in progress

[jalview.git] / forester / java / src / org / forester / sdi / TestGSDI.java

diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java
index 91ac13a..6480281 100644 (file)
--- a/forester/java/src/org/forester/sdi/TestGSDI.java
+++ b/forester/java/src/org/forester/sdi/TestGSDI.java
@@ -50,7 +50,7 @@ public final class TestGSDI {
     }
 
     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() {
@@ -128,17 +128,20 @@ public final class TestGSDI {
             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
@@ -147,17 +150,20 @@ public final class 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
@@ -166,17 +172,20 @@ public final class 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
@@ -185,13 +194,16 @@ public final class 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
@@ -200,19 +212,24 @@ public final class 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]),"
@@ -265,7 +282,8 @@ public final class TestGSDI {
             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])" );
@@ -279,7 +297,8 @@ public final class TestGSDI {
             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])" );
@@ -293,7 +312,8 @@ public final class TestGSDI {
             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])" );
@@ -307,7 +327,8 @@ public final class TestGSDI {
             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])" );
@@ -321,10 +342,12 @@ public final class TestGSDI {
             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])" );
@@ -338,10 +361,12 @@ public final class TestGSDI {
             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])" );
@@ -355,10 +380,12 @@ public final class TestGSDI {
             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])" );
@@ -372,10 +399,11 @@ public final class TestGSDI {
             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;
             }
@@ -390,11 +418,12 @@ public final class TestGSDI {
             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])" );