JAL-2996 JAL-3053 ~ | : [] {} () treated as gap characters.

[jalview.git] / src / jalview / util / Comparison.java

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 94d6300..aa6bcd4 100644 (file)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -40,8 +40,29 @@ public class Comparison
 
   public static final char GAP_DASH = '-';
 
-  public static final String GapChars = new String(new char[] { GAP_SPACE,
-      GAP_DOT, GAP_DASH });
+  public static final char GAP_TILDE = '~';
+
+  public static final char GAP_PIPE = '|';
+
+  public static final char GAP_COLON = ':';
+
+  public static final char GAP_LPAREN = '(';
+
+  public static final char GAP_RPAREN = ')';
+
+  public static final char GAP_LSQBR = '[';
+
+  public static final char GAP_RSQBR = ']';
+
+  public static final char GAP_LBRACE = '{';
+
+  public static final char GAP_RBRACE = '}';
+
+  public static final String GapChars = new String(
+          new char[]
+          { GAP_SPACE, GAP_DOT, GAP_DASH, GAP_TILDE, GAP_PIPE, GAP_COLON,
+              GAP_LPAREN,
+              GAP_RPAREN, GAP_LSQBR, GAP_RSQBR, GAP_LBRACE, GAP_RBRACE });
 
   /**
    * DOCUMENT ME!
@@ -71,7 +92,8 @@ public class Comparison
    *          int
    * @return float
    */
-  public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+  public static float compare(SequenceI ii, SequenceI jj, int start,
+          int end)
   {
     String si = ii.getSequenceAsString();
     String sj = jj.getSequenceAsString();
@@ -97,8 +119,8 @@ public class Comparison
     {
       for (int j = 0; j < jlen; j++)
       {
-        if (si.substring(start + j, start + j + 1).equals(
-                sj.substring(start + j, start + j + 1)))
+        if (si.substring(start + j, start + j + 1)
+                .equals(sj.substring(start + j, start + j + 1)))
         {
           match++;
         }
@@ -112,8 +134,8 @@ public class Comparison
     {
       for (int j = 0; j < jlen; j++)
       {
-        if (si.substring(start + j, start + j + 1).equals(
-                sj.substring(start + j, start + j + 1)))
+        if (si.substring(start + j, start + j + 1)
+                .equals(sj.substring(start + j, start + j + 1)))
         {
           match++;
         }
@@ -150,7 +172,8 @@ public class Comparison
    * @deprecated use PIDModel.computePID()
    */
   @Deprecated
-  public final static float PID(String seq1, String seq2, int start, int end)
+  public final static float PID(String seq1, String seq2, int start,
+          int end)
   {
     return PID(seq1, seq2, start, end, true, false);
   }
@@ -253,7 +276,24 @@ public class Comparison
    */
   public static final boolean isGap(char c)
   {
-    return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false;
+    switch (c)
+    {
+    case GAP_SPACE:
+    case GAP_DOT:
+    case GAP_DASH:
+    case GAP_TILDE:
+    case GAP_PIPE:
+    case GAP_COLON:
+    case GAP_LPAREN:
+    case GAP_RPAREN:
+    case GAP_LSQBR:
+    case GAP_RSQBR:
+    case GAP_LBRACE:
+    case GAP_RBRACE:
+      return true;
+    default:
+      return false;
+    }
   }
 
   /**
@@ -388,7 +428,7 @@ public class Comparison
     {
       return false;
     }
-    List<SequenceI> flattened = new ArrayList<SequenceI>();
+    List<SequenceI> flattened = new ArrayList<>();
     for (SequenceI[] ss : seqs)
     {
       for (SequenceI s : ss)
@@ -396,8 +436,8 @@ public class Comparison
         flattened.add(s);
       }
     }
-    final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
-            .size()]);
+    final SequenceI[] oneDArray = flattened
+            .toArray(new SequenceI[flattened.size()]);
     return isNucleotide(oneDArray);
   }