktop extends jalview.jbgui.GDesktop if (QuitHandler.quitCancelled()) { jalview.bin.Console.debug("Desktop aborting quit"); - return null; + return; } if (dialogExecutor != null) @@ -1415,8 +1464,6 @@ public class Desktop extends jalview.jbgui.GDesktop // instance.dispose(); } instance.quit(); - - return null; // Void }; return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit, @@ -1432,7 +1479,7 @@ 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) @@ -1564,7 +1611,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } Jalview.setCurrentAlignFrame(null); - System.out.println("ALL CLOSED"); + jalview.bin.Console.info("ALL CLOSED"); /* * reset state of singleton objects as appropriate (clear down session state @@ -1915,7 +1962,6 @@ public class Desktop extends jalview.jbgui.GDesktop } } }, "Project Loader").start(); - return null; }); chooser.showOpenDialog(this); @@ -3086,7 +3132,11 @@ public class Desktop extends jalview.jbgui.GDesktop String title = "View of desktop"; ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, title); - exporter.doExport(of, this, width, height, title); + try { + exporter.doExport(of, this, width, height, title); + } catch (ImageOutputException ioex) { + jalview.bin.Console.error("Unexpected error whilst writing Jalview desktop snapshot as EPS",ioex); + } } /** @@ -3526,4 +3576,17 @@ public class Desktop extends jalview.jbgui.GDesktop jalview.bin.Console.debug(Cache.getStackTraceString(e)); } } + + /** + * closes the current instance window, disposes and forgets about it. + */ + public static void closeDesktop() + { + if (Desktop.instance != null) { + Desktop.instance.closeAll_actionPerformed(null); + Desktop.instance.setVisible(false); + Desktop.instance.dispose(); + Desktop.instance = null; + } + } }