JAL-2591 More rationalising of hiddencols

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 681c777..a75adbb 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;
@@ -598,24 +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;
 
@@ -1797,7 +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(
@@ -1910,7 +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);
@@ -1925,8 +1926,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       copiedHiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int[] region : viewport.getAlignment().getHiddenColumns()
-              .getListOfCols())
+      for (int[] region : viewport.getAlignment().getHiddenColumns())
       {
         copiedHiddenColumns.addElement(new int[] {
             region[0] - hiddenOffset, region[1] - hiddenOffset });
@@ -2732,7 +2732,7 @@ 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()));
@@ -2824,25 +2824,31 @@ 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))