JAL-3732 - sequences can be moved up/down in cursor mode via alt-up/down arrow

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4810a96..4be7d0e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -538,7 +538,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1,
+                    evt.isShiftDown() && !evt.isAltDown());
           }
           break;
 
@@ -549,9 +550,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1,
+                    evt.isShiftDown() && !evt.isAltDown());
           }
-
           break;
 
         case KeyEvent.VK_LEFT:
@@ -562,7 +563,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
           }
 
           break;
@@ -574,7 +575,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
           }
           break;
 
@@ -1170,7 +1171,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
-              { fileName, format }));
+              { file, format }));
 
     }
     else
@@ -1199,48 +1200,49 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // create backupfiles object and get new temp filename destination
-        Cache.log.debug("ALIGNFRAME making backupfiles object for " + file);
+        Cache.log.trace("ALIGNFRAME making backupfiles object for " + file);
         BackupFiles backupfiles = new BackupFiles(file);
 
         try
         {
-          Cache.log.debug("ALIGNFRAME setting PrintWriter");
-          PrintWriter out = new PrintWriter(
-                  new FileWriter(backupfiles.getTempFilePath()));
+          String tempFilePath = backupfiles.getTempFilePath();
+          Cache.log.trace(
+                  "ALIGNFRAME setting PrintWriter to " + tempFilePath);
+          PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
 
-          Cache.log.debug("ALIGNFRAME using temp file "
-                  + backupfiles.getTempFilePath());
+          Cache.log.trace(
+                  "ALIGNFRAME about to write to temp file " + tempFilePath);
 
           out.print(output);
-          Cache.log.debug("ALIGNFRAME about to close file");
+          Cache.log.trace("ALIGNFRAME about to close file");
           out.close();
-          Cache.log.debug("ALIGNFRAME closed file");
+          Cache.log.trace("ALIGNFRAME closed file");
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
                   "label.successfully_saved_to_file_in_format", new Object[]
-                  { fileName, format.getName() }));
+                  { file, format.getName() }));
         } catch (IOException e)
         {
           success = false;
           Cache.log.error(
                   "ALIGNFRAME Something happened writing the temp file");
           Cache.log.error(e.getMessage());
-          Cache.log.debug(e.getStackTrace());
+          Cache.log.debug(Cache.getStackTraceString(e));
 
         } catch (Exception ex)
         {
           success = false;
           Cache.log.error(
-                  "ALIGNFRAME Something else happened writing the temp file");
+                  "ALIGNFRAME Something unexpected happened writing the temp file");
           Cache.log.error(ex.getMessage());
-          Cache.log.debug(ex.getStackTrace());
+          Cache.log.debug(Cache.getStackTraceString(ex));
         }
 
         backupfiles.setWriteSuccess(success);
         Cache.log.debug("ALIGNFRAME writing temp file was "
-                + (success ? "" : "not ") + "successful");
+                + (success ? "" : "NOT ") + "successful");
         // do the backup file roll and rename the temp file to actual file
-        Cache.log.debug("ALIGNFRAME about to rollBackupsAndRenameTempFile");
+        Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
         success = backupfiles.rollBackupsAndRenameTempFile();
         Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
                 + (success ? "" : "un") + "successfully");
@@ -1254,7 +1256,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         JvOptionPane.showInternalMessageDialog(this, MessageManager
                 .formatMessage("label.couldnt_save_file", new Object[]
-                { fileName }),
+                { file }),
                 MessageManager.getString("label.error_saving_file"),
                 JvOptionPane.WARNING_MESSAGE);
       }
@@ -1747,10 +1749,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode 
    * 
    * @param up
-   *          DOCUMENT ME!
+   *          or down (if !up)
    */
   public void moveSelectedSequences(boolean up)
   {
@@ -1758,8 +1760,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (sg == null)
     {
-      return;
+      if (viewport.cursorMode) 
+      {
+        sg = new SequenceGroup();
+        sg.addSequence(viewport.getAlignment()
+                .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
+      } else {
+        return;
+      }
+    }
+    
+    if (sg.getSize() < 1)
+    {
+        return;
     }
+    
+    // TODO: JAL-3733 - add an event to the undo buffer for this !
+    
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true, false);
@@ -1768,19 +1785,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   synchronized void slideSequences(boolean right, int size)
   {
     List<SequenceI> sg = new ArrayList<>();
-    if (viewport.cursorMode)
-    {
-      sg.add(viewport.getAlignment()
-              .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
-    }
-    else if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() != viewport
-                    .getAlignment().getHeight())
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
+            .getSize() != viewport.getAlignment().getHeight())
     {
       sg = viewport.getSelectionGroup()
               .getSequences(viewport.getHiddenRepSequences());
     }
 
+    if (sg.size() == 0 && viewport.cursorMode)
+    {
+      sg.add(viewport.getAlignment()
+              .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
+    }
+
     if (sg.size() < 1)
     {
       return;
@@ -2478,7 +2495,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
+    viewport.setSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
@@ -2715,15 +2732,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens a Finder dialog
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    new Finder();
+    new Finder(alignPanel);
   }
 
   /**