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Great! Contracts is working. Fixing some misspecified ones. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5854 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-05-23 21:00:52 +00:00
parent 833dff658a
commit c7f4674fe2
1 changed files with 6 additions and 6 deletions
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12
java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
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@ -64,8 +64,8 @@ public class MannWhitneyU {
* @param lessThanOther - either Set1 or Set2
* @return - u-based z-approximation, and p-value associated with the test (p-value is exact for small n,m)
*/
@Requires({"validateObservations(observations)", "lessThanOther != null"})
@Ensures({"result != null", "! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"})
@Requires({"lessThanOther != null"})
@Ensures({"validateObservations(observations) || Double.isNaN(result.getFirst())","result != null", "! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"})
public Pair<Double,Double> runOneSidedTest(USet lessThanOther) {
long u = calculateOneSidedU(observations, lessThanOther);
int n = lessThanOther == USet.SET1 ? sizeSet1 : sizeSet2;
@ -84,7 +84,7 @@ public class MannWhitneyU {
* @return a pair holding the u and p-value.
*/
@Ensures({"result != null", "! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"})
@Requires({"validateObservations(observations)"})
//@Requires({"validateObservations(observations)"})
public Pair<Double,Double> runTwoSidedTest() {
Pair<Long,USet> uPair = calculateTwoSidedU(observations);
long u = uPair.first;
@ -218,7 +218,7 @@ public class MannWhitneyU {
* @param observed - the observed data
* @return the minimum of the U counts (set1 dominates 2, set 2 dominates 1)
*/
@Requires({"observed != null", "observed.size() > 0", "validateObservations(observed)"})
@Requires({"observed != null", "observed.size() > 0"})
@Ensures({"result != null","result.first > 0"})
public static Pair<Long,USet> calculateTwoSidedU(TreeSet<Pair<Number,USet>> observed) {
int set1SeenSoFar = 0;
@ -255,7 +255,7 @@ public class MannWhitneyU {
* @param dominator - the set that is hypothesized to be stochastically dominating
* @return the u-statistic associated with the hypothesis that dominator stochastically dominates the other set
*/
@Requires({"observed != null","dominator != null","observed.size() > 0","validateObservations(observed)"})
@Requires({"observed != null","dominator != null","observed.size() > 0"})
@Ensures({"result >= 0"})
public static long calculateOneSidedU(TreeSet<Pair<Number,USet>> observed,USet dominator) {
long otherBeforeDominator = 0l;
@ -281,7 +281,7 @@ public class MannWhitneyU {
* @param twoSided: whether the test is two sided or not. The recursive formula is symmetric, multiply by two for two-sidedness.
* @return the probability under the hypothesis that all sequences are equally likely of finding a set-two entry preceding a set-one entry "u" times.
*/
@Requires({"m > 0","n > 0","u > 0"})
@Requires({"m > 0","n > 0","u >= 0"})
@Ensures({"result != null","! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"})
public static Pair<Double,Double> calculatePRecursively(int n, int m, long u, boolean twoSided) {
if ( m > 8 && n > 5 ) { throw new StingException(String.format("Please use the appropriate (normal or sum of uniform) approximation. Values n: %d, m: %d",n,m)); }