move all Alignment classes into alignment source code sub-folder

iqtree · May 6, 2017 · 4052ba5 · 4052ba5
1 parent acf2016
commit 4052ba5
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Showing 38 changed files with 43 additions and 34 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -471,6 +471,7 @@ endif()
 add_definitions("-I${EIGEN3_INCLUDE_DIR} -DUSE_EIGEN3")
 add_subdirectory(model)
 add_subdirectory(gsl)
+add_subdirectory(alignment)
 
 ##################################################################
 # the main executable
@@ -492,8 +493,6 @@ if (IQTREE_FLAGS MATCHES "mpi")
 endif()
 
 add_executable(iqtree
-alignment.cpp alignment.h
-alignmentpairwise.cpp alignmentpairwise.h
 circularnetwork.cpp circularnetwork.h
 eigendecomposition.cpp eigendecomposition.h
 greedy.cpp greedy.h
@@ -502,7 +501,6 @@ gurobiwrapper.cpp gurobiwrapper.h
 gzstream.cpp gzstream.h
 hashsplitset.cpp hashsplitset.h
 iqtree.cpp iqtree.h
-maalignment.cpp maalignment.h
 matree.cpp matree.h
 mexttree.cpp mexttree.h
 mpdablock.cpp mpdablock.h
@@ -536,9 +534,6 @@ split.cpp split.h
 splitgraph.cpp splitgraph.h
 splitset.cpp splitset.h
 stoprule.cpp stoprule.h
-superalignment.cpp superalignment.h
-superalignmentpairwise.cpp superalignmentpairwise.h
-superalignmentpairwiseplen.cpp superalignmentpairwiseplen.h
 supernode.cpp supernode.h
 tinatree.cpp tinatree.h
 tools.cpp tools.h
@@ -579,7 +574,7 @@ 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 PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+        set_target_properties(iqtree ncl lbfgsb whtest sprng vectorclass model alignment PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
     endif()
     set_target_properties(kernelsse pll PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
 	if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
@@ -635,7 +630,7 @@ if (NOT IQTREE_FLAGS MATCHES "single")
 endif()
 
 # basic linking librararies
-target_link_libraries(iqtree pll ncl lbfgsb whtest sprng vectorclass model gsl ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
+target_link_libraries(iqtree pll ncl lbfgsb whtest sprng vectorclass model gsl alignment ${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
@@ -0,0 +1,14 @@
+add_library(alignment
+alignment.cpp
+alignment.h
+alignmentpairwise.cpp
+alignmentpairwise.h
+maalignment.cpp
+maalignment.h
+superalignment.cpp
+superalignment.h
+superalignmentpairwise.cpp
+superalignmentpairwise.h
+superalignmentpairwiseplen.cpp
+superalignmentpairwiseplen.h
+)
diff --git a/alignment.cpp → alignment/alignment.cpp b/alignment.cpp → alignment/alignment.cpp
diff --git a/alignment.h → alignment/alignment.h b/alignment.h → alignment/alignment.h
diff --git a/alignmentpairwise.cpp → alignment/alignmentpairwise.cpp b/alignmentpairwise.cpp → alignment/alignmentpairwise.cpp
diff --git a/alignmentpairwise.h → alignment/alignmentpairwise.h b/alignmentpairwise.h → alignment/alignmentpairwise.h
diff --git a/maalignment.cpp → alignment/maalignment.cpp b/maalignment.cpp → alignment/maalignment.cpp
diff --git a/maalignment.h → alignment/maalignment.h b/maalignment.h → alignment/maalignment.h
diff --git a/superalignment.cpp → alignment/superalignment.cpp b/superalignment.cpp → alignment/superalignment.cpp
diff --git a/superalignment.h → alignment/superalignment.h b/superalignment.h → alignment/superalignment.h
diff --git a/superalignmentpairwise.cpp → alignment/superalignmentpairwise.cpp b/superalignmentpairwise.cpp → alignment/superalignmentpairwise.cpp
diff --git a/superalignmentpairwise.h → alignment/superalignmentpairwise.h b/superalignmentpairwise.h → alignment/superalignmentpairwise.h
diff --git a/superalignmentpairwiseplen.cpp → alignment/superalignmentpairwiseplen.cpp b/superalignmentpairwiseplen.cpp → alignment/superalignmentpairwiseplen.cpp
diff --git a/superalignmentpairwiseplen.h → alignment/superalignmentpairwiseplen.h b/superalignmentpairwiseplen.h → alignment/superalignmentpairwiseplen.h
diff --git a/candidateset.h b/candidateset.h
@@ -24,7 +24,7 @@
 #define CANDIDATESET_H_
 //#include "phylotree.h"
 #include "tools.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 #include "mtreeset.h"
 #include <stack>
 #include "checkpoint.h"

diff --git a/constrainttree.h b/constrainttree.h
@@ -12,7 +12,7 @@
 #define CONSTRAINTTREE_H
 
 #include "mtree.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 
 struct NNIMove;
 

diff --git a/mexttree.cpp b/mexttree.cpp
@@ -18,7 +18,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 #include "mexttree.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 
 void MExtTree::generateRandomTree(TreeGenType tree_type, Params &params, bool binary) {
 	Alignment *alignment = NULL;

diff --git a/model/modelfactory.h b/model/modelfactory.h
@@ -25,7 +25,7 @@
 #include "rateheterogeneity.h"
 #include "modelsblock.h"
 #include "checkpoint.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 
 const double MIN_BRLEN_SCALE = 0.01;
 const double MAX_BRLEN_SCALE = 100.0;

diff --git a/model/modelmarkov.h b/model/modelmarkov.h
@@ -23,7 +23,7 @@
 #include "phylotree.h"
 #include "modelsubst.h"
 #include "optimization.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 #include "eigendecomposition.h"
 #include <complex>
 

diff --git a/model/partitionmodel.cpp b/model/partitionmodel.cpp
@@ -18,7 +18,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 #include "partitionmodel.h"
-#include "superalignment.h"
+#include "alignment/superalignment.h"
 #include "model/rategamma.h"
 
 PartitionModel::PartitionModel()

diff --git a/mtreeset.cpp b/mtreeset.cpp
@@ -18,7 +18,7 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 #include "mtreeset.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 #include "gzstream.h"
 
 MTreeSet::MTreeSet()

diff --git a/mtreeset.h b/mtreeset.h
@@ -22,7 +22,7 @@
 
 #include "mtree.h"
 #include "splitgraph.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 
 void readIntVector(const char *file_name, int burnin, int max_count, IntVector &vec);
 

diff --git a/ngs.h b/ngs.h
@@ -22,7 +22,7 @@
 #define NGS_H
 
 #include "phylotree.h"
-#include "alignmentpairwise.h"
+#include "alignment/alignmentpairwise.h"
 #include "model/ratemeyerdiscrete.h"
 
 /*

diff --git a/parsmultistate.cpp b/parsmultistate.cpp
@@ -21,7 +21,7 @@
 #include "phylotree.h"
 #include "tinatree.h"
 #include "parsmultistate.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 
 void doParsMultiState(Params &params) {
 	cout << "Here\n";

diff --git a/pattern.cpp b/pattern.cpp
@@ -10,7 +10,7 @@
 //
 //
 #include "pattern.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 
 Pattern::Pattern()
         : vector<StateType>()

diff --git a/pda.cpp b/pda.cpp
@@ -56,7 +56,7 @@
 #include "ngs.h"
 #include "parsmultistate.h"
 #include "gss.h"
-#include "maalignment.h" //added by MA
+#include "alignment/maalignment.h" //added by MA
 #include "ncbitree.h"
 #include "ecopd.h"
 #include "upperbounds.h"

diff --git a/phyloanalysis.cpp b/phyloanalysis.cpp
@@ -28,8 +28,8 @@
 #include "phylosupertree.h"
 #include "phylosupertreeplen.h"
 #include "phyloanalysis.h"
-#include "alignment.h"
-#include "superalignment.h"
+#include "alignment/alignment.h"
+#include "alignment/superalignment.h"
 #include "iqtree.h"
 #include "phylotreemixlen.h"
 #include "model/modelmarkov.h"

diff --git a/phylokernel.h b/phylokernel.h
@@ -11,7 +11,7 @@
 #include "phylotree.h"
 //#include "vectorclass/vectorclass.h"
 //#include "vectorclass/vectormath_exp.h"
-#include "superalignment.h"
+#include "alignment/superalignment.h"
 
 #ifdef __SSE2__
 inline Vec2d horizontal_add(Vec2d x[2]) {

diff --git a/phylosupertree.cpp b/phylosupertree.cpp
@@ -18,8 +18,8 @@
  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
  ***************************************************************************/
 #include "phylosupertree.h"
-#include "superalignment.h"
-#include "superalignmentpairwise.h"
+#include "alignment/superalignment.h"
+#include "alignment/superalignmentpairwise.h"
 #include "msetsblock.h"
 #include "myreader.h"
 #include "phylotesting.h"

diff --git a/phylosupertree.h b/phylosupertree.h
@@ -22,7 +22,7 @@
 
 #include "iqtree.h"
 #include "supernode.h"
-#include "superalignment.h"
+#include "alignment/superalignment.h"
 
 
 /**

diff --git a/phylosupertreeplen.cpp b/phylosupertreeplen.cpp
@@ -6,7 +6,7 @@
  */
 
 #include "phylosupertreeplen.h"
-#include "superalignmentpairwiseplen.h"
+#include "alignment/superalignmentpairwiseplen.h"
 #include "model/partitionmodelplen.h"
 #include <string.h>
 #include "timeutil.h"

diff --git a/phylosupertreeplen.h b/phylosupertreeplen.h
@@ -10,7 +10,7 @@
 
 #include "phylosupertree.h"
 #include "model/partitionmodel.h"
-#include "superalignmentpairwise.h"
+#include "alignment/superalignmentpairwise.h"
 
 /**
  * this is to classify the cases which happen on the subtree

diff --git a/phylotree.cpp b/phylotree.cpp
@@ -22,7 +22,7 @@
 #include "phylotree.h"
 #include "bionj.h"
 //#include "rateheterogeneity.h"
-#include "alignmentpairwise.h"
+#include "alignment/alignmentpairwise.h"
 #include <algorithm>
 #include <limits>
 #include "timeutil.h"

diff --git a/phylotree.h b/phylotree.h
@@ -34,7 +34,7 @@
 //#define EIGEN_TUNE_FOR_CPU_CACHE_SIZE (8*512*512)
 //#include <Eigen/Core>
 #include "mtree.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 #include "model/modelsubst.h"
 #include "model/modelfactory.h"
 #include "phylonode.h"

diff --git a/pllnni.cpp b/pllnni.cpp
@@ -33,7 +33,7 @@
 
 #include "phylotree.h"
 #include "pllnni.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 
 /* program options */
 int nni0;

diff --git a/quartet.cpp b/quartet.cpp
@@ -12,7 +12,7 @@
 #include "phylotree.h"
 #include "phylosupertree.h"
 #include "model/partitionmodel.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 #if 0 // (HAS-bla)
 #include "tools.h"
 #endif

diff --git a/tools.cpp b/tools.cpp
@@ -35,7 +35,7 @@
 #include "timeutil.h"
 #include "gzstream.h"
 #include "MPIHelper.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 
 VerboseMode verbose_mode;
 

diff --git a/upperbounds.h b/upperbounds.h
@@ -13,7 +13,7 @@
 */
 #include "iqtree.h"
 #include "mexttree.h"
-#include "alignment.h"
+#include "alignment/alignment.h"
 #include "phylotree.h"
 
 class PhyloTree;