Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 99580ae..5e16397 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;
 
@@ -1199,23 +1200,23 @@ 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
         {
           String tempFilePath = backupfiles.getTempFilePath();
-          Cache.log.debug(
+          Cache.log.trace(
                   "ALIGNFRAME setting PrintWriter to " + tempFilePath);
           PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
 
-          Cache.log.debug(
+          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[]
@@ -1232,7 +1233,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           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(Cache.getStackTraceString(ex));
         }
@@ -1241,7 +1242,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Cache.log.debug("ALIGNFRAME writing temp file was "
                 + (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");
@@ -1769,19 +1770,19 @@ 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;
@@ -2479,7 +2480,7 @@ 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
@@ -2716,15 +2717,14 @@ 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);
   }
 
   /**