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IB-2 COP F2 base case #1484

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a374aca
IB-2: Test scenario: COP of an F1 with itself
nahuel-soldevilla Sep 12, 2023
5a344e6
IB-2: Fix edge case where root nodes have number of progenitors = -1
nahuel-soldevilla Sep 12, 2023
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8 changes: 6 additions & 2 deletions src/main/java/org/generationcp/middleware/api/germplasm/pedigree/cop/CopCalculation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -248,7 +248,7 @@ public double coefficientOfInbreeding(final GermplasmTreeNode g) {
* D
*/
GermplasmTreeNode source = g.getMaleParentNode();
while (!isUnknown(source) && isDerivative(source)) {
while (hasSourceParent(source)) {
source = source.getMaleParentNode();
}
/*
Expand Down Expand Up @@ -388,7 +388,7 @@ private int countInbreedingGenerations(final GermplasmTreeNode g) {
}

int count = 1;
while (!isUnknown(source) && isDerivative(source) && !isUnknown(source.getMaleParentNode())) {
while (hasSourceParent(source)) {
count++;
source = source.getMaleParentNode();
}
Expand Down Expand Up @@ -540,6 +540,10 @@ private static boolean isUnknown(final GermplasmTreeNode node) {
return node == null || node.getGid() == UNKNOWN_GID;
}

private static boolean hasSourceParent(final GermplasmTreeNode source) {
return !isUnknown(source) && isDerivative(source) && !isUnknown(source.getMaleParentNode());
}

/**
*
* @param g1
Expand Down
123 changes: 123 additions & 0 deletions src/test/java/org/generationcp/middleware/api/germplasm/pedigree/cop/CopServiceImplTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,129 @@ public void testCoefficientOfInbreeding_KnownSource() {
assertThat(this.copService.coefficientOfInbreeding(p6.getGid(), BTypeEnum.SELF_FERTILIZING), is(31 / 32d));
}

/**
* <pre>
* AA BB CC DD
* EE FF
* GG
*
* gid1 gid2 cop
* "AA" "AA" 1
* "BB" "AA" 0
* "BB" "BB" 1
* "CC" "AA" 0
* "CC" "BB" 0
* "CC" "CC" 1
* "DD" "AA" 0
* "DD" "BB" 0
* "DD" "CC" 0
* "DD" "DD" 1
* "EE" "AA" 0.5
* "EE" "BB" 0.5
* "EE" "CC" 0
* "EE" "DD" 0
* "EE" "EE" 0.5
* "FF" "AA" 0
* "FF" "BB" 0
* "FF" "CC" 0.5
* "FF" "DD" 0.5
* "FF" "EE" 0
* "FF" "FF" 0.5
* "GG" "AA" 0.25
* "GG" "BB" 0.25
* "GG" "CC" 0.25
* "GG" "DD" 0.25
* "GG" "EE" 0.25
* "GG" "FF" 0.25
* "GG" "GG" 0.5
* </pre>
*
*/
@Test
public void testCase_SelfFertilizingF2() {
this.btype = BTypeEnum.SELF_FERTILIZING;

final Germplasm aa = this.createGermplasm("AA", 0, 0, 0);
final Germplasm bb = this.createGermplasm("BB", 0, 0, 0);
final Germplasm cc = this.createGermplasm("CC", 0, 0, 0);
final Germplasm dd = this.createGermplasm("DD", 0, 0, 0);
final Germplasm ee = this.createGermplasm("EE", 2, aa.getGid(), bb.getGid());
final Germplasm ff = this.createGermplasm("FF", 2, cc.getGid(), dd.getGid());
final Germplasm gg = this.createGermplasm("GG", 2, ee.getGid(), ff.getGid());

assertThat(this.copService.coefficientOfParentage(aa.getGid(), aa.getGid(), this.btype), is(1d));
assertThat(this.copService.coefficientOfParentage(bb.getGid(), aa.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(bb.getGid(), bb.getGid(), this.btype), is(1d));
assertThat(this.copService.coefficientOfParentage(cc.getGid(), aa.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(cc.getGid(), bb.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(cc.getGid(), cc.getGid(), this.btype), is(1d));
assertThat(this.copService.coefficientOfParentage(dd.getGid(), aa.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(dd.getGid(), bb.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(dd.getGid(), cc.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(dd.getGid(), dd.getGid(), this.btype), is(1d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), aa.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), bb.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), cc.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), dd.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), ee.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), aa.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), bb.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), cc.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), dd.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), ee.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), ff.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), aa.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), bb.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), cc.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), dd.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), ee.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), ff.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), gg.getGid(), this.btype), is(1 / 2d));
}

@Test
public void testCase_SelfFertilizingF2WithIncorrectProgenitorNumberForF0() {
this.btype = BTypeEnum.SELF_FERTILIZING;

final Germplasm aa = this.createGermplasm("AA", -1, 0, 0);
final Germplasm bb = this.createGermplasm("BB", -1, 0, 0);
final Germplasm cc = this.createGermplasm("CC", -1, 0, 0);
final Germplasm dd = this.createGermplasm("DD", -1, 0, 0);
final Germplasm ee = this.createGermplasm("EE", 2, aa.getGid(), bb.getGid());
final Germplasm ff = this.createGermplasm("FF", 2, cc.getGid(), dd.getGid());
final Germplasm gg = this.createGermplasm("GG", 2, ee.getGid(), ff.getGid());

assertThat(this.copService.coefficientOfParentage(aa.getGid(), aa.getGid(), this.btype), is(1d));
assertThat(this.copService.coefficientOfParentage(bb.getGid(), aa.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(bb.getGid(), bb.getGid(), this.btype), is(1d));
assertThat(this.copService.coefficientOfParentage(cc.getGid(), aa.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(cc.getGid(), bb.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(cc.getGid(), cc.getGid(), this.btype), is(1d));
assertThat(this.copService.coefficientOfParentage(dd.getGid(), aa.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(dd.getGid(), bb.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(dd.getGid(), cc.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(dd.getGid(), dd.getGid(), this.btype), is(1d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), aa.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), bb.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), cc.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), dd.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ee.getGid(), ee.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), aa.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), bb.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), cc.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), dd.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), ee.getGid(), this.btype), is(0d));
assertThat(this.copService.coefficientOfParentage(ff.getGid(), ff.getGid(), this.btype), is(1 / 2d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), aa.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), bb.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), cc.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), dd.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), ee.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), ff.getGid(), this.btype), is(1 / 4d));
assertThat(this.copService.coefficientOfParentage(gg.getGid(), gg.getGid(), this.btype), is(1 / 2d));
}


private Germplasm createGermplasm(final String name, final int gnpgs, final int gpid1, final int gpid2) {
final Name preferredName = new Name();
preferredName.setNval(name);
Expand Down