Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 2646ede..f914108 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -22,6 +22,9 @@ package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -43,6 +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;
@@ -169,14 +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)
@@ -219,9 +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());
 
@@ -1924,7 +1928,8 @@ 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 });
@@ -2730,7 +2735,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
-            .getAlignment().getSequenceAt(0), null);
+            .getAlignment().getSequenceAt(0));
 
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.getAlignment()));
@@ -2822,25 +2827,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void averageDistanceTreeMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
+    newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
+            "Average distance tree using PID");
   }
 
   public void neighbourTreeMenuItem_actionPerformed()
   {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+    newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
+            "Neighbour joining tree using PID");
   }
 
   protected void njTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+    newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
+            .getBlosum62().getName(),
+            "Neighbour joining tree using BLOSUM62");
   }
 
   protected void avTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+    newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
+            .getBlosum62().getName(),
+            "Average distance tree using BLOSUM62");
   }
 
-  void NewTreePanel(String type, String pwType, String title)
+  void newTreePanel(String type, String pwType, String title)
   {
     // are the sequences aligned?
     if (!viewport.getAlignment().isAligned(false))
@@ -4198,9 +4209,10 @@ 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)