Add method to SequenceUtil to clean the protein sequence

[jabaws.git] / datamodel / compbio / data / sequence / SequenceUtil.java

diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java
index d0a6cd7..4d61d2a 100644 (file)
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -170,6 +170,17 @@ public final class SequenceUtil {
        }\r
 \r
        /**\r
+        * Remove all non AA chars from the sequence\r
+        * \r
+        * @param sequence\r
+        *            the sequence to clean\r
+        * @return cleaned sequence\r
+        */\r
+       public static String cleanProteinSequence(String sequence) {\r
+               return SequenceUtil.NON_AA.matcher(sequence).replaceAll("");\r
+       }\r
+\r
+       /**\r
         * @param sequence\r
         * @return true is the sequence is a protein sequence, false overwise\r
         */\r