JAL-1807 explicit imports (jalview.gui)

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

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index dcddf88..292b970 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,13 +20,17 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPairwiseAlignPanel;
+import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.event.ActionEvent;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -37,7 +41,7 @@ import jalview.util.MessageManager;
 public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
 
-  AlignViewport av;
+  AlignmentViewport av;
 
   Vector sequences;
 
@@ -47,7 +51,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * @param av
    *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignmentViewport av)
   {
     super();
     this.av = av;
@@ -97,13 +101,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
-                .getStart(), as.getS1().getEnd());
-        sequences.add(seq);
-
-        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
-                .getStart(), as.getS2().getEnd());
-        sequences.add(seq);
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq2());
       }
     }
 
@@ -114,8 +113,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
       for (int i = 0; i < count; i++)
       {
-        jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
-                + seqs[i].getName());
+        Format.print(System.out, "%s \n",
+                ("" + i) + " " + seqs[i].getName());
       }
 
       System.out.println("\n");
@@ -124,8 +123,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       {
         for (int j = 0; j < i; j++)
         {
-          jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
-                  / totscore);
+          Format.printDouble(System.out, "%7.3f", scores[i][j] / totscore);
         }
       }