JAL-1551 spotlessApply

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 981a060..fb3bbc0 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;
@@ -431,7 +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
@@ -799,26 +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 (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);
 
-        new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
+    }
+    else
+    {
+      try
+      {
+        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);
+
+          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);
     }
   }