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

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

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 1326647..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)
   {