JAL-3820 Create and use 'Jalview app' symblinks to java executable. Fixes grouped...

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ba7665b..1c55476 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -105,6 +105,10 @@ 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;
@@ -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));
       }
     }
@@ -799,26 +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 (Desktop.jalviewClipboard[2] != null)
+      {
+        HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+        af.viewport.setHiddenColumns(hc);
+      }
+
+      Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
 
-      if (contents != null)
+    }
+    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);
     }
   }
 
@@ -1436,8 +1484,7 @@ 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.out.println("Desktop exiting.");
-    System.exit(0);
+    Jalview.exit("Desktop exiting.", 0);
   }
 
   private void storeLastKnownDimensions(String string, Rectangle jc)