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Added some methods to return the cross-talk partner base of a given base or base index. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@400 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-14 14:49:12 +00:00
parent eb4b4a053b
commit 40ea22eb17
1 changed files with 42 additions and 0 deletions
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42
java/src/org/broadinstitute/sting/utils/BaseUtils.java
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@ -1,6 +1,17 @@
package org.broadinstitute.sting.utils;
/**
* BaseUtils contains some basic utilities for manipulating nucleotides.
*
* @author Kiran Garimella
*/
public class BaseUtils {
/**
* Converts a simple base to a base index
*
* @param base [AaCcGgTt]
* @return 0, 1, 2, 3, or -1 if the base can't be understood
*/
static public int simpleBaseToBaseIndex(char base) {
switch (base) {
case 'A':
@ -19,6 +30,12 @@ public class BaseUtils {
}
}
/**
* Converts a base index to a simple base
*
* @param baseIndex 0, 1, 2, 3
* @return A, C, G, T, or '.' if the index can't be understood
*/
static public char baseIndexToSimpleBase(int baseIndex) {
switch (baseIndex) {
case 0: return 'A';
@ -28,4 +45,29 @@ public class BaseUtils {
default: return '.';
}
}
/**
* Converts a base index to a base index representing its cross-talk partner
*
* @param baseIndex 0, 1, 2, 3
* @return 1, 0, 3, 2, or -1 if the index can't be understood
*/
static public int crossTalkPartnerIndex(int baseIndex) {
switch (baseIndex) {
case 0: return 1; // A -> C
case 1: return 0; // C -> A
case 2: return 3; // G -> T
case 3: return 2; // T -> G
default: return -1;
}
}
/**
* Converts a base to the base representing its cross-talk partner
* @param base [AaCcGgTt]
* @return C, A, T, G, or '.' if the base can't be understood
*/
static public char crossTalkPartnerBase(char base) {
return baseIndexToSimpleBase(crossTalkPartnerIndex(simpleBaseToBaseIndex(base)));
}
}