Merge branch 'develop' into features/JAL-2393customMatrices

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

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index a8ad086..22e1ab7 100644 (file)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -34,11 +34,11 @@ public class Comparison
 
   private static final int TO_UPPER_CASE = 'a' - 'A';
 
-  private static final char GAP_SPACE = ' ';
+  public static final char GAP_SPACE = ' ';
 
-  private static final char GAP_DOT = '.';
+  public static final char GAP_DOT = '.';
 
-  private static final char GAP_DASH = '-';
+  public static final char GAP_DASH = '-';
 
   public static final String GapChars = new String(new char[] { GAP_SPACE,
       GAP_DOT, GAP_DASH });
@@ -135,7 +135,9 @@ public class Comparison
    * @param s2
    *          SequenceI
    * @return float
+   * @deprecated use PIDModel.computePID()
    */
+  @Deprecated
   public final static float PID(String seq1, String seq2)
   {
     return PID(seq1, seq2, 0, seq1.length());
@@ -144,6 +146,10 @@ public class Comparison
   static final int caseShift = 'a' - 'A';
 
   // Another pid with region specification
+  /**
+   * @deprecated use PIDModel.computePID()
+   */
+  @Deprecated
   public final static float PID(String seq1, String seq2, int start, int end)
   {
     return PID(seq1, seq2, start, end, true, false);
@@ -165,7 +171,9 @@ public class Comparison
    * @param ungappedOnly
    *          - if true - only count PID over ungapped columns
    * @return
+   * @deprecated use PIDModel.computePID()
    */
+  @Deprecated
   public final static float PID(String seq1, String seq2, int start,
           int end, boolean wcGaps, boolean ungappedOnly)
   {
@@ -416,18 +424,24 @@ public class Comparison
     return isNucleotide(oneDArray);
   }
 
-  public static boolean compareChars(char c1, char c2, boolean caseSensitive)
+  /**
+   * Compares two residues either case sensitively or case insensitively
+   * depending on the caseSensitive flag
+   * 
+   * @param c1
+   *          first char
+   * @param c2
+   *          second char to compare with
+   * @param caseSensitive
+   *          if true comparison will be case sensitive otherwise its not
+   * @return
+   */
+  public static boolean isSameResidue(char c1, char c2,
+          boolean caseSensitive)
   {
-    boolean sameCase = (Character.isUpperCase(c1) && Character
-            .isUpperCase(c2))
-            || (Character.isLowerCase(c1) && Character.isLowerCase(c2));
-    if (sameCase)
-    {
-      return c1 == c2;
-    }
-    else if (caseSensitive)
+    if (caseSensitive)
     {
-      return false;
+      return (c1 == c2);
     }
     else
     {