import org.forester.development.DevelopmentTools;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sdi.SDI.TaxonomyComparisonBase;
+import org.forester.util.ForesterUtil;
public final class TestGSDI {
+ private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
+ + "test_data" + ForesterUtil.getFileSeparator();
+
private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
p.setRooted( true );
}
private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) {
- return PhylogenyMethods.getInstance().obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
+ return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent();
}
public static boolean test() {
private static boolean testGSDI_general() {
try {
- final PhylogenyMethods pm = PhylogenyMethods.getInstance();
+
+ final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
+ + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
+ + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
+ + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
+ + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
+ + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
+ + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
+ + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
+ + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
+ + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
+ + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
+ + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
+ + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
+ + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
+ + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
+ + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
+ + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
+ final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
+ s2.setRooted( true );
final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
s1.setRooted( true );
final Phylogeny g1 = TestGSDI
.createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
final GSDI sdi1 = new GSDI( g1, s1, false );
+ // Archaeopteryx.createApplication( g1 );
+ // Archaeopteryx.createApplication( s1 );
if ( sdi1.getDuplicationsSum() != 1 ) {
return false;
}
- if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
.isSpeciationOrDuplication() ) {
return false;
}
- if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) {
+ if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isDuplication() ) ) {
return false;
}
- if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g2 = TestGSDI
if ( sdi2.getDuplicationsSum() != 0 ) {
return false;
}
- if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
+ if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
.isSpeciationOrDuplication() ) {
return false;
}
- if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g3 = TestGSDI
if ( sdi3.getDuplicationsSum() != 0 ) {
return false;
}
- if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
+ if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
.isSpeciationOrDuplication() ) {
return false;
}
- if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g4 = TestGSDI
if ( sdi4.getDuplicationsSum() != 1 ) {
return false;
}
- if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
+ if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent()
+ .isDuplication() ) {
return false;
}
- if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g5 = TestGSDI
if ( sdi5.getDuplicationsSum() != 3 ) {
return false;
}
- if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
+ if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent()
+ .isDuplication() ) {
return false;
}
- if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
+ if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent()
+ .isDuplication() ) {
return false;
}
- if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
+ if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent()
+ .isDuplication() ) {
return false;
}
- if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
return false;
}
- final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
- + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
- + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
- + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
- + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
- + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
- + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
- + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
- + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
- + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
- + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
- + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
- + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
- + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
- + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
- + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
- + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
- final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
- s2.setRooted( true );
final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" );
final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
if ( sdi2_0.getDuplicationsSum() != 0 ) {
if ( sdi2_0.getSpeciationsSum() != 1 ) {
return false;
}
- if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
if ( sdi2_1.getSpeciationsSum() != 1 ) {
return false;
}
- if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
if ( sdi2_2.getSpeciationsSum() != 1 ) {
return false;
}
- if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
if ( sdi2_3.getSpeciationsSum() != 0 ) {
return false;
}
- if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData()
+ .getEvent().isDuplication() ) {
return false;
}
final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
if ( sdi2_4.getSpeciationsSum() != 2 ) {
return false;
}
- if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
if ( sdi2_5.getSpeciationsSum() != 2 ) {
return false;
}
- if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
if ( sdi2_6.getSpeciationsSum() != 2 ) {
return false;
}
- if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
if ( sdi2_7.getSpeciationsSum() != 1 ) {
return false;
}
- if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
- if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
+ if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
.isSpeciationOrDuplication() ) {
return false;
}
if ( sdi2_8.getSpeciationsSum() != 1 ) {
return false;
}
- if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
+ if ( !PhylogenyMethods.calculateLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
.isSpeciationOrDuplication() ) {
return false;
}
- if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ if ( !PhylogenyMethods.calculateLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
return false;
}
final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
final Phylogeny g2_22 = TestGSDI
.createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" );
final GSDI sdi2_22 = new GSDI( g2_22, s2, false );
+ //Archaeopteryx.createApplication( g2_22 );
+ //Archaeopteryx.createApplication( s2 );
if ( sdi2_22.getDuplicationsSum() != 0 ) {
return false;
}
if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
return false;
}
+ final Phylogeny g2_33_d = TestGSDI
+ .createPhylogeny( "((((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?],(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?])" );
+ final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false );
+ if ( sdi2_33_d.getDuplicationsSum() != 3 ) {
+ return false;
+ }
+ if ( sdi2_33_d.getSpeciationOrDuplicationEventsSum() != 14 ) {
+ return false;
+ }
+ if ( sdi2_33_d.getSpeciationsSum() != 6 ) {
+ return false;
+ }
final Phylogeny g2_34 = TestGSDI
.createPhylogeny( "(((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4])" );
final GSDI sdi2_34 = new GSDI( g2_34, s2, false );
if ( sdi7_4_2.getSpeciationsSum() != 5 ) {
return false;
}
- // final String g2_0_ =
- // "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
- // final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[
- // 0 ];
- // g2_0.setRooted( true );
- // final GSDI sdi2_0 = new GSDI( g2_0, s2, false );
- // if ( sdi2_0.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // final String g2_1_= "";
- // final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[
- // 0 ];
- // g2_1.setRooted( true );
- // final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
- // if ( sdi2_1.getDuplicationsSum() != 0 ) {
- // return false;
- // }
+ final String g2_0_ = "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))";
+ final Phylogeny g2_0p = TestGSDI.createPhylogeny( g2_0_ );
+ g2_0.setRooted( true );
+ final GSDI sdi2_0p = new GSDI( g2_0p, s2, false );
+ if ( sdi2_0p.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ //--
+ final Phylogeny tol_143_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + "tol_143.xml" )[ 0 ];
+ final Phylogeny gene_tree_tax_code_4_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gene_tree_tax_code_4.xml" )[ 0 ];
+ final GSDI gsdi_143_4_1 = new GSDI( gene_tree_tax_code_4_.copy(), tol_143_.copy(), false, true, true );
+ if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) {
+ return false;
+ }
+ if ( gsdi_143_4_1.getSpeciationsSum() != 28 ) {
+ return false;
+ }
+ if ( gsdi_143_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_gene_tree_sn_wnt = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ];
+ gsdi_test_gene_tree_sn_wnt.setRooted( true );
+ final GSDI a = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), tol_143_.copy(), false, true, true );
+ if ( a.getDuplicationsSum() != 33 ) {
+ return false;
+ }
+ if ( a.getSpeciationsSum() != 31 ) {
+ return false;
+ }
+ if ( a.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( a.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( a.getMappedExternalSpeciesTreeNodes().size() != 26 ) {
+ return false;
+ }
+ if ( a.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_species_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_species_tree_sn.xml" )[ 0 ];
+ final GSDI b = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
+ gsdi_test_species_tree_sn_xml.copy(),
+ false,
+ true,
+ true );
+ if ( b.getDuplicationsSum() != 8 ) {
+ return false;
+ }
+ if ( b.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( b.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( b.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( b.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
+ return false;
+ }
+ if ( b.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+ return false;
+ }
+ if ( b.getStrippedExternalGeneTreeNodes().size() != 87 ) {
+ return false;
+ }
+ if ( b.getStrippedSpeciesTreeNodes().size() != 17 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_species_tree_sn_nh = TestGSDI
+ .createPhylogeny( "((((((('Homo sapiens','Mus musculus')Euarchontoglires,'Petromyzon marinus')Vertebrata,'Nematostella vectensis')'Bilateria Cnidaria',(('Mycosphaerella graminicola','Mycosphaerella pini')Mycosphaerella,'Saccharomyces cerevisiae')'Pezizomycotina Saccharomycetales')Opisthokonta,('Plasmodium chabaudi','Plasmodium falciparum','Plasmodium yoelii yoelii')Plasmodium)Eukaryota,'Pyrococcus horikoshii')Neomura,(('Kineococcus radiotolerans','Kocuria rhizophila','Streptomyces coelicolor','Thermobifida fusca','Microlunatus phosphovorus'),'Bacteroides thetaiotaomicron'))'cellular organisms';" );
+ PhylogenyMethods.transferNodeNameToField( gsdi_test_species_tree_sn_nh,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ true );
+ final GSDI c = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
+ gsdi_test_species_tree_sn_nh.copy(),
+ false,
+ true,
+ true );
+ if ( c.getDuplicationsSum() != 8 ) {
+ return false;
+ }
+ if ( c.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( c.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( c.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( c.getMappedExternalSpeciesTreeNodes().size() != 2 ) {
+ return false;
+ }
+ if ( c.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+ return false;
+ }
+ if ( c.getStrippedExternalGeneTreeNodes().size() != 87 ) {
+ return false;
+ }
+ if ( c.getStrippedSpeciesTreeNodes().size() != 15 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_gene_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_gene_tree_codes.xml" )[ 0 ];
+ final Phylogeny gsdi_test_species_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_species_tree_codes.xml" )[ 0 ];
+ final GSDI d = new GSDI( gsdi_test_gene_tree_codes_xml.copy(),
+ gsdi_test_species_tree_codes_xml.copy(),
+ false,
+ true,
+ true );
+ if ( d.getDuplicationsSum() != 21 ) {
+ return false;
+ }
+ if ( d.getSpeciationsSum() != 28 ) {
+ return false;
+ }
+ if ( d.getSpeciationOrDuplicationEventsSum() != 6 ) {
+ return false;
+ }
+ if ( d.getTaxCompBase() != TaxonomyComparisonBase.CODE ) {
+ return false;
+ }
+ if ( d.getMappedExternalSpeciesTreeNodes().size() != 17 ) {
+ return false;
+ }
+ if ( d.getReMappedScientificNamesFromGeneTree().size() != 0 ) {
+ return false;
+ }
+ if ( d.getStrippedExternalGeneTreeNodes().size() != 12 ) {
+ return false;
+ }
+ if ( d.getStrippedSpeciesTreeNodes().size() != 3 ) {
+ return false;
+ }
+ //--
+ final Phylogeny gsdi_test_gene_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
+ + "gsdi_test_gene_tree_sn.xml" )[ 0 ];
+ final GSDI e = new GSDI( gsdi_test_gene_tree_sn_xml.copy(),
+ gsdi_test_species_tree_sn_xml.copy(),
+ false,
+ true,
+ true );
+ if ( e.getDuplicationsSum() != 7 ) {
+ return false;
+ }
+ if ( e.getSpeciationsSum() != 9 ) {
+ return false;
+ }
+ if ( e.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( e.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+ return false;
+ }
+ if ( e.getMappedExternalSpeciesTreeNodes().size() != 12 ) {
+ return false;
+ }
+ if ( e.getReMappedScientificNamesFromGeneTree().size() != 8 ) {
+ return false;
+ }
+ if ( e.getStrippedExternalGeneTreeNodes().size() != 3 ) {
+ return false;
+ }
+ if ( e.getStrippedSpeciesTreeNodes().size() != 7 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testGSDIR_general() {
+ try {
+
+ final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4]),"
+ + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4]),"
+ + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4]),"
+ + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),("
+ + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4]),"
+ + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4]),"
+ + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4]),"
+ + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),("
+ + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4]),"
+ + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4]),"
+ + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4]),"
+ + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),("
+ + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4]),"
+ + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4]),"
+ + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4]),"
+ + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])"
+ + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])";
+ final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ];
+ s2.setRooted( true );
+ final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])";
+ final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ];
+ s1.setRooted( true );
+ final Phylogeny g1 = TestGSDI
+ .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" );
+ final GSDIR sdi1 = new GSDIR( g1, s1, false, 1 );
+ // Archaeopteryx.createApplication( g1 );
+ // Archaeopteryx.createApplication( s1 );
+ if ( sdi1.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isDuplication() ) ) {
+ return false;
+ }
+ if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent()
+ .isSpeciation() ) {
+ return false;
+ }
+
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
return true;
}
+
+ public static void main( final String[] args ) {
+ if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
+ System.out.println( "binary failed" );
+ }
+ if ( !TestGSDI.testGSDI_general() ) {
+ System.out.println( "general failed" );
+ }
+ if ( !TestGSDI.testGSDIR_general() ) {
+ System.out.println( "general re-rooting failed" );
+ }
+ else {
+ System.out.println( "OK" );
+ }
+ // boolean success = test();
+ // if ( success ) {
+ // System.out.println( "OK" );
+ // }
+ // else {
+ // System.out.println( "failed" );
+ // }
+ }
}
git://source.jalview.org / jalview.git / blobdiff