X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=ed44d4ad8d5c54201613435700401b32de275d18;hb=7d6575e94bed92bc06043d432576e3a39e8a8e75;hp=bd4cc223152a38191ca5fccff936147c4f68744e;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index bd4cc22..ed44d4a 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -51,6 +51,8 @@ public class AlignSeq
 
   public static final String DNA = "dna";
 
+  private static final String NEWLINE = System.lineSeparator();
+
   static String[] dna =
   { "A", "C", "G", "T", "-" };
 
@@ -363,8 +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)
     {
@@ -579,21 +581,28 @@ public class AlignSeq
     int nochunks = ((aseq1.length - count) / len) + 1;
     pid = 0;
 
-    output.append("Score = " + score[maxi][maxj] + "\n");
-    output.append("Length of alignment = " + (aseq1.length - count) + "\n");
+    output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE);
+    output.append("Length of alignment = ")
+            .append(String.valueOf(aseq1.length - count)).append(NEWLINE);
     output.append("Sequence ");
     output.append(new Format("%" + maxid + "s").form(s1.getName()));
-    output.append(" :  " + s1.getStart() + " - " + s1.getEnd()
-            + " (Sequence length = " + s1str.length() + ")\n");
+    output.append(" :  ").append(String.valueOf(s1.getStart()))
+            .append(" - ").append(String.valueOf(s1.getEnd()));
+    output.append(" (Sequence length = ")
+            .append(String.valueOf(s1str.length())).append(")")
+            .append(NEWLINE);
     output.append("Sequence ");
     output.append(new Format("%" + maxid + "s").form(s2.getName()));
-    output.append(" :  " + s2.getStart() + " - " + s2.getEnd()
-            + " (Sequence length = " + s2str.length() + ")\n\n");
+    output.append(" :  ").append(String.valueOf(s2.getStart()))
+            .append(" - ").append(String.valueOf(s2.getEnd()));
+    output.append(" (Sequence length = ")
+            .append(String.valueOf(s2str.length())).append(")")
+            .append(NEWLINE).append(NEWLINE);
 
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
-      output.append(new Format("%" + (maxid) + "s").form(s1id) + " ");
+      output.append(new Format("%" + (maxid) + "s").form(s1id)).append(" ");
 
       for (int i = 0; i < len; i++)
       {
@@ -603,8 +612,8 @@ public class AlignSeq
         }
       }
 
-      output.append("\n");
-      output.append(new Format("%" + (maxid) + "s").form(" ") + " ");
+      output.append(NEWLINE);
+      output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
 
       // Print out the matching chars
       for (int i = 0; i < len; i++)
@@ -612,7 +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++;
@@ -638,9 +647,9 @@ public class AlignSeq
       }
 
       // Now print the second aligned sequence
-      output = output.append("\n");
-      output = output.append(new Format("%" + (maxid) + "s").form(s2id)
-              + " ");
+      output = output.append(NEWLINE);
+      output = output.append(new Format("%" + (maxid) + "s").form(s2id))
+              .append(" ");
 
       for (int i = 0; i < len; i++)
       {
@@ -650,12 +659,12 @@ public class AlignSeq
         }
       }
 
-      output = output.append("\n\n");
+      output.append(NEWLINE).append(NEWLINE);
     }
 
     pid = pid / (aseq1.length - count) * 100;
     output = output.append(new Format("Percentage ID = %2.2f\n\n")
-            .form(pid));
+            .formDouble(pid));
 
     try
     {
@@ -698,7 +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();
@@ -1001,7 +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;
@@ -1068,7 +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;
   }