JAL-1807 disambiguated method signatures with numeric primitive args

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 2ef1c76..f76e801 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.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.
  * 
@@ -20,6 +20,13 @@
  */
 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;
@@ -32,13 +39,6 @@ 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;
-
 /**
  * 
  * 
@@ -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", "-" };
 
@@ -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++)
@@ -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();
@@ -804,19 +813,23 @@ 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())
     {