add information content calculations

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index cd1e1a9..02d30bb 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -46,6 +46,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
@@ -172,14 +173,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }
 
   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
-          ColumnSelection columnSelection, JalviewLite applet,
+          HiddenColumns hidden, JalviewLite applet,
           String title, boolean embedded)
   {
-    this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+    this(al, hiddenSeqs, hidden, applet, title, embedded, true);
   }
 
   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
-          ColumnSelection columnSelection, JalviewLite applet,
+          HiddenColumns hidden, JalviewLite applet,
           String title, boolean embedded, boolean addToDisplay)
   {
     if (applet != null)
@@ -222,9 +223,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.hideSequence(hiddenSeqs);
     }
-    if (columnSelection != null)
+    if (hidden != null)
     {
-      viewport.setColumnSelection(columnSelection);
+      viewport.getAlignment().setHiddenColumns(hidden);
     }
     viewport.setScaleAboveWrapped(scaleAbove.getState());
 
@@ -600,24 +601,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     case KeyEvent.VK_PAGE_UP:
       if (viewport.getWrapAlignment())
       {
-        alignPanel.scrollUp(true);
+        ranges.scrollUp(true);
       }
       else
       {
-        alignPanel.setScrollValues(ranges.getStartRes(),
-                2 * ranges.getStartSeq() - ranges.getEndSeq());
+        ranges.pageUp();
       }
       break;
 
     case KeyEvent.VK_PAGE_DOWN:
       if (viewport.getWrapAlignment())
       {
-        alignPanel.scrollUp(false);
+        ranges.scrollUp(false);
       }
       else
       {
-        alignPanel
-                .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
+        ranges.pageDown();
       }
       break;
 
@@ -1799,7 +1798,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   synchronized void slideSequences(boolean right, int size)
   {
-    List<SequenceI> sg = new Vector<SequenceI>();
+    List<SequenceI> sg = new Vector<>();
     if (viewport.cursorMode)
     {
       sg.add(viewport.getAlignment().getSequenceAt(
@@ -1912,7 +1911,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     SequenceGroup sg = viewport.getSelectionGroup();
     copiedSequences = new StringBuffer();
-    Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
+    Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
     for (int i = 0; i < sg.getSize(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
@@ -1927,7 +1926,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       copiedHiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+      for (int[] region : viewport.getAlignment().getHiddenColumns()
+              .getHiddenRegions())
       {
         copiedHiddenColumns.addElement(new int[] {
             region[0] - hiddenOffset, region[1] - hiddenOffset });
@@ -4207,9 +4207,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * @param csel
    *          - columns to be selected on the alignment
    */
-  public void select(SequenceGroup sel, ColumnSelection csel)
+  public void select(SequenceGroup sel, ColumnSelection csel,
+          HiddenColumns hidden)
   {
-    alignPanel.seqPanel.selection(sel, csel, null);
+    alignPanel.seqPanel.selection(sel, csel, hidden, null);
   }
 
   public void scrollTo(int row, int column)