X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=ed44d4ad8d5c54201613435700401b32de275d18;hb=5bd245162908974e3c96329da6a803598341bae1;hp=5612133cb95ef77c1b2aec9931d7c687b7b90870;hpb=d69ae82ef958ae5bd67481d0b018a1db3662d4ae;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 5612133..ed44d4a 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,13 +20,6 @@
  */
 package jalview.analysis;
 
-import java.awt.Color;
-import java.awt.Graphics;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.StringTokenizer;
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
@@ -39,6 +32,13 @@ import jalview.util.Format;
 import jalview.util.MapList;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Graphics;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
+
 /**
  * 
  * 
@@ -365,8 +365,8 @@ public class AlignSeq
    */
   private void SeqInit(String string1, String string2)
   {
-    s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
-    s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
+    s1str = extractGaps(Comparison.GapChars, string1);
+    s2str = extractGaps(Comparison.GapChars, string2);
 
     if (s1str.length() == 0 || s2str.length() == 0)
     {
@@ -621,7 +621,7 @@ public class AlignSeq
         if ((i + (j * len)) < astr1.length())
         {
           if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
-                  && !jalview.util.Comparison.isGap(astr1.charAt(i
+                  && !Comparison.isGap(astr1.charAt(i
                           + (j * len))))
           {
             pid++;
@@ -664,7 +664,7 @@ public class AlignSeq
 
     pid = pid / (aseq1.length - count) * 100;
     output = output.append(new Format("Percentage ID = %2.2f\n\n")
-            .form(pid));
+            .formDouble(pid));
 
     try
     {
@@ -707,7 +707,7 @@ public class AlignSeq
           Format.print(System.out, "%3s", s1str.substring(i, i + 1));
         }
 
-        Format.print(System.out, "%3d ", mat[i][j] / 10);
+        Format.printLong(System.out, "%3d ", mat[i][j] / 10);
       }
 
       System.out.println();
@@ -1010,7 +1010,7 @@ public class AlignSeq
    * 
    * @return mapping from positions in S1 to corresponding positions in S2
    */
-  public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
+  public Mapping getMappingFromS1(boolean allowmismatch)
   {
     ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
     int pdbpos = s2.getStart() + getSeq2Start() - 2;
@@ -1077,7 +1077,7 @@ public class AlignSeq
     }
     MapList map = new MapList(mapseq1, mapseq2, 1, 1);
 
-    jalview.datamodel.Mapping mapping = new Mapping(map);
+    Mapping mapping = new Mapping(map);
     mapping.setTo(s2);
     return mapping;
   }