JAL-2504 use (and update) defaults for new feature only if not supplied

[jalview.git] / src / jalview / appletgui / SeqPanel.java

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 60c53dd..d46cc34 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -25,6 +25,7 @@ import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -180,19 +181,22 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
     if (av.hasHiddenColumns()
-            && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+            && !av.getAlignment().getHiddenColumns()
+                    .isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
-      while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+      while (!av.getAlignment().getHiddenColumns()
+              .isVisible(seqCanvas.cursorX)
               && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-              || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+              || !av.getAlignment().getHiddenColumns()
+                      .isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -228,16 +232,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     else
     {
       ViewportRanges ranges = av.getRanges();
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       while (seqCanvas.cursorY < ranges.getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > ranges.getEndSeq())
+      while (seqCanvas.cursorY > ranges.getEndSeq())
       {
         ap.scrollUp(false);
       }
-      while (seqCanvas.cursorX < av.getColumnSelection()
-              .adjustForHiddenColumns(ranges.getStartRes()))
+      while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges
+              .getStartRes()))
       {
 
         if (!ap.scrollRight(false))
@@ -245,8 +250,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           break;
         }
       }
-      while (seqCanvas.cursorX > av.getColumnSelection()
-              .adjustForHiddenColumns(ranges.getEndRes()))
+      while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges
+              .getEndRes()))
       {
         if (!ap.scrollRight(true))
         {
@@ -570,7 +575,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       if (features != null && features.length > 0)
       {
         seqCanvas.getFeatureRenderer().amendFeatures(
-                new SequenceI[] { sequence }, features, false, ap, null);
+                new SequenceI[] { sequence }, features, false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -638,7 +643,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(res);
     }
 
     return res;
@@ -959,7 +965,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           fontSize = 1;
         }
 
-        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av.setFont(
+                new Font(av.font.getName(), av.font.getStyle(), fontSize),
+                true);
         av.setCharWidth(oldWidth);
       }
       else
@@ -1131,8 +1139,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (av.hasHiddenColumns())
     {
       fixedColumns = true;
-      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+      int y1 = av.getAlignment().getHiddenColumns()
+              .getHiddenBoundaryLeft(startres);
+      int y2 = av.getAlignment().getHiddenColumns()
+              .getHiddenBoundaryRight(startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1203,8 +1213,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           if (sg.getSize() == av.getAlignment().getHeight())
           {
-            if ((av.hasHiddenColumns() && startres < av
-                    .getColumnSelection().getHiddenBoundaryRight(startres)))
+            if ((av.hasHiddenColumns() && startres < av.getAlignment()
+                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
@@ -1787,7 +1797,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    */
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          SelectionSource source)
+          HiddenColumns hidden, SelectionSource source)
   {
     // TODO: fix this hack - source of messages is align viewport, but SeqPanel
     // handles selection messages...
@@ -1804,7 +1814,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
      * Check for selection in a view of which this one is a dna/protein
      * complement.
      */
-    if (selectionFromTranslation(seqsel, colsel, source))
+    if (selectionFromTranslation(seqsel, colsel, hidden, source))
     {
       return;
     }
@@ -1870,15 +1880,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          av.getColumnSelection().setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel,
+                  av.getAlignment().getHiddenColumns());
         }
       }
       repaint |= av.isColSelChanged(true);
     }
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getColumnSelection()
-                    .getHiddenColumns() == null))
+            && (av.getColumnSelection() == null || av.getAlignment()
+                    .getHiddenColumns().getHiddenRegions() == null))
     {
       System.err.println("Bad things");
     }
@@ -1938,7 +1949,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    * @param source
    */
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
-          ColumnSelection colsel, SelectionSource source)
+          ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     if (!(source instanceof AlignViewportI))
     {
@@ -1961,9 +1973,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     /*
      * Map column selection
      */
-    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
-            av);
+    // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+    // av);
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
+    MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
+    av.getAlignment().setHiddenColumns(hs);
 
     ap.scalePanelHolder.repaint();
     ap.repaint();