Removed binary clone tree

Author: melkebir

CMakeLists.txt

@@ -8,8 +8,6 @@ set( generatemigrationtrees_src
   src/generatemigrationtreesmain.cpp
   src/utils.cpp
   src/nonbinaryclonetree.cpp
-  src/clonetree.cpp
-  src/binarytree.cpp
   src/basetree.cpp
   src/migrationtree.cpp
   src/gabowmyers.cpp
@@ -18,8 +16,6 @@ set( generatemigrationtrees_src
 set( generatemigrationtrees_hdr
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
   src/migrationtree.h
   src/gabowmyers.h
@@ -28,9 +24,6 @@ set( generatemigrationtrees_hdr
 set( pmh_hdr
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
-  src/basetree.h
   src/ilpsolver.h
 #  src/ilppmhsolver.h
   src/migrationgraph.h
@@ -41,8 +34,6 @@ set( simulation_hdr
   src/simulation/celltree.h
   src/simulation/beta_distribution.hpp
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
   src/migrationtree.h
   src/migrationgraph.h
@@ -53,8 +44,6 @@ set( simulation_hdr
 set( simulation_src
   src/utils.cpp
   src/nonbinaryclonetree.cpp
-  src/clonetree.cpp
-  src/binarytree.cpp
   src/basetree.cpp
   src/migrationtree.cpp
   src/migrationgraph.cpp
@@ -67,17 +56,13 @@ set( simulation_src
 set( pmh_src
   src/pmh.cpp
   src/utils.cpp
-  src/clonetree.cpp
   src/nonbinaryclonetree.cpp
-  src/binarytree.cpp
   src/basetree.cpp
   src/ilpsolver.cpp
 #  src/ilppmhsolver.cpp
   src/migrationgraph.cpp
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
   src/ilpsolver.h
   src/migrationgraph.h
@@ -86,8 +71,6 @@ set( pmh_src
 set( pmh_pr_hdr
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
   src/ilpsolver.h
   src/ilpbinarizationsolver.h
@@ -99,9 +82,7 @@ set( pmh_pr_hdr
 set( pmh_pr_src
   src/pmh_pr.cpp
   src/utils.cpp
-  src/clonetree.cpp
   src/nonbinaryclonetree.cpp
-  src/binarytree.cpp
   src/basetree.cpp
   src/ilpsolver.cpp
   src/ilpbinarizationsolver.cpp
@@ -112,8 +93,6 @@ set( pmh_pr_src
   src/migrationgraph.cpp
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
   src/ilpsolver.h
   src/ilpbinarizationsolver.h
@@ -126,8 +105,6 @@ set( generatemutationtrees_hdr
   src/basematrix.h
   src/frequencymatrix.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/enumeratecanonicalclonetrees.h
   src/enumeratemutationtrees.h
   src/spruce/matrix.h
@@ -157,11 +134,7 @@ set( generatemutationtrees_src
   src/basetree.h
   src/basetree.cpp
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/nonbinaryclonetree.cpp
-  src/clonetree.cpp
-  src/binarytree.cpp
   src/rootedcladisticnoisysparseenumeration.h
   src/rootedcladisticnoisysparseenumeration.cpp
   src/spruce/matrix.h
@@ -197,8 +170,6 @@ set( ms_hdr
   src/basematrix.h
   src/frequencymatrix.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/spruce/matrix.h
   src/spruce/realmatrix.h
   src/spruce/realtensor.h
@@ -230,11 +201,7 @@ set( ms_src
   src/msenumeration.h
   src/msenumeration.cpp
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/nonbinaryclonetree.cpp
-  src/clonetree.cpp
-  src/binarytree.cpp
   src/rootedcladisticnoisysparseenumeration.h
   src/rootedcladisticnoisysparseenumeration.cpp
   src/migrationgraph.cpp
@@ -293,8 +260,6 @@ set( cluster_src
 set( pmh_cti_hdr
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
   src/ilpsolver.h
   src/migrationgraph.h
@@ -307,9 +272,7 @@ set( pmh_cti_hdr
 set( pmh_cti_src
   src/pmh_cti.cpp
   src/utils.cpp
-  src/clonetree.cpp
   src/nonbinaryclonetree.cpp
-  src/binarytree.cpp
   src/basetree.cpp
   src/ilpsolver.cpp
   src/ilpsolverext.cpp
@@ -319,8 +282,6 @@ set( pmh_cti_src
   src/gabowmyers.cpp
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
   src/ilpsolverext.h
   src/ilpsolver.h
@@ -362,43 +323,33 @@ set( pmh_cti_src
 set( visualizeclonetree_hdr
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
 )
 
 set( visualizeclonetree_src
   src/visualizeclonetreemain.cpp
   src/utils.cpp
-  src/clonetree.cpp
   src/nonbinaryclonetree.cpp
-  src/binarytree.cpp
   src/basetree.cpp
 )
 
 set( robinson_foulds_hdr
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
 )
 
 set( robinson_foulds_src
   src/rfmain.cpp
   src/utils.cpp
-  src/clonetree.cpp
   src/nonbinaryclonetree.cpp
-  src/binarytree.cpp
   src/basetree.cpp
 )
 
 set( visualizemigrationgraph_hdr
   src/migrationgraph.h
   src/utils.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
-  src/binarytree.h
   src/basetree.h
   src/migrationtree.h
   src/gabowmyers.h
@@ -408,8 +359,6 @@ set( visualizemigrationgraph_src
   src/migrationgraph.cpp
   src/utils.cpp
   src/nonbinaryclonetree.cpp
-  src/clonetree.cpp
-  src/binarytree.cpp
   src/basetree.cpp
   src/migrationtree.cpp
   src/gabowmyers.cpp
@@ -418,28 +367,24 @@ set( visualizemigrationgraph_src
 
 set( pmh_sankoff_hdr
   src/basetree.h
-  src/binarytree.h
   src/utils.h
   src/mpbase.h
   src/sankoff.h
   src/charactertree.h
   src/nonbinaryclonetree.h
-  src/clonetree.h
   src/sankofflabeling.h
   src/migrationgraph.h
 )
 
 set( pmh_sankoff_src
   src/basetree.cpp
-  src/binarytree.cpp
   src/utils.cpp
   src/mpbase.cpp
   src/sankoff.cpp
   src/charactertree.cpp
   src/pmh_sankoff.cpp
   src/nonbinaryclonetree.cpp
   src/sankofflabeling.cpp
-  src/clonetree.cpp
   src/migrationgraph.cpp
 )