X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=241eeebdd2cfc09bbc11a790468d7de98cf4846e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=96c9b72219d39dcc665f987e80374bc89c488feb;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 96c9b72..241eeeb 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -51,13 +51,13 @@ public class AlignSeq
 
   public static final String DNA = "dna";
 
-  static String[] dna =
-  { "A", "C", "G", "T", "-" };
+  private static final String NEWLINE = System.lineSeparator();
+
+  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;
 
@@ -449,7 +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 }));
     }
   }
 
@@ -579,21 +580,28 @@ 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 +611,8 @@ 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++)
@@ -638,9 +646,9 @@ 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++)
       {
@@ -650,7 +658,7 @@ public class AlignSeq
         }
       }
 
-      output = output.append("\n\n");
+      output.append(NEWLINE).append(NEWLINE);
     }
 
     pid = pid / (aseq1.length - count) * 100;
@@ -804,19 +812,23 @@ public class AlignSeq
   }
 
   /**
-   * DOCUMENT ME!
+   * Returns the given sequence with all of the given gap characters removed.
    * 
-   * @param gapChar
-   *          DOCUMENT ME!
+   * @param gapChars
+   *          a string of characters to be treated as gaps
    * @param seq
-   *          DOCUMENT ME!
+   *          the input sequence
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
-  public static String extractGaps(String gapChar, String seq)
+  public static String extractGaps(String gapChars, String seq)
   {
-    StringTokenizer str = new StringTokenizer(seq, gapChar);
-    StringBuffer newString = new StringBuffer();
+    if (gapChars == null || seq == null)
+    {
+      return null;
+    }
+    StringTokenizer str = new StringTokenizer(seq, gapChars);
+    StringBuilder newString = new StringBuilder(seq.length());
 
     while (str.hasMoreTokens())
     {
@@ -1084,8 +1096,8 @@ 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>();
@@ -1093,7 +1105,7 @@ public class AlignSeq
     {
       ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
       ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
-  
+
       for (SequenceI sq : ochains)
       {
         SequenceI bestm = null;
@@ -1101,8 +1113,7 @@ 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();
@@ -1128,7 +1139,8 @@ 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();)
@@ -1139,9 +1151,12 @@ 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);