[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Wed Mar 21 12:22:56 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv15695/src/main/ca/ucalgary/seahawk/util

Modified Files:
	Sequence.java 
Log Message:
Made sequence finding more lenient w.r.t. whitespace
moby-live/Java/src/main/ca/ucalgary/seahawk/util Sequence.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/Sequence.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/Sequence.java	2007/02/08 16:59:58	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/Sequence.java	2007/03/21 16:22:56	1.3
@@ -12,6 +12,7 @@
      * @return true if ACGTUX comprise > 2/3 of the sequence, and all non-IUPAC letters comprise less than 5%
      */
     public static boolean isNucleicAcid(String sequence){
+        sequence = sequence.replaceAll("\\s", "");
 	String naChars = sequence.replaceAll("[^acgtunxACGTUNX]", "");
 	String nonNAChars = sequence.replaceAll("[acgtumrwsykvhdbnxACGTUMRWSYKVHDBNX \\-\t\r\n]", "");
 	double seqLen = (double) sequence.length(); // not int, because we don't want integer division
@@ -20,6 +21,7 @@
     }
 
     public static boolean isDNA(String sequence){
+        sequence = sequence.replaceAll("\\s", "");
 	String dnaChars = sequence.replaceAll("[^acgtnxACGTNX]", "");
 	String nonDNAChars = sequence.replaceAll("[acgtmrwsykvhdbnxACGTMRWSYKVHDBNX \\-\t\r\n]", "");
 	double seqLen = (double) sequence.length(); // not int, because we don't want integer division
@@ -27,6 +29,7 @@
     }
 
     public static boolean isRNA(String sequence){
+        sequence = sequence.replaceAll("\\s", "");
 	String rnaChars = sequence.replaceAll("[^acgunxACGUNX]", "");
 	String nonRNAChars = sequence.replaceAll("[acgumrwsykvhdbnxACGUMRWSYKVHDBNX \\-\t\r\n]", "");
 	double seqLen = (double) sequence.length(); // not int, because we don't want integer division
@@ -34,6 +37,7 @@
     }
 
     public static boolean isProtein(String sequence){
+        sequence = sequence.replaceAll("\\s", "");
 	String protChars = sequence.replaceAll("[^ARNDCQEGHILKMFPSTWYVBZXarndcqeghilkmfpstwyvbz*]", "");
 	String nonProtChars = sequence.replaceAll("[ARNDCQEGHILKMFPSTWYVBZXarndcqeghilkmfpstwyvbz \\-\t\r\n]", "");
 	double seqLen = (double) sequence.length(); // not int, because we don't want integer division