diff --git a/data/bpcomp b/data/bpcomp
deleted file mode 100755
index a4e4d057..00000000
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diff --git a/data/cvrep b/data/cvrep
deleted file mode 100755
index b905bb93..00000000
Binary files a/data/cvrep and /dev/null differ
diff --git a/data/pb_mpi b/data/pb_mpi
deleted file mode 100755
index 2b9d0f5f..00000000
Binary files a/data/pb_mpi and /dev/null differ
diff --git a/data/readpb_mpi b/data/readpb_mpi
deleted file mode 100755
index 431f4a77..00000000
Binary files a/data/readpb_mpi and /dev/null differ
diff --git a/data/tracecomp b/data/tracecomp
deleted file mode 100755
index bbc5b104..00000000
Binary files a/data/tracecomp and /dev/null differ
diff --git a/sources/BipartitionList.cpp b/sources/BipartitionList.cpp
index 5aa27a98..411f6901 100644
--- a/sources/BipartitionList.cpp
+++ b/sources/BipartitionList.cpp
@@ -13,6 +13,7 @@ along with PhyloBayes. If not, see .
**********************/
+#include
#include "phylo.h"
// ---------------------------------------------------------------------------------
@@ -57,7 +58,7 @@ double BPCompare(string* ChainName, int P, string reftreename, int burnin, int e
}
}
BipartitionList** bplist = new BipartitionList*[P];
- TaxaParameters* taxaparam = 0;
+ TaxaParameters* taxaparam = 0;
BipartitionList* refbplist = 0;
if (verbose) {
@@ -141,13 +142,14 @@ double BPCompare(string* ChainName, int P, string reftreename, int burnin, int e
int bpsize = mergedbplist->GetSize();
- double diff[bpsize];
- double refdiff[bpsize];
- double prob[Q][bpsize];
- double length[Q][bpsize];
- double meanprob[bpsize];
- double refprob[bpsize];
- double reflength[bpsize];
+ vector diff(bpsize);
+ vector refdiff(bpsize);
+ vector > prob(Q, vector(bpsize));
+ vector > length(Q, vector(bpsize));
+ vector meanprob(bpsize);
+ vector refprob(bpsize);
+ vector reflength(bpsize);
+
for (int k=0; k burnin) {
if (rootonly) {
@@ -635,10 +637,10 @@ int BipartitionList::IsEqualTo(BipartitionList* comp) {
void BipartitionList::Prune(PBTree* inTree) {
-
+
if (inTree->IsDichotomous()) {
cerr << "in BipartitionList::Prune : warning, tree is dichotomous\n";
- }
+ }
Flush();
inTree->GetRoot()->BipartitionPruning(this);
Modulo();
@@ -647,7 +649,7 @@ void BipartitionList::Prune(PBTree* inTree) {
void BipartitionList::PruneWithSupports(PBTree* inTree) {
-
+
Flush();
inTree->GetRoot()->BipartitionPruningWithSupports(this);
Modulo();
@@ -664,7 +666,7 @@ BipartitionList::BipartitionList( TreeList* inTreeList, double* weightarray, dou
mParam = inTreeList->GetParameters();
BasicAllocation();
-
+
for (int i=0; iGetSize(); i++) {
BipartitionList tempList(mParam);
inTreeList->GetTree(i)->Trichotomise();
@@ -694,7 +696,7 @@ BipartitionList::~BipartitionList() {
delete[] mCompatibleArray;
}
-
+
// ---------------------------------------------------------------------------------
// Sort(); // reverse order !
// ---------------------------------------------------------------------------------
@@ -723,12 +725,12 @@ void BipartitionList::Sort() {
}
}
}
-
+
// ---------------------------------------------------------------------------------
// GetHisto();
// ---------------------------------------------------------------------------------
-
+
void BipartitionList::GetHisto(int* histo, int ncat) {
for (int i=0; iPermutTaxa(permut);
- }
+ }
delete[] permut;
}
return ok;
@@ -781,7 +783,7 @@ int BipartitionList::RegisterWith(TaxaParameters* inParam) {
// ---------------------------------------------------------------------------------
void BipartitionList::Truncate(double cutoff) {
-
+
int i=0;
while ( (i= cutoff)) {
i++;
@@ -802,21 +804,21 @@ void BipartitionList::Flush(){
mSize = 0;
mWeight = 0;
}
-
+
// ---------------------------------------------------------------------------------
// Pop()
// ---------------------------------------------------------------------------------
void BipartitionList::Pop(){
-
+
if (! mSize) {
cerr << "error in BipartitionList : pop called on list of size 0\n";
exit(1);
}
mSize--;
}
-
+
// ---------------------------------------------------------------------------------
// Modulo
@@ -890,20 +892,20 @@ void BipartitionList::Suppress(const Bipartition& bp) {
mBipartitionArray[i]->Suppress(bp);
}
}
-
+
// ---------------------------------------------------------------------------------
// GetIndex()
// ---------------------------------------------------------------------------------
int BipartitionList::GetIndex(const Bipartition& inPartition){
-
+
int i=0;
while ( (i mAllocatedSize) {
Reallocate();
@@ -1077,7 +1079,7 @@ void BipartitionList::WriteToStream(ostream& os, int header, int verbose) {
if (header) {
mParam->WriteToStream(os);
}
- os << "BipartitionList\n";
+ os << "BipartitionList\n";
os << "Size " << mSize << '\n';
os << "Weight " << mWeight << '\n';
os << '\n';
@@ -1113,12 +1115,12 @@ void BipartitionList::ReadFromStream(istream& is) {
mParam->ReadFromStream(is);
}
else if (temp == "BipartitionList") {
-
+
int size;
is >> temp >> size >> temp >> mWeight;
cerr << size << '\n';
mSize = 0;
-
+
for (int i=0; i> temp;
}
}
-
diff --git a/sources/Makefile b/sources/Makefile
index 5bd96727..6f002212 100644
--- a/sources/Makefile
+++ b/sources/Makefile
@@ -1,6 +1,6 @@
CC=mpic++
-CPPFLAGS= -w -O3 -c
-LDFLAGS= -O3
+CPPFLAGS= -w -O3 -flto -c
+LDFLAGS= -O3 -flto
SRCS= TaxonSet.cpp Tree.cpp Random.cpp SequenceAlignment.cpp CodonSequenceAlignment.cpp \
StateSpace.cpp CodonStateSpace.cpp ZippedSequenceAlignment.cpp SubMatrix.cpp \
GTRSubMatrix.cpp CodonSubMatrix.cpp linalg.cpp Chrono.cpp BranchProcess.cpp \