X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=369721d8c2b325fa0d4bec3a20ce73f9824906f3;hb=0ebcd487f08f9873987d9a32edce7df47aa27927;hp=5612133cb95ef77c1b2aec9931d7c687b7b90870;hpb=d69ae82ef958ae5bd67481d0b018a1db3662d4ae;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 5612133..369721d 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;
+
 /**
  * 
  * 
@@ -53,13 +53,11 @@ public class AlignSeq
 
   private static final String NEWLINE = System.lineSeparator();
 
-  static String[] dna =
-  { "A", "C", "G", "T", "-" };
+  static String[] dna = { "A", "C", "G", "T", "-" };
 
   // "C", "T", "A", "G", "-"};
-  static String[] pep =
-  { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
-      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
+  static String[] pep = { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I",
+      "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
 
   int[][] score;
 
@@ -451,7 +449,8 @@ public class AlignSeq
     else
     {
       output.append("Wrong type = dna or pep only");
-      throw new Error(MessageManager.formatMessage("error.unknown_type_dna_or_pep", new String[]{type2}));
+      throw new Error(MessageManager.formatMessage(
+              "error.unknown_type_dna_or_pep", new String[] { type2 }));
     }
   }
 
@@ -578,7 +577,8 @@ public class AlignSeq
       }
     }
     int len = 72 - maxid - 1;
-    int nochunks = ((aseq1.length - count) / len) + 1;
+    int nochunks = ((aseq1.length - count) / len)
+            + ((aseq1.length - count) % len > 0 ? 1 : 0);
     pid = 0;
 
     output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE);
@@ -663,9 +663,8 @@ public class AlignSeq
     }
 
     pid = pid / (aseq1.length - count) * 100;
-    output = output.append(new Format("Percentage ID = %2.2f\n\n")
+    output = output.append(new Format("Percentage ID = %2.2f\n")
             .form(pid));
-
     try
     {
       os.print(output.toString());
@@ -949,6 +948,7 @@ public class AlignSeq
   public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
           int psize)
   {
+    // TODO method dosen't seem to be referenced anywhere delete??
     int max = -1000;
     int min = 1000;
 
@@ -1097,8 +1097,8 @@ public class AlignSeq
    */
   public static List<List<? extends Object>> replaceMatchingSeqsWith(
           List<SequenceI> seqs, List<AlignmentAnnotation> annotations,
-          List<SequenceI> ochains,
-          AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
+          List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
+          boolean removeOldAnnots)
   {
     List<SequenceI> orig = new ArrayList<SequenceI>(), repl = new ArrayList<SequenceI>();
     List<AlignSeq> aligs = new ArrayList<AlignSeq>();
@@ -1106,7 +1106,7 @@ public class AlignSeq
     {
       ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
       ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
-  
+
       for (SequenceI sq : ochains)
       {
         SequenceI bestm = null;
@@ -1114,8 +1114,7 @@ public class AlignSeq
         int bestscore = 0;
         for (SequenceI msq : al.getSequences())
         {
-          AlignSeq aseq = doGlobalNWAlignment(msq, sq,
-                  dnaOrProtein);
+          AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein);
           if (bestm == null || aseq.getMaxScore() > bestscore)
           {
             bestscore = aseq.getMaxScore();
@@ -1141,7 +1140,8 @@ public class AlignSeq
           sq.setName(sp.getName());
           sq.setDescription(sp.getDescription());
           Mapping sp2sq;
-          sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+          sq.transferAnnotation(sp,
+                  sp2sq = aligns.get(q).getMappingFromS1(false));
           aligs.add(aligns.get(q));
           int inspos = -1;
           for (int ap = 0; ap < annotations.size();)
@@ -1152,9 +1152,12 @@ public class AlignSeq
               {
                 inspos = ap;
               }
-              if (removeOldAnnots) {
+              if (removeOldAnnots)
+              {
                 annotations.remove(ap);
-              } else {
+              }
+              else
+              {
                 AlignmentAnnotation alan = annotations.remove(ap);
                 alan.liftOver(sq, sp2sq);
                 alan.setSequenceRef(sq);