private static boolean testExternalNodeBasedCoverage() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final String ps1 =
"((((A:0.1,B:0.7):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,X:2.0)";
final Phylogeny p1 = factory.create(ps1, new NHXParser())[0];
final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>();
final List<String> names = new ArrayList<String>();
phylogenies.add(p1);
names.add("A");
names.add("A");
final CoverageCalculationOptions options =
new ExternalNodeBasedCoverageMethodOptions(
"org.forester.pccx.BranchCountingBasedScoringMethod");
final CoverageCalculator cc =
CoverageCalculator.getInstance(new ExternalNodeBasedCoverageMethod(), options);
Coverage cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(),
(1.0 + 1.0 / 2 + 1.0 / 3 + 1.0 / 4 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 / 5)
/ 9)) {
return false;
}
names.add("B");
names.add("B");
cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(),
(1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 / 7 + 1.0 / 5) / 9)) {
return false;
}
names.add("G");
cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(),
(1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 / 4 + 1.0 / 4 + 1.0 + 1.0 / 2 + 1.0 / 4) / 9)) {
return false;
}
names.add("E");
cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(),
(1.0 + 1.0 + 1.0 / 3 + 1.0 / 4 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0 / 4) / 9)) {
return false;
}
names.add("X");
cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(),
(1.0 + 1.0 + 1.0 / 3 + 1.0 / 3 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0) / 9)) {
return false;
}
names.add("C");
names.add("C");
names.add("C");
cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(), (1.0 + 1.0 + 1.0 + 1.0 / 3 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0) / 9)) {
return false;
}
names.add("D");
cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(), (1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 / 2 + 1.0 + 1.0 / 2 + 1.0) / 9)) {
return false;
}
names.add("F");
cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(), (1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 / 2 + 1.0) / 9)) {
return false;
}
names.add("H");
cov = cc.calculateCoverage(phylogenies, names, false);
if (!TestPccx.isEqual(
cov.getScore(), (1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0 + 1.0) / 9)) {
return false;
}
final CoverageExtender ce = new BasicExternalNodeBasedCoverageExtender();
List<String> l =
ce.find(
phylogenies,
null,
0,
new ExternalNodeBasedCoverageMethodOptions(
"org.forester.pccx.BranchCountingBasedScoringMethod"),
null);
if (!l.get(0).equals("X")) {
return false;
}
if (!l.get(1).equals("A")) {
return false;
}
if (!l.get(2).equals("E")) {
return false;
}
if (!l.get(3).equals("G")) {
return false;
}
if (!l.get(4).equals("C")) {
return false;
}
if (!l.get(5).equals("D")) {
return false;
}
if (!l.get(6).equals("B")) {
return false;
}
if (!l.get(7).equals("F")) {
return false;
}
if (!l.get(8).equals("H")) {
return false;
}
final List<String> already_covered = new ArrayList<String>();
already_covered.add("A");
already_covered.add("X");
already_covered.add("H");
already_covered.add("C");
l =
ce.find(
phylogenies,
already_covered,
0,
new ExternalNodeBasedCoverageMethodOptions(
"org.forester.pccx.BranchCountingBasedScoringMethod"),
null);
if (!l.get(0).equals("E")) {
return false;
}
if (!l.get(1).equals("D")) {
return false;
}
if (!l.get(2).equals("B")) {
return false;
}
if (!l.get(3).equals("F")) {
return false;
}
if (!l.get(4).equals("G")) {
return false;
}
final String ps2 =
"((((A:0.1,B:0.7):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,X:2.0)";
final String ps3 =
"((((A:0.1,B:0.1):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,X:2.0)";
final String ps4 =
"((((A:0.1,B:0.05):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,X:2.0)";
final Phylogeny p2 = factory.create(ps2, new NHXParser())[0];
final Phylogeny p3 = factory.create(ps3, new NHXParser())[0];
final Phylogeny p4 = factory.create(ps4, new NHXParser())[0];
final List<Phylogeny> phylogenies2 = new ArrayList<Phylogeny>();
final List<String> names2 = new ArrayList<String>();
phylogenies2.add(p2);
phylogenies2.add(p3);
phylogenies2.add(p4);
names2.add("A");
names2.add("A");
final CoverageCalculationOptions options2 =
new ExternalNodeBasedCoverageMethodOptions(
"org.forester.pccx.BranchLengthBasedScoringMethod");
final CoverageCalculator cc2 =
CoverageCalculator.getInstance(new ExternalNodeBasedCoverageMethod(), options2);
Coverage cov2 = cc2.calculateCoverage(phylogenies2, names2, false);
final double nf =
1
/ (1 / 0.1 + 1 / 0.7 + 1 / 1.0 + 1 / 1.7 + 1 / 0.3 + 1 / 0.4 + 1 / 0.5 + 1 / 0.6
+ 1 / 2.0);
if (!TestPccx.isEqual(
cov2.getScore(),
(1 / 0.1
+ (1 / 0.8 + 1 / 0.2 + 1 / 0.15) / 3
+ 1 / 1.3
+ 1 / 4.0
+ 1 / 6.4
+ 1 / 6.5
+ 1 / 6.7
+ 1 / 6.8
+ 1 / 5.6)
* nf)) {
return false;
}
names2.add("C");
cov2 = cc2.calculateCoverage(phylogenies2, names2, false);
if (!TestPccx.isEqual(
cov2.getScore(),
(1 / 0.1
+ (1 / 0.8 + 1 / 0.2 + 1 / 0.15) / 3
+ 1 / 1.0
+ 1 / 4.0
+ 1 / 6.4
+ 1 / 6.5
+ 1 / 6.7
+ 1 / 6.8
+ 1 / 5.6)
* nf)) {
return false;
}
names2.add("E");
cov2 = cc2.calculateCoverage(phylogenies2, names2, false);
if (!TestPccx.isEqual(
cov2.getScore(),
(1 / 0.1
+ (1 / 0.8 + 1 / 0.2 + 1 / 0.15) / 3
+ 1 / 1.0
+ +1 / 4.0
+ 1 / 0.3
+ 1 / 0.7
+ 1 / 3.1
+ 1 / 3.2
+ 1 / 4.8)
* nf)) {
return false;
}
final CoverageCalculationOptions options_log =
new ExternalNodeBasedCoverageMethodOptions(
"org.forester.pccx.LogBranchLengthBasedScoringMethod");
final CoverageCalculator cclog =
CoverageCalculator.getInstance(new ExternalNodeBasedCoverageMethod(), options_log);
final Coverage cov_log = cclog.calculateCoverage(phylogenies2, names2, false);
if (!TestPccx.isEqual(cov_log.getScore(), 0.8534252108361485)) {
return false;
}
final String ps10 =
"((((A:0.1,B:0.7):0.2,C:1.0):2.0,D:1.7):1.3,((E:0.3,F:0.4):1.1,(G:0.5,H:0.6):1.2):1.4,((((I:0.1,J:0.7):0.2,K:1.0):2.0,L:1.7):1.3,((M:0.3,N:0.4,O:0.1,P:0.2):1.1,(Q:0.5,R:0.6):1.2):1.4,S:2.0):2.0)";
final Phylogeny p10 = factory.create(ps10, new NHXParser())[0];
final List<Phylogeny> phylogenies10 = new ArrayList<Phylogeny>();
final List<String> names10 = new ArrayList<String>();
phylogenies10.add(p10);
names10.add("A");
names10.add("B");
names10.add("N");
names10.add("O");
final CoverageCalculationOptions options10 =
new ExternalNodeBasedCoverageMethodOptions(
"org.forester.pccx.BranchCountingBasedScoringMethod");
final CoverageCalculator cc10 =
CoverageCalculator.getInstance(new ExternalNodeBasedCoverageMethod(), options10);
cc10.calculateCoverage(phylogenies10, names10, true);
} catch (final Exception e) {
e.printStackTrace(System.out);
return false;
}
return true;
}
