JAL-3878 update branch from 2.12 merge from 2.11.2

[jalview.git] / src / jalview / gui / PairwiseAlignPanel.java

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index d081794..f33b2d6 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -21,13 +21,13 @@
 package jalview.gui;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.AlignViewportI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPairwiseAlignPanel;
 import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.event.ActionEvent;
 import java.util.Vector;
@@ -43,7 +43,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private static final String DASHES = "---------------------\n";
 
-  AlignmentViewport av;
+  AlignViewportI av;
 
   Vector<SequenceI> sequences;
 
@@ -51,28 +51,27 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * Creates a new PairwiseAlignPanel object.
    * 
    * @param viewport
-   *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignmentViewport viewport)
+  public PairwiseAlignPanel(AlignViewportI viewport)
   {
     super();
     this.av = viewport;
 
-    sequences = new Vector<SequenceI>();
+    sequences = new Vector<>();
 
     SequenceGroup selectionGroup = viewport.getSelectionGroup();
     boolean isSelection = selectionGroup != null
             && selectionGroup.getSize() > 0;
     AlignmentView view = viewport.getAlignmentView(isSelection);
     // String[] seqStrings = viewport.getViewAsString(true);
-    String[] seqStrings = view.getSequenceStrings(viewport
-            .getGapCharacter());
+    String[] seqStrings = view
+            .getSequenceStrings(viewport.getGapCharacter());
 
     SequenceI[] seqs;
     if (isSelection)
     {
-      seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
-              .getGapCharacter())[0];
+      seqs = (SequenceI[]) view
+              .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
     }
     else
     {
@@ -109,8 +108,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         }
         first = false;
         as.printAlignment(System.out);
-        scores[i][j] = as.getMaxScore()
-                / as.getASeq1().length;
+        scores[i][j] = as.getMaxScore() / as.getASeq1().length;
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
@@ -140,8 +138,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
     for (int i = 0; i < seqs.length; i++)
     {
-      System.out.println(String.format("%3d %s", i + 1,
-              seqs[i].getDisplayId(true)));
+      System.out.println(
+              String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
     }
 
     /*