move all Tree classes into tree sub-folder

iqtree · May 6, 2017 · 78e5e63 · 78e5e63
1 parent 4052ba5
commit 78e5e63
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Showing 99 changed files with 119 additions and 93 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -472,18 +472,19 @@ add_definitions("-I${EIGEN3_INCLUDE_DIR} -DUSE_EIGEN3")
 add_subdirectory(model)
 add_subdirectory(gsl)
 add_subdirectory(alignment)
+add_subdirectory(tree)
 
 ##################################################################
 # the main executable
 ##################################################################
 
-add_library(kernelsse phylokernelsse.cpp)
+add_library(kernelsse tree/phylokernelsse.cpp)
 
 if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
-add_library(kernelavx phylotreeavx.cpp)
-add_library(kernelfma phylokernelfma.cpp)
+add_library(kernelavx tree/phylotreeavx.cpp)
+add_library(kernelfma tree/phylokernelfma.cpp)
 if (IQTREE_FLAGS MATCHES "512")
-    add_library(kernelavx512 phylokernelavx512.cpp)
+    add_library(kernelavx512 tree/phylokernelavx512.cpp)
     add_definitions(-DINCLUDE_AVX512)
 endif()
 endif()
@@ -500,54 +501,30 @@ gss.cpp gss.h
 gurobiwrapper.cpp gurobiwrapper.h
 gzstream.cpp gzstream.h
 hashsplitset.cpp hashsplitset.h
-iqtree.cpp iqtree.h
-matree.cpp matree.h
-mexttree.cpp mexttree.h
 mpdablock.cpp mpdablock.h
 msetsblock.cpp msetsblock.h
 msplitsblock.cpp msplitsblock.h
 modelsblock.cpp modelsblock.h
-mtree.cpp mtree.h
-mtreeset.cpp mtreeset.h
-ncbitree.cpp ncbitree.h
 ngs.cpp ngs.h
-node.cpp node.h
 optimization.cpp optimization.h
 parsmultistate.cpp parsmultistate.h
-pattern.cpp pattern.h
 pda.cpp
 pdnetwork.cpp pdnetwork.h
-pdtree.cpp pdtree.h
-pdtreeset.cpp pdtreeset.h
 phyloanalysis.cpp phyloanalysis.h
-phylonode.cpp phylonode.h
-phylonodemixlen.cpp phylonodemixlen.h
-phylosupertree.cpp phylosupertree.h
-phylotree.cpp phylotree.h
-phylotreesse.cpp phylokernel.h phylokernelnew.h
-phylotreepars.cpp
-phylokernelnonrev.cpp phylokernelnonrev.h
-phylotreemixlen.cpp phylotreemixlen.h
 pruning.cpp pruning.h
-quartet.cpp
 split.cpp split.h
 splitgraph.cpp splitgraph.h
 splitset.cpp splitset.h
 stoprule.cpp stoprule.h
-supernode.cpp supernode.h
-tinatree.cpp tinatree.h
 tools.cpp tools.h
 whtest_wrapper.cpp whtest_wrapper.h
 lpwrapper.c lpwrapper.h
 pllnni.cpp pllnni.h
-phylosupertreeplen.cpp phylosupertreeplen.h
 phylotesting.cpp phylotesting.h
 ecopd.cpp ecopd.h
-ecopdmtreeset.cpp ecopdmtreeset.h
 graph.cpp graph.h
 candidateset.cpp candidateset.h
 checkpoint.cpp checkpoint.h
-constrainttree.cpp constrainttree.h
 MPIHelper.cpp MPIHelper.h
 memslot.cpp memslot.h
 )
@@ -574,7 +551,7 @@ endif(ZLIB_FOUND)
 
 if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
     if (NOT IQTREE_FLAGS MATCHES "nosse")
-        set_target_properties(iqtree ncl lbfgsb whtest sprng vectorclass model alignment PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+        set_target_properties(iqtree ncl lbfgsb whtest sprng vectorclass model alignment tree PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
     endif()
     set_target_properties(kernelsse pll PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
 	if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
@@ -630,7 +607,7 @@ if (NOT IQTREE_FLAGS MATCHES "single")
 endif()
 
 # basic linking librararies
-target_link_libraries(iqtree pll ncl lbfgsb whtest sprng vectorclass model gsl alignment ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
+target_link_libraries(iqtree pll ncl lbfgsb whtest sprng vectorclass model gsl alignment tree ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
 
 if (NOT IQTREE_FLAGS MATCHES "nosse")
     target_link_libraries(iqtree kernelsse)

diff --git a/alignment/CMakeLists.txt b/alignment/CMakeLists.txt
@@ -1,4 +1,6 @@
 add_library(alignment
+pattern.cpp
+pattern.h
 alignment.cpp
 alignment.h
 alignmentpairwise.cpp

diff --git a/alignment/alignmentpairwise.cpp b/alignment/alignmentpairwise.cpp
@@ -18,7 +18,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 #include "alignmentpairwise.h"
-#include "phylosupertree.h"
+#include "tree/phylosupertree.h"
 
 AlignmentPairwise::AlignmentPairwise()
         : Alignment(), Optimization()

diff --git a/alignment/alignmentpairwise.h b/alignment/alignmentpairwise.h
@@ -21,7 +21,7 @@
 #define ALIGNMENTPAIRWISE_H
 
 #include "optimization.h"
-#include "phylotree.h"
+#include "tree/phylotree.h"
 
 /**
 Pairwise alignment

diff --git a/pattern.cpp → alignment/pattern.cpp b/pattern.cpp → alignment/pattern.cpp
diff --git a/pattern.h → alignment/pattern.h b/pattern.h → alignment/pattern.h
diff --git a/alignment/superalignment.cpp b/alignment/superalignment.cpp
@@ -19,9 +19,9 @@
  ***************************************************************************/
 
 #include <stdarg.h>
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "superalignment.h"
-#include "phylosupertree.h"
+#include "tree/phylosupertree.h"
 
 SuperAlignment::SuperAlignment() : Alignment() {
     max_num_states = 0;

diff --git a/alignment/superalignmentpairwise.h b/alignment/superalignmentpairwise.h
@@ -22,7 +22,7 @@
 
 #include "alignmentpairwise.h"
 #include "superalignment.h"
-#include "phylosupertree.h"
+#include "tree/phylosupertree.h"
 
 /**
 	@author BUI Quang Minh <minh.bui@univie.ac.at>

diff --git a/alignment/superalignmentpairwiseplen.h b/alignment/superalignmentpairwiseplen.h
@@ -9,7 +9,7 @@
 #ifndef iqtree_superalignmentpairwiseplen_h
 #define iqtree_superalignmentpairwiseplen_h
 
-#include "phylosupertreeplen.h"
+#include "tree/phylosupertreeplen.h"
 #include "superalignmentpairwise.h"
 
 

diff --git a/candidateset.cpp b/candidateset.cpp
@@ -6,7 +6,7 @@
  *  Email: nltung@gmail.com
  */
 
-#include "iqtree.h"
+#include "tree/iqtree.h"
 #include "candidateset.h"
 #include "MPIHelper.h"
 

diff --git a/candidateset.h b/candidateset.h
@@ -25,7 +25,7 @@
 //#include "phylotree.h"
 #include "tools.h"
 #include "alignment/alignment.h"
-#include "mtreeset.h"
+#include "tree/mtreeset.h"
 #include <stack>
 #include "checkpoint.h"
 

diff --git a/ecopd.cpp b/ecopd.cpp
@@ -9,8 +9,8 @@
 #include "ecopd.h"
 #include "split.h"
 #include "pdnetwork.h"
-#include "mtreeset.h"
-#include "ecopdmtreeset.h"
+#include "tree/mtreeset.h"
+#include "tree/ecopdmtreeset.h"
 #include "graph.h"
 
 

diff --git a/ecopd.h b/ecopd.h
@@ -8,9 +8,9 @@
 #ifndef ECOPD_H
 #define ECOPD_H
 
-#include "mtree.h"
-#include "mtreeset.h"
-#include "ecopdmtreeset.h"
+#include "tree/mtree.h"
+#include "tree/mtreeset.h"
+#include "tree/ecopdmtreeset.h"
 #include "pdnetwork.h"
 
 /* ===============================================================================

diff --git a/greedy.h b/greedy.h
@@ -20,7 +20,7 @@
 #ifndef GREEDY_H
 #define GREEDY_H
 
-#include "pdtree.h"
+#include "tree/pdtree.h"
 
 /**
 Implementation of greedy algorithm with complexity O(n*logk)

diff --git a/gss.cpp b/gss.cpp
@@ -25,7 +25,7 @@
 #include "gss.h"
 #include "lpwrapper.h"
 #include "gurobiwrapper.h"
-#include "mtreeset.h"
+#include "tree/mtreeset.h"
 
 
 GSSNetwork::GSSNetwork(Params &params) : PDNetwork(params) {

diff --git a/memslot.cpp b/memslot.cpp
@@ -19,7 +19,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "memslot.h"
 
 const int MEM_LOCKED = 1;

diff --git a/model/modelfactorymixlen.cpp b/model/modelfactorymixlen.cpp
@@ -5,7 +5,7 @@
  *      Author: minh
  */
 
-#include "phylotreemixlen.h"
+#include "tree/phylotreemixlen.h"
 #include "timeutil.h"
 #include "tools.h"
 #include "model/modelfactorymixlen.h"

diff --git a/model/modelmarkov.h b/model/modelmarkov.h
@@ -20,7 +20,7 @@
 #ifndef MODELMARKOV_H
 #define MODELMARKOV_H
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "modelsubst.h"
 #include "optimization.h"
 #include "alignment/alignment.h"

diff --git a/model/modelmixture.h b/model/modelmixture.h
@@ -8,7 +8,7 @@
 #ifndef MODELMIXTURE_H_
 #define MODELMIXTURE_H_
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "modelsubst.h"
 #include "modelmarkov.h"
 #include "modelsblock.h"

diff --git a/model/partitionmodel.h b/model/partitionmodel.h
@@ -20,7 +20,7 @@
 #ifndef PARTITIONMODEL_H
 #define PARTITIONMODEL_H
 
-#include "phylosupertree.h"
+#include "tree/phylosupertree.h"
 #include "modelfactory.h"
 
 /**

diff --git a/model/partitionmodelplen.h b/model/partitionmodelplen.h
@@ -9,7 +9,7 @@
 #ifndef iqtree_partitionmodelplen_h
 #define iqtree_partitionmodelplen_h
 
-#include "phylosupertreeplen.h"
+#include "tree/phylosupertreeplen.h"
 #include "model/partitionmodel.h"
 
 class PartitionModelPlen : public PartitionModel

diff --git a/model/ratefree.cpp b/model/ratefree.cpp
@@ -5,7 +5,7 @@
  *      Author: minh
  */
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "ratefree.h"
 #include "rateinvar.h"
 

diff --git a/model/rategamma.cpp b/model/rategamma.cpp
@@ -19,7 +19,7 @@
  *   Free Software Foundation, Inc.,                                       *
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "rategamma.h"
 #include <cmath>
 

diff --git a/model/rateheterogeneity.cpp b/model/rateheterogeneity.cpp
@@ -18,7 +18,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "rateheterogeneity.h"
 
 

diff --git a/model/rateheterotachy.cpp b/model/rateheterotachy.cpp
@@ -6,7 +6,7 @@
 //
 //
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "rateheterotachy.h"
 
 RateHeterotachy::RateHeterotachy(int ncat, string params, PhyloTree *tree) : RateHeterogeneity() {

diff --git a/model/rateinvar.h b/model/rateinvar.h
@@ -20,7 +20,7 @@
 #ifndef RATEINVAR_H
 #define RATEINVAR_H
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "rateheterogeneity.h"
 
 const double MIN_PINVAR = 1e-6;

diff --git a/model/ratekategory.cpp b/model/ratekategory.cpp
@@ -17,7 +17,7 @@
 */
 
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "ratekategory.h"
 
 RateKategory::RateKategory(int ncat, PhyloTree *tree)

diff --git a/model/ratemeyerdiscrete.cpp b/model/ratemeyerdiscrete.cpp
@@ -18,7 +18,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "ratemeyerdiscrete.h"
 //#include "kmeans/KMeans.h"
 //#include "modeltest_wrapper.h"

diff --git a/model/ratemeyerhaeseler.cpp b/model/ratemeyerhaeseler.cpp
@@ -17,7 +17,7 @@
  *   Free Software Foundation, Inc.,                                       *
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "ratemeyerhaeseler.h"
 
 

diff --git a/model/ratemeyerhaeseler.h b/model/ratemeyerhaeseler.h
@@ -22,7 +22,7 @@
 
 #include "rateheterogeneity.h"
 #include "tools.h"
-#include "iqtree.h"
+#include "tree/iqtree.h"
 
 
 /**

diff --git a/ngs.h b/ngs.h
@@ -21,7 +21,7 @@
 #ifndef NGS_H
 #define NGS_H
 
-#include "phylotree.h"
+#include "tree/phylotree.h"
 #include "alignment/alignmentpairwise.h"
 #include "model/ratemeyerdiscrete.h"
 

diff --git a/parsmultistate.cpp b/parsmultistate.cpp
@@ -18,8 +18,8 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 
-#include "phylotree.h"
-#include "tinatree.h"
+#include "tree/phylotree.h"
+#include "tree/tinatree.h"
 #include "parsmultistate.h"
 #include "alignment/alignment.h"