JAL-2490 tidy code and tests for feature export in Jalview format

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 681c777..b8700e1 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;
@@ -1444,12 +1447,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (format.equalsIgnoreCase("Jalview"))
     {
       features = formatter.printJalviewFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols());
+              .getSequencesArray(), getDisplayedFeatureCols(), true);
     }
     else
     {
       features = formatter.printGffFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols());
+              .getSequencesArray(), getDisplayedFeatureCols(), true);
     }
 
     if (displayTextbox)
@@ -1926,7 +1929,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       copiedHiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
       for (int[] region : viewport.getAlignment().getHiddenColumns()
-              .getListOfCols())
+              .getHiddenRegions())
       {
         copiedHiddenColumns.addElement(new int[] {
             region[0] - hiddenOffset, region[1] - hiddenOffset });
@@ -2732,7 +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()));
@@ -2824,25 +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))