From: Andrei Zavada <johnhom...@gmail.com>
---
mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp | 106 ++++++++++-----------
.../seqan/basic/basic_allocator_chunkpool.h | 2 +-
.../projects/library/seqan/basic/basic_holder.h | 10 +-
.../library/seqan/file/file_format_cgviz.h | 2 +-
.../projects/library/seqan/file/file_format_embl.h | 4 +-
.../library/seqan/file/file_format_fasta_align.h | 6 +-
.../projects/library/seqan/file/file_format_mmap.h | 6 +-
.../projects/library/seqan/file/file_format_sam.h | 4 +-
.../seqan/graph_algorithms/graph_algorithm.h | 18 ++--
.../seqan/graph_algorithms/graph_algorithm_hmm.h | 14 +--
.../graph_algorithms/graph_algorithm_lis_his.h | 2 +-
.../seqan/graph_align/graph_align_hirschberg.h | 4 +-
.../seqan/graph_msa/graph_align_tcoffee_base.h | 12 +--
.../seqan/graph_msa/graph_align_tcoffee_distance.h | 8 +-
.../graph_msa/graph_align_tcoffee_guidetree.h | 10 +-
.../seqan/graph_msa/graph_align_tcoffee_io.h | 36 +++----
.../seqan/graph_msa/graph_align_tcoffee_library.h | 10 +-
.../seqan/graph_msa/graph_align_tcoffee_msa.h | 8 +-
.../graph_msa/graph_align_tcoffee_progressive.h | 16 ++--
.../graph_msa/graph_align_tcoffee_refinement.h | 10 +-
.../library/seqan/graph_types/graph_drawing.h | 10 +-
.../seqan/graph_types/graph_impl_automaton.h | 10 +-
.../library/seqan/graph_types/graph_impl_hmm.h | 14 +--
.../library/seqan/graph_types/graph_impl_oracle.h | 8 +-
.../library/seqan/graph_types/graph_impl_tree.h | 8 +-
.../library/seqan/graph_types/graph_impl_trie.h | 8 +-
.../seqan/graph_types/graph_impl_wordgraph.h | 4 +-
.../projects/library/seqan/map/map_skiplist.h | 6 +-
.../projects/library/seqan/map/sumlist_skip.h | 14 +--
.../seqan/modifier/modifier_alphabet_expansion.h | 4 +-
.../graph_algorithm_refine_exact_iterative.h | 10 +-
.../refinement/graph_algorithm_refine_inexact.h | 4 +-
.../library/seqan/refinement/graph_impl_align.h | 38 ++++----
.../projects/library/seqan/sequence/lexical.h | 4 +-
.../library/seqan/sequence/sequence_multiple.h | 2 +-
.../projects/library/seqan/sequence/string_base.h | 24 ++---
.../library/seqan/sequence/string_packed.h | 2 +-
37 files changed, 229 insertions(+), 229 deletions(-)
diff --git a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
index 64fe0f7..7a3ba64 100644
--- a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
+++ b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
@@ -398,7 +398,7 @@ _cc_visit_g_ranked(Graph<TSpec> const& g,
TSize &maxdist)
{
//SEQAN_CHECKPOINT
- typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type
TAdjacencyIterator;
+ // typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type
TAdjacencyIterator;
typedef typename EdgeDescriptor<Graph<TSpec> >::Type TEdgeDescriptor;
typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type
TOutEdgeIterator;
//Add all edges from u to ccedges
@@ -525,8 +525,8 @@
connected_components_by_genome_ranked_RECURSIVE(Graph<TSpec> const& g,
typedef std::multimap<TSize,TVertexDescriptor> TGenomeVertexMap;
- typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type
TAdjacencyIterator;
- typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type
TOutEdgeIterator;
+ // typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type
TAdjacencyIterator;
+ // typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type
TOutEdgeIterator;
clear(components);
resizeVertexMap(g,components);
@@ -626,7 +626,7 @@ connected_components_by_genome_ranked(Graph<TSpec> const& g,
typedef std::multimap<TSize,TVertexDescriptor> TGenomeVertexMap;
- typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type
TAdjacencyIterator;
+ // typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type
TAdjacencyIterator;
typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type
TOutEdgeIterator;
clear(components);
@@ -840,13 +840,13 @@ typename Size<Graph<TSpec> >::Type
connected_components_ranked(Graph<TSpec> const& g,
TComponents& components){
//SEQAN_CHECKPOINT
- typedef typename Size<Graph<TSpec> >::Type TSize;
+ // typedef typename Size<Graph<TSpec> >::Type TSize;
typedef typename Iterator<Graph<TSpec>, EdgeIterator>::Type TEdgeIterator;
typedef typename Iterator<Graph<TSpec>, VertexIterator>::Type
TVertexIterator;
typedef typename VertexDescriptor<Graph<TSpec> >::Type TVertexDescriptor;
typedef typename EdgeDescriptor<Graph<TSpec> >::Type TEdgeDescriptor;
- typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type
TAdjacencyIterator;
+ // typedef typename Iterator<Graph<TSpec>, AdjacencyIterator>::Type
TAdjacencyIterator;
typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type
TOutEdgeIterator;
clear(components);
@@ -1021,7 +1021,7 @@ alignmentEvaluationCustom(Graph<Alignment<TStringSet,
TCargo, TSpec> > const& g,
TSize& totalLen)
{
//SEQAN_CHECKPOINT
- typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+ // typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename Value<TScore>::Type TScoreValue;
typedef typename Value<typename Value<TStringSet>::Type>::Type
TAlphabet;
TSize alphSize = ValueSize<TAlphabet>::VALUE;
@@ -1155,8 +1155,8 @@ void doReadBlockFile(const std::string & filename,
bool checkbounds){
std::ifstream file;
file.open(filename.c_str(), std::ios_base::in | std::ios_base::binary);
- typedef std::ifstream TFile;
- typedef Value<TFile>::Type TValue;
+ // typedef std::ifstream TFile;
+ // typedef Value<TFile>::Type TValue;
std::string line;
std::vector<unsigned int> currblock;
std::vector<unsigned int> currlcb;
@@ -1164,7 +1164,7 @@ void doReadBlockFile(const std::string & filename,
std::map<std::string,char> sequenceOrientMap;
std::map<std::string,std::pair<unsigned int, unsigned int> >
sequenceCoordsMap;
std::map<String<char>,int> seqNamesIdxMap;
- for(int i=0;i<length(sequenceNames);++i){
+ for(size_t i=0;i<length(sequenceNames);++i){
seqNamesIdxMap[sequenceNames[i]]=i;
}
@@ -1713,7 +1713,7 @@ void convertCC2Blocks(TGraph &g,
typedef typename Size<TGraph>::Type TSize;
typedef std::pair<TIdType, TSize> TKey;
typedef std::map<TKey, TVertexDescriptor> TPosToVertexMap;
- typedef FragmentInfo<TIdType, TSize> TFragmentInfo;
+ // typedef FragmentInfo<TIdType, TSize> TFragmentInfo;
// data_pvMap is an STL Map to retrieve a vertex given SeqId, Position
// first.first == seqId
@@ -2126,7 +2126,7 @@ void buildMatchesFromGraph(TGraph &g,
typedef typename Size<StringSet<TString, TSpec> >::Type TSize;
typedef Fragment<> TFragment;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
TEdgeIterator itE(g);
@@ -2456,7 +2456,7 @@ bool getLCBProps(TGraph &g,
unsigned int &alnlen,
TVertexOrientMap &vertexOrientMap){
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
std::vector<unsigned int>::const_iterator vit;
std::vector<unsigned int>::const_iterator vit_end;
bool seqPresent=false;
@@ -2587,7 +2587,7 @@ void retrieveLCBSegments(TGraph & g,
if(lcbid>0){};
//Vars
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
//Need to trim seqSet to members and subsequences present in the current LCB
//Map to track old seqid to newseqid
@@ -2598,7 +2598,7 @@ void retrieveLCBSegments(TGraph & g,
typename std::set<TVertexDescriptor>::iterator pos;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
typename std::vector<TVertexDescriptor>::const_iterator vit;
typename std::vector<TVertexDescriptor>::const_iterator vit_end;
@@ -2711,7 +2711,7 @@ void retrieveLCBSegments(TGraph & g,
//All coordinates for fragments
//must be relative to the orientation determined previously
//offsets array is always relative to the matching strand
- typedef Fragment<> TFragment;
+ // typedef Fragment<> TFragment;
buildMatchesFromGraph(g,
seqSetv,
@@ -3146,23 +3146,23 @@ void generateLCBs(Graph<Alignment<TStringSet, TCargo,
TSpec> > &g,
<< numVertices(g) << " "
<< numEdges(g) << std::endl;
#endif
- typedef Dna5 TAlphabet;
- typedef typename Value<TScore>::Type TScoreValue;
+ // typedef Dna5 TAlphabet;
+ // typedef typename Value<TScore>::Type TScoreValue;
typedef typename Size<TStringSet>::Type TSize;
- typedef typename Value<TStringSet1>::Type TString;
- typedef typename Value<TNames>::Type TName;
+ // typedef typename Value<TStringSet1>::Type TString;
+ // typedef typename Value<TNames>::Type TName;
//typedef Graph<Alignment<TStringSet, TSize> > TGraph;
//Using int to support negative edge scores
typedef Graph<Alignment<TStringSet, int> > TGraph;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename EdgeType<TGraph>::Type TEdgeStump;
- typedef typename Iterator<String<TEdgeStump*> const, Rooted>::Type
TIterConst;
- typedef typename Iterator<String<TEdgeStump*>, Rooted>::Type TIter;
+ // typedef typename EdgeType<TGraph>::Type TEdgeStump;
+ // typedef typename Iterator<String<TEdgeStump*> const, Rooted>::Type
TIterConst;
+ // typedef typename Iterator<String<TEdgeStump*>, Rooted>::Type TIter;
//
- typedef std::map<unsigned int, unsigned int> TComponentLength;
+ // typedef std::map<unsigned int, unsigned int> TComponentLength;
// Strongly Connected Components, topological sort, and length of each
component
typedef String<unsigned int> TComponentMap;
@@ -3485,7 +3485,7 @@ void getGuideTree(TSequenceSet &seqSet,
typedef String<TAlphabet> TSequence;
//Parse subtree
TDistanceMatrix currdistanceMatrix;
- typedef typename Value<TDistanceMatrix>::Type TValue;
+ // typedef typename Value<TDistanceMatrix>::Type TValue;
typedef typename Iterator<TDistanceMatrix>::Type TMatrixIterator;
//This assumes the best estimate is obtained by kmers across whole genome
@@ -3550,8 +3550,8 @@ s_score alignSingleLCB(TGraph &currG,
TStringSet &currseqs,
TGuideTree &currguideTree,
MsaOptions<Dna5 , TScore> const& msaOpt){
- typedef typename Value<TScore>::Type TScoreValue;
- typedef Dna5 TAlphabet;
+ // typedef typename Value<TScore>::Type TScoreValue;
+ // typedef Dna5 TAlphabet;
//Currently disabled
bool inlinerefine= (msaOpt.refine=="true") ? true : false; //Compute
iterative refinement inline
if(lcbid>0){}
@@ -3788,8 +3788,8 @@ std::vector<s_score> alignLCBs(TGraph &g,
typedef Dna5 TAlphabet;
typedef String<TDistanceValue> TDistanceMatrix;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename Value<TScore>::Type TScoreValue;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename Value<TScore>::Type TScoreValue;
std::vector<s_score> allscores;
TDistanceMatrix distanceMatrix;
@@ -4180,9 +4180,9 @@ void wholeGenomeAlignment(TGraph &g,
TVMap &vertexOrientMap,
TStream &strmmaf,
TIMap &aintervals){
- typedef Dna5 TAlphabet;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef Dna5 TAlphabet;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
//Perform consistency scoring
//Do not add any edges to the graph
//Simple score existing match edges for consistency
@@ -4253,11 +4253,11 @@ void wholeGenomeAlignment(TGraph &g,
process_mem_usage(vm, rss);
cout << "VM: " << vm << "; RSS: " << rss << endl;
#endif
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename EdgeType<TGraph>::Type TEdgeStump;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeType<TGraph>::Type TEdgeStump;
typename std::vector<std::vector<unsigned int> >::const_iterator lit;
- typedef Fragment<> TFragment;
- typedef String<TAlphabet> TSequence;
+ // typedef Fragment<> TFragment;
+ // typedef String<TAlphabet> TSequence;
//Retrieve LCBs from the complete alignment graph $g
std::vector<s_score> allscores = alignLCBs(g,
LCBs,
@@ -4552,19 +4552,19 @@
singlepass_wholeGenomeAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gA
TIntervals &aintervals,
MsaOptions<Dna5 , TScore> const& msaOpt)
{
- typedef Dna5 TAlphabet;
+ // typedef Dna5 TAlphabet;
typedef typename Value<TScore>::Type TScoreValue;
typedef typename Size<TStringSet>::Type TSize;
- typedef typename Value<TStringSet1>::Type TString;
- typedef typename Value<TNames>::Type TName;
+ // typedef typename Value<TStringSet1>::Type TString;
+ // typedef typename Value<TNames>::Type TName;
//typedef Graph<Alignment<TStringSet, TSize> > TGraph;
//Using int to support negative edge scores
typedef Graph<Alignment<TStringSet, int> > TGraph;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef double TDistanceValue;
+ // typedef double TDistanceValue;
#ifdef SEQAN_PROFILE
std::cerr << "Mugsy WGA" << std::endl;
@@ -4841,10 +4841,10 @@
singlepass_wholeGenomeAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gA
std::string outfile(msaOpt.outfile);
strmmaf.open(std::string(outfile+".maf").c_str(), std::ios_base::out |
std::ios_base::trunc);
_streamWrite(strmmaf,"##maf version=1 scoring=mugsy");
- typedef String<unsigned int> TComponentMap;
- typedef typename Value<TComponentMap>::Type TComponent;
- typedef typename Position<TGraph>::Type TPos;
- typedef SVABlock<TComponent,unsigned,TVertexDescriptor,unsigned> TBlock;
+ // typedef String<unsigned int> TComponentMap;
+ // typedef typename Value<TComponentMap>::Type TComponent;
+ // typedef typename Position<TGraph>::Type TPos;
+ // typedef SVABlock<TComponent,unsigned,TVertexDescriptor,unsigned> TBlock;
std::vector<std::vector<TVertexDescriptor> > lcbs;
std::map<TVertexDescriptor,char> vertexOrientMap;
@@ -4904,15 +4904,15 @@ findDuplications(Graph<Alignment<TStringSet, TCargo,
TSpec> >& gAlign,
typedef Dna5 TAlphabet;
typedef typename Value<TScore>::Type TScoreValue;
typedef typename Size<TStringSet>::Type TSize;
- typedef typename Value<TStringSet1>::Type TString;
- typedef typename Value<TNames>::Type TName;
+ // typedef typename Value<TStringSet1>::Type TString;
+ // typedef typename Value<TNames>::Type TName;
//Using int to support negative edge scores
typedef Graph<Alignment<TStringSet, int> > TGraph;
typedef typename Id<TGraph>::Type TId;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
//
- typedef std::map<unsigned int, unsigned int> TComponentLength;
+ // typedef std::map<unsigned int, unsigned int> TComponentLength;
// Strongly Connected Components, topological sort, and length of each
component
typedef String<unsigned int> TComponentMap;
@@ -4923,7 +4923,7 @@ findDuplications(Graph<Alignment<TStringSet, TCargo,
TSpec> >& gAlign,
typedef typename Value<TComponentMap>::Type TComponent;
typedef std::pair<TId, TSize> TKey;
typedef std::map<TKey, TVertexDescriptor> TPosToVertexMap;
- typedef FragmentInfo<TId, TSize> TFragmentInfo;
+ // typedef FragmentInfo<TId, TSize> TFragmentInfo;
typedef double TDistanceValue;
#ifdef SEQAN_PROFILE
@@ -5231,7 +5231,7 @@ findDuplications(Graph<Alignment<TStringSet, TCargo,
TSpec> >& gAlign,
int numcc = connected_components(runG,runccmap);
std::cerr << "Determined " << numcc << " LCBs from a graph of runs: " <<
numVertices(runG) << std::endl;
- typedef std::vector<TVertexDescriptor> TLCB;
+ // typedef std::vector<TVertexDescriptor> TLCB;
std::vector<std::vector<TVertexDescriptor> > runs;
std::vector<std::vector<TVertexDescriptor> > LCBs;
//List of runs in an LCB
@@ -5386,8 +5386,8 @@ findDuplications(Graph<Alignment<TStringSet, TCargo,
TSpec> >& gAlign,
}
getGuideTree(currseqs,curridset,seqguideTrees,currguideTree);
- typedef Fragment<> TFragment;
- typedef String<TAlphabet> TSequence;
+ // typedef Fragment<> TFragment;
+ // typedef String<TAlphabet> TSequence;
std::cout << "Aligning LCB " << lcbid << " with " << length(currseqs) <<
std::endl;
assert(curridset.size()>0);
diff --git
a/mugsy-seqan/projects/library/seqan/basic/basic_allocator_chunkpool.h
b/mugsy-seqan/projects/library/seqan/basic/basic_allocator_chunkpool.h
index c50f86a..fff78d6 100644
--- a/mugsy-seqan/projects/library/seqan/basic/basic_allocator_chunkpool.h
+++ b/mugsy-seqan/projects/library/seqan/basic/basic_allocator_chunkpool.h
@@ -223,7 +223,7 @@ deallocate(Allocator<ChunkPool<SIZE, MAX_COUNT,
TParentAllocator> > & me,
SEQAN_CHECKPOINT
SEQAN_ASSERT(count > 0)
- typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >
TAllocator;
+ // typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >
TAllocator;
if ((sizeof(TValue) != SIZE) || (count > MAX_COUNT))
{//no blocking
diff --git a/mugsy-seqan/projects/library/seqan/basic/basic_holder.h
b/mugsy-seqan/projects/library/seqan/basic/basic_holder.h
index c4c54c0..2710fe3 100644
--- a/mugsy-seqan/projects/library/seqan/basic/basic_holder.h
+++ b/mugsy-seqan/projects/library/seqan/basic/basic_holder.h
@@ -1038,7 +1038,7 @@ inline typename Reference<Holder<TValue, Tristate> >::Type
value(Holder<TValue, Tristate> & me)
{
SEQAN_CHECKPOINT
- typedef Holder<TValue, Tristate> THolder;
+ // typedef Holder<TValue, Tristate> THolder;
if (empty(me))
{
@@ -1068,7 +1068,7 @@ assignValue(Holder<TValue, Tristate> & me,
TSource const & value_)
{
SEQAN_CHECKPOINT
- typedef typename Value<Holder<TValue, Tristate> >::Type THostValue;
+ // typedef typename Value<Holder<TValue, Tristate> >::Type THostValue;
if (empty(me))
{
create(me, value_);
@@ -1555,7 +1555,7 @@ setValue(Holder<TValue, Tristate2> & me,
TValue & value_)
{
SEQAN_CHECKPOINT
- typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
+ // typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
clear(me);
me.data_value = & value_;
@@ -1581,7 +1581,7 @@ SEQAN_CHECKPOINT
me.data_state = THolder::OWNER;
}
- typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
+ // typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
return *(me.data_value);
}
template <typename TValue>
@@ -1605,7 +1605,7 @@ assignValue(Holder<TValue, Tristate2> & me,
TSource const & value_)
{
SEQAN_CHECKPOINT
- typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
+ // typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
if (empty(me))
{
create(me, value_);
diff --git a/mugsy-seqan/projects/library/seqan/file/file_format_cgviz.h
b/mugsy-seqan/projects/library/seqan/file/file_format_cgviz.h
index 2e588d9..54928cd 100644
--- a/mugsy-seqan/projects/library/seqan/file/file_format_cgviz.h
+++ b/mugsy-seqan/projects/library/seqan/file/file_format_cgviz.h
@@ -63,7 +63,7 @@ void _write_impl(TFile& target, Align<TSource, TSpec>& align,
TStringContainer&
SEQAN_CHECKPOINT
typedef Align<TSource, TSpec> const TAlign;
- typedef typename Row<TAlign>::Type TRow;
+ // typedef typename Row<TAlign>::Type TRow;
typedef typename Position<typename Rows<TAlign>::Type>::Type
TRowsPosition;
typedef typename Position<TAlign>::Type TPosition;
TRowsPosition row_count = length(rows(align));
diff --git a/mugsy-seqan/projects/library/seqan/file/file_format_embl.h
b/mugsy-seqan/projects/library/seqan/file/file_format_embl.h
index 2419bda..3d8cf61 100644
--- a/mugsy-seqan/projects/library/seqan/file/file_format_embl.h
+++ b/mugsy-seqan/projects/library/seqan/file/file_format_embl.h
@@ -309,7 +309,7 @@ SEQAN_CHECKPOINT
SEQAN_TASSERT(length(key)==2);
typedef typename Iterator<String<TValue,TSpec>,Standard>::Type
TIterator;
- typedef typename Position<String<TValue,TSpec> >::Type TPosition;
+ // typedef typename Position<String<TValue,TSpec> >::Type TPosition;
clear(data);
if(empty(meta))
@@ -373,7 +373,7 @@ readFeature(TString & str,
SEQAN_CHECKPOINT
typedef typename Iterator<TString,Standard>::Type TIterator;
- typedef typename Position<TString>::Type TPosition;
+ // typedef typename Position<TString>::Type TPosition;
clear(data);
if(empty(str) || start_pos >= length(str))
diff --git a/mugsy-seqan/projects/library/seqan/file/file_format_fasta_align.h
b/mugsy-seqan/projects/library/seqan/file/file_format_fasta_align.h
index 2507990..c00a6bf 100644
--- a/mugsy-seqan/projects/library/seqan/file/file_format_fasta_align.h
+++ b/mugsy-seqan/projects/library/seqan/file/file_format_fasta_align.h
@@ -138,8 +138,8 @@ SEQAN_CHECKPOINT
TSize numRows=length(beg_end_length) / 3;
resize(rows(align), numRows); //rows
- typedef Align<TSource, TSpec> TAlign;
- typedef typename Row<TAlign>::Type TRow;
+ // typedef Align<TSource, TSpec> TAlign;
+ // typedef typename Row<TAlign>::Type TRow;
for(TSize i=0;i<numRows;++i) {
TSize begin = beg_end_length[i*3];
@@ -253,7 +253,7 @@ void _write_impl(TFile& file, Align<TSource, TSpec>& align,
TStringContainer& id
typedef Align<TSource, TSpec> const TAlign;
typedef typename Row<TAlign>::Type TRow;
typedef typename Position<typename Rows<TAlign>::Type>::Type
TRowsPosition;
- typedef typename Position<TAlign>::Type TPosition;
+ // typedef typename Position<TAlign>::Type TPosition;
TRowsPosition row_count = length(rows(align));
for(TRowsPosition i=0;i<row_count;++i) {
diff --git a/mugsy-seqan/projects/library/seqan/file/file_format_mmap.h
b/mugsy-seqan/projects/library/seqan/file/file_format_mmap.h
index fd9c9bb..5734097 100644
--- a/mugsy-seqan/projects/library/seqan/file/file_format_mmap.h
+++ b/mugsy-seqan/projects/library/seqan/file/file_format_mmap.h
@@ -129,7 +129,7 @@ namespace SEQAN_NAMESPACE_MAIN
Fasta)
{
typedef String<TValue, MMap<TConfig> >
TString;
- typedef StringSet<TString, ConcatDirect<TDelimiter> >
TStringSet;
+ // typedef StringSet<TString, ConcatDirect<TDelimiter> >
TStringSet;
typedef typename Iterator<TString const, Standard>::Type
TIterator;
clear(me.limits);
@@ -278,7 +278,7 @@ typedef Tag<TagFastq_> const Fastq;
Fastq)
{
typedef String<TValue, MMap<TConfig> >
TString;
- typedef StringSet<TString, ConcatDirect<TDelimiter> >
TStringSet;
+ // typedef StringSet<TString, ConcatDirect<TDelimiter> >
TStringSet;
typedef typename Iterator<TString const, Standard>::Type
TIterator;
clear(me.limits);
@@ -556,7 +556,7 @@ typedef Tag<TagFastq_> const Fastq;
QSeq)
{
typedef String<TValue, MMap<TConfig> >
TString;
- typedef StringSet<TString, ConcatDirect<TDelimiter> >
TStringSet;
+ // typedef StringSet<TString, ConcatDirect<TDelimiter> >
TStringSet;
typedef typename Iterator<TString const, Standard>::Type
TIterator;
clear(me.limits);
diff --git a/mugsy-seqan/projects/library/seqan/file/file_format_sam.h
b/mugsy-seqan/projects/library/seqan/file/file_format_sam.h
index d41eed3..f8d951f 100644
--- a/mugsy-seqan/projects/library/seqan/file/file_format_sam.h
+++ b/mugsy-seqan/projects/library/seqan/file/file_format_sam.h
@@ -223,8 +223,8 @@ namespace SEQAN_NAMESPACE_MAIN {
typedef Align<DnaString, TGapsSpec> const TAlign;
typedef typename Row<TAlign>::Type TRow;
- typedef typename Position<typename Rows<TAlign>::Type>::Type
TRowsPosition;
- typedef typename Position<TAlign>::Type TPosition;
+ // typedef typename Position<typename Rows<TAlign>::Type>::Type
TRowsPosition;
+ // typedef typename Position<TAlign>::Type TPosition;
typedef typename Iterator<typename Row<TAlign>::Type const,
Standard>::Type TIter;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm.h
b/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm.h
index 91ad0aa..a0c9422 100644
--- a/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm.h
+++ b/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm.h
@@ -90,7 +90,7 @@ breadth_first_search(Graph<TSpec> const& g,
{
SEQAN_CHECKPOINT
typedef Graph<TSpec> TGraph;
- typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+ // typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
typedef typename Value<TPredecessorMap>::Type TPredVal;
typedef typename Value<TDistanceMap>::Type TDistVal;
@@ -202,7 +202,7 @@ depth_first_search(Graph<TSpec> const& g,
SEQAN_CHECKPOINT
typedef Graph<TSpec> TGraph;
typedef typename Size<TGraph>::Type TSize;
- typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+ // typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename Value<TPredecessorMap>::Type TPredVal;
@@ -315,7 +315,7 @@ strongly_connected_components(Graph<TSpec> const& g_source,
typedef Graph<TSpec> TGraph;
typedef typename Size<TGraph>::Type TSize;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+ // typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
typedef typename Value<TComponents>::Type TCompVal;
resizeVertexMap(g_source,components);
@@ -425,7 +425,7 @@ connected_components(Graph<TSpec> const& g_source,
SEQAN_CHECKPOINT
typedef typename Size<Graph<TSpec> >::Type TSize;
- typedef typename Iterator<Graph<TSpec>, EdgeIterator>::Type
TEdgeIterator;
+ // typedef typename Iterator<Graph<TSpec>, EdgeIterator>::Type
TEdgeIterator;
typedef typename Iterator<Graph<TSpec>, VertexIterator>::Type
TVertexIterator;
typedef typename VertexDescriptor<Graph<TSpec> >::Type
TVertexDescriptor;
clear(components);
@@ -858,8 +858,8 @@ dag_shortest_path(Graph<TSpec> const& g,
TDistanceMap& distance)
{
SEQAN_CHECKPOINT
- typedef typename EdgeDescriptor<Graph<TSpec> >::Type TEdgeDescriptor;
- typedef typename Iterator<Graph<TSpec>, EdgeIterator>::Type
TEdgeIterator;
+ // typedef typename EdgeDescriptor<Graph<TSpec> >::Type TEdgeDescriptor;
+ // typedef typename Iterator<Graph<TSpec>, EdgeIterator>::Type
TEdgeIterator;
typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type
TOutEdgeIterator;
typedef typename Iterator<String<TVertexDescriptor>, Rooted>::Type
TStringIterator;
@@ -924,7 +924,7 @@ bellman_ford_algorithm(Graph<TSpec> const& g,
typedef typename Size<Graph<TSpec> >::Type TSize;
// Initialization
- typedef typename EdgeDescriptor<Graph<TSpec> >::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<Graph<TSpec> >::Type TEdgeDescriptor;
typedef typename Iterator<Graph<TSpec>, VertexIterator>::Type
TVertexIterator;
typedef typename Iterator<Graph<TSpec>, OutEdgeIterator>::Type
TOutEdgeIterator;
resizeVertexMap(g,predecessor);
@@ -994,7 +994,7 @@ dijkstra(Graph<TSpec> const& g,
{
SEQAN_CHECKPOINT
typedef Graph<TSpec> TGraph;
- typedef typename Size<TGraph>::Type TSize;
+ // typedef typename Size<TGraph>::Type TSize;
typedef typename Value<TDistanceMap>::Type TDistVal;
typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
@@ -1489,7 +1489,7 @@ ford_fulkerson(Graph<TSpec> const& g,
SEQAN_CHECKPOINT
typedef Graph<TSpec> TGraph;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+ // typedef typename Iterator<TGraph, VertexIterator>::Type
TVertexIterator;
typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
typedef typename Value<TFlowMap>::Type TFlow;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm_hmm.h
b/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm_hmm.h
index ab82a15..d933b9c 100644
--- a/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm_hmm.h
+++ b/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm_hmm.h
@@ -611,8 +611,8 @@ __parameterEstimator(Graph<Hmm<TAlphabet, TProbability,
TSpec> >& hmm,
SEQAN_CHECKPOINT
typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
typedef typename Size<TGraph>::Type TSize;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
typedef typename Value<TTransitionCounter>::Type TCounterValue;
@@ -650,8 +650,8 @@ estimationWithStates(Graph<Hmm<TAlphabet, TProbability,
TSpec> >& hmm,
typedef typename Size<TGraph>::Type TSize;
typedef typename Value<TStateSeqSet>::Type TStateSeq;
typedef typename Value<TStateSeq>::Type TState;
- typedef typename Value<TSequenceSet>::Type TSequence;
- typedef typename Value<TSequence>::Type TChar;
+ // typedef typename Value<TSequenceSet>::Type TSequence;
+ // typedef typename Value<TSequence>::Type TChar;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
// Initialization
@@ -794,10 +794,10 @@ __baumWelchAlgorithm(Graph<Hmm<TAlphabet, TProbability,
TSpec > >& hmm,
SEQAN_CHECKPOINT
typedef Graph<Hmm<TAlphabet, TProbability, TSpec> > TGraph;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
- typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+ // typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
typedef String<TProbability> TCountString;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm_lis_his.h
b/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm_lis_his.h
index 77d1d84..54c3bb8 100644
---
a/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm_lis_his.h
+++
b/mugsy-seqan/projects/library/seqan/graph_algorithms/graph_algorithm_lis_his.h
@@ -101,7 +101,7 @@ longestIncreasingSubsequence(TString const& str,
TPositions& pos) {
// The trace-back graph
typedef Graph<Directed<void, WithoutEdgeId> > TGraph;
- typedef Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
+ // typedef Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
TGraph g;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_align/graph_align_hirschberg.h
b/mugsy-seqan/projects/library/seqan/graph_align/graph_align_hirschberg.h
index 1eea65b..54e52f7 100644
--- a/mugsy-seqan/projects/library/seqan/graph_align/graph_align_hirschberg.h
+++ b/mugsy-seqan/projects/library/seqan/graph_align/graph_align_hirschberg.h
@@ -124,9 +124,9 @@ _align_hirschberg(TTrace& trace,
typedef String<TScoreValue> TColumn;
typedef typename Iterator<TTrace, Standard>::Type TTraceIter;
typedef typename Value<TStringSet const>::Type TString;
- typedef typename Iterator<TString const, Standard>::Type TStringIter;
+ // typedef typename Iterator<TString const, Standard>::Type TStringIter;
typedef typename Size<TString>::Type TSize;
- typedef typename Value<TString>::Type TCharacter;
+ // typedef typename Value<TString>::Type TCharacter;
typedef unsigned char TTraceValue;
// TraceBack values
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_base.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_base.h
index 652f48d..cb37411 100644
--- a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_base.h
+++ b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_base.h
@@ -209,9 +209,9 @@ buildAlignmentGraph(String<TFragment, TSpec1>& matches,
FrequencyCounting)
{
SEQAN_CHECKPOINT
- typedef String<TFragment, TSpec1> TFragmentString;
- typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TOutGraph;
- typedef typename Size<TFragmentString>::Type TSize;
+ // typedef String<TFragment, TSpec1> TFragmentString;
+ // typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TOutGraph;
+ // typedef typename Size<TFragmentString>::Type TSize;
// Initialization
clearVertices(outGraph);
@@ -375,7 +375,7 @@ inline void
{
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
- typedef typename Size<TGraph>::Type TSize;
+ // typedef typename Size<TGraph>::Type TSize;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
@@ -992,7 +992,7 @@ alignmentEvaluation(Graph<Alignment<TStringSet, TCargo,
TSpec> > const& g,
TSize& len)
{
SEQAN_CHECKPOINT
- typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+ // typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename Value<TScore>::Type TScoreValue;
typedef typename Value<typename Value<TStringSet>::Type>::Type
TAlphabet;
TSize alphSize = ValueSize<TAlphabet>::VALUE;
@@ -1113,7 +1113,7 @@ convertAlignment(Align<TSource, TSpec2> const& align,
Graph<Alignment<TStringSet, TCargo, TSpec> >&
gAlign)
{
typedef Align<TSource, TSpec2> const TAlign;
- typedef typename Value<TSource>::Type TAlphabet;
+ // typedef typename Value<TSource>::Type TAlphabet;
typedef typename Size<TAlign>::Type TSize;
typedef typename Row<TAlign>::Type TRow;
typedef typename Iterator<TRow, Standard>::Type TRowIterator;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_distance.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_distance.h
index 9a26358..92354f2 100644
---
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_distance.h
+++
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_distance.h
@@ -68,10 +68,10 @@ getDistanceMatrix(Graph<Alignment<TStringSet, TCargo,
TSpec> >& g,
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename Size<TGraph>::Type TSize;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
typedef typename Value<TMatrix>::Type TValue;
// Initialization
@@ -128,7 +128,7 @@ getDistanceMatrix(Graph<Alignment<TStringSet, TCargo,
TSpec> >& g,
KmerDistance)
{
SEQAN_CHECKPOINT
- typedef typename Value<TMatrix>::Type TValue;
+ // typedef typename Value<TMatrix>::Type TValue;
typedef typename Iterator<TMatrix, Standard>::Type TMatrixIterator;
getKmerSimilarityMatrix(stringSet(g), distanceMatrix, ktup,
TAlphabet());
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_guidetree.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_guidetree.h
index 64ef1ad..298d48c 100644
---
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_guidetree.h
+++
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_guidetree.h
@@ -427,7 +427,7 @@ _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >&
pairGraph,
SEQAN_CHECKPOINT
typedef Graph<Undirected<TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+ // typedef typename Iterator<TGraph, VertexIterator>::Type
TVertexIterator;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
TVertexDescriptor s = sourceVertex(pairGraph,best);
@@ -461,7 +461,7 @@ _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >&
pairGraph,
SEQAN_CHECKPOINT
typedef Graph<Undirected<TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+ // typedef typename Iterator<TGraph, VertexIterator>::Type
TVertexIterator;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
TVertexDescriptor s = sourceVertex(pairGraph,best);
@@ -494,7 +494,7 @@ _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >&
pairGraph,
SEQAN_CHECKPOINT
typedef Graph<Undirected<TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+ // typedef typename Iterator<TGraph, VertexIterator>::Type
TVertexIterator;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
TCargo infCargo = _getInfinity<TCargo>();
@@ -530,7 +530,7 @@ _upgmaTreeMerge(Graph<Undirected<TCargo, TSpec> >&
pairGraph,
SEQAN_CHECKPOINT
typedef Graph<Undirected<TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename Iterator<TGraph, VertexIterator>::Type TVertexIterator;
+ // typedef typename Iterator<TGraph, VertexIterator>::Type
TVertexIterator;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
TCargo infCargo = _getInfinity<TCargo>();
@@ -568,7 +568,7 @@ upgmaTree(String<TStringValue, TStringSpec>& mat,
typedef typename Size<TGraph>::Type TSize;
typedef String<TStringValue, TStringSpec> TMatrix;
typedef typename Value<TMatrix>::Type TValue;
- typedef typename Iterator<TMatrix>::Type TMatrixIter;
+ // typedef typename Iterator<TMatrix>::Type TMatrixIter;
// First initialization
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_io.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_io.h
index 1522cb4..2152046 100644
--- a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_io.h
+++ b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_io.h
@@ -225,7 +225,7 @@ read(TFile & file,
{
SEQAN_CHECKPOINT
typedef typename Size<TNames>::Type TSize;
- typedef typename Position<TFile>::Type TPosition;
+ // typedef typename Position<TFile>::Type TPosition;
typedef typename Value<TFile>::Type TValue;
TValue c;
@@ -262,7 +262,7 @@ void write(TFile & file,
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename Value<TStringSet>::Type TString;
typedef typename Size<TStringSet>::Type TSize;
@@ -344,8 +344,8 @@ read(TFile & file,
FastaAlign)
{
SEQAN_CHECKPOINT
- typedef typename Size<TNames>::Type TSize;
- typedef TSize TWord;
+ // typedef typename Size<TNames>::Type TSize;
+ // typedef TSize TWord;
typedef typename Value<TFile>::Type TValue;
TValue c;
@@ -388,8 +388,8 @@ _collectSegmentMatches(String<TValue, TSpec2> const& mat,
TValue gapChar = gapValue<TValue>();
// Create the anchor graph
- typedef String<TFragment, TSpec> TFragmentString;
- typedef typename Iterator<TFragmentString>::Type TFragmentStringIter;
+ // typedef String<TFragment, TSpec> TFragmentString;
+ // typedef typename Iterator<TFragmentString>::Type TFragmentStringIter;
typedef std::pair<TSize, TSize> TResiduePair;
typedef std::set<TResiduePair> TResiduePairSet;
String<TResiduePairSet> resPair;
@@ -461,8 +461,8 @@ template<typename TValue, typename TSpec2, typename
TFragment, typename TSpec, t
TValue gapChar = gapValue<TValue>();
// Create the anchor graph
- typedef String<TFragment, TSpec> TFragmentString;
- typedef typename Iterator<TFragmentString>::Type TFragmentStringIter;
+ // typedef String<TFragment, TSpec> TFragmentString;
+ // typedef typename Iterator<TFragmentString>::Type TFragmentStringIter;
typedef std::pair<TSize, TSize> TResiduePair;
typedef std::set<TResiduePair> TResiduePairSet;
String<TResiduePairSet> resPair;
@@ -581,7 +581,7 @@ template<typename TValue, typename TSpec2, typename
TFragment, typename TSpec, t
}
}
}
- typedef Fragment<TSize, ExactReversableFragment<TSpec> > TFragmentRev;
+ // typedef Fragment<TSize, ExactReversableFragment<TSpec> > TFragmentRev;
if(rev){
#ifdef DEBUGGING
std::cout << "REVMATCH" << std::endl;
@@ -1041,7 +1041,7 @@ read(TFile & file,
strSet,
seq1, seq2);
//Perform some simple checks for correctness of seq ids
- typedef String<Fragment<> > TFragmentString;
+ // typedef String<Fragment<> > TFragmentString;
typedef String<Fragment<> > TAlignmentString;
typedef typename Iterator<TAlignmentString,Standard>::Type
TAliIterator;
TAliIterator ali_it = begin(matches,Standard())+ali_counter;
@@ -1237,8 +1237,8 @@ void write(TFile & file,
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename Value<TStringSet>::Type TString;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename Value<TStringSet>::Type TString;
typedef typename Size<TStringSet>::Type TSize;
TStringSet& str = stringSet(g);
@@ -1430,10 +1430,10 @@ read(TFile & file,
SEQAN_CHECKPOINT
typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGuideTree>::Type TEdgeDescriptor;
- typedef typename Size<TGuideTree>::Type TSize;
+ // typedef typename EdgeDescriptor<TGuideTree>::Type TEdgeDescriptor;
+ // typedef typename Size<TGuideTree>::Type TSize;
typedef typename Id<TGuideTree>::Type TId;
- typedef typename Position<TFile>::Type TPosition;
+ // typedef typename Position<TFile>::Type TPosition;
typedef typename Value<TFile>::Type TValue;
typedef typename Value<TNames>::Type TName;
TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
@@ -1617,9 +1617,9 @@ write(TFile & file,
bool collapseRoot,
NewickFormat)
{
- typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
- typedef typename Size<TGuideTree>::Type TSize;
- typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
+ // typedef Graph<Tree<TCargo, TSpec> > TGuideTree;
+ // typedef typename Size<TGuideTree>::Type TSize;
+ // typedef typename VertexDescriptor<TGuideTree>::Type
TVertexDescriptor;
String<char> myNewickString;
_buildNewickString(guideTree, names, myNewickString,
getRoot(guideTree), collapseRoot);
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_library.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_library.h
index fb429ad..410b221 100644
--- a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_library.h
+++ b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_library.h
@@ -195,8 +195,8 @@ appendSegmentMatches(StringSet<TString, Dependent<TSpec> >
const& str,
typedef String<TSize2, TSpec2> TPairList;
typedef typename Size<TStringSet>::Type TSize;
typedef typename Id<TStringSet>::Type TId;
- typedef typename Value<TSegmentMatches>::Type TFragment;
- typedef typename Value<TScores>::Type TScoreValue;
+ // typedef typename Value<TSegmentMatches>::Type TFragment;
+ // typedef typename Value<TScores>::Type TScoreValue;
typedef typename Iterator<TPairList, Standard>::Type TPairIter;
// Pairwise longest common subsequence
@@ -276,10 +276,10 @@ appendSegmentMatches(StringSet<TString, Dependent<TSpec>
> const& str,
Kmer_Library)
{
SEQAN_CHECKPOINT
- typedef StringSet<TString, Dependent<TSpec> > TStringSet;
+ // typedef StringSet<TString, Dependent<TSpec> > TStringSet;
typedef typename Value<TScores>::Type TScoreValue;
typedef typename Value<TSegmentMatches>::Type TFragment;
- typedef typename Id<TStringSet>::Type TId;
+ // typedef typename Id<TStringSet>::Type TId;
typedef String<TSize> TTupelString;
typedef String<TTupelString> TTupelStringSet;
@@ -368,7 +368,7 @@ appendSegmentMatches(StringSet<TString, Dependent<TSpec> >
const& str,
SEQAN_CHECKPOINT
typedef StringSet<TString, Dependent<TSpec> > TStringSet;
typedef String<TSize2, TSpec2> TPairList;
- typedef typename Size<TStringSet>::Type TSize;
+ // typedef typename Size<TStringSet>::Type TSize;
typedef typename Id<TStringSet>::Type TId;
typedef typename Iterator<TPairList, Standard>::Type TPairIter;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_msa.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_msa.h
index 320e76a..7588098 100644
--- a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_msa.h
+++ b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_msa.h
@@ -219,7 +219,7 @@ globalMsaAlignment(Graph<Alignment<TStringSet, TCargo,
TSpec> >& gAlign,
typedef typename Value<TScore>::Type TScoreValue;
typedef typename Size<TStringSet>::Type TSize;
typedef Graph<Alignment<TStringSet, TSize> > TGraph;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
typedef double TDistanceValue;
@@ -367,8 +367,8 @@ inline void
globalMsaAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& gAlign,
TScore const& scoreObject)
{
- typedef typename Value<TStringSet>::Type TString;
- typedef typename Value<TString>::Type TAlphabet;
+ // typedef typename Value<TStringSet>::Type TString;
+ // typedef typename Value<TString>::Type TAlphabet;
TStringSet sequenceSet = stringSet(gAlign);
String<String<char> > sequenceNames;
fill(sequenceNames, length(sequenceSet), String<char>("tmpName"));
@@ -444,7 +444,7 @@ void
_debugRefinedMatches(TGraph& g)
{
typedef typename Id<TGraph>::Type TId;
- typedef typename Size<TGraph>::Type TSize;
+ // typedef typename Size<TGraph>::Type TSize;
typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
std::cout << "Refined matches" << std::endl;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_progressive.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_progressive.h
index 0577884..040013b 100644
---
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_progressive.h
+++
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_progressive.h
@@ -343,10 +343,10 @@ heaviestMatching(Graph<Alignment<TStringSet, TCargo,
TSpec> > const& g,
TSize seqsInStr1 = length(str1[0]);
TSize seqsInStr2 = length(str2[0]);
typedef typename Value<TString>::Type TVertexSet;
- typedef typename Iterator<TString const, Rooted>::Type TStringIter;
- typedef typename Iterator<TString, Rooted>::Type TSIter;
+ // typedef typename Iterator<TString const, Rooted>::Type TStringIter;
+ // typedef typename Iterator<TString, Rooted>::Type TSIter;
typedef typename Iterator<TVertexSet const, Rooted>::Type
TVertexSetIter;
- typedef typename Iterator<TVertexSet, Rooted>::Type TIter;
+ // typedef typename Iterator<TVertexSet, Rooted>::Type TIter;
clear(align);
// Retrieve all matches
String<bool> matchedVertices;
@@ -415,11 +415,11 @@ _recursiveProgressiveMatching(Graph<Alignment<TStringSet,
TCargo, TSpec> >& g,
TVertexDescriptor
const root,
TSequence& alignSeq)
{
- typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
- typedef typename Size<TGraph>::Type TSize;
- typedef typename Id<TGraph>::Type TId;
+ // typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
+ // typedef typename Size<TGraph>::Type TSize;
+ // typedef typename Id<TGraph>::Type TId;
typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type
TAdjacencyIterator;
- typedef typename Iterator<TGuideTree, DfsPreorder>::Type
TDfsPreorderIterator;
+ // typedef typename Iterator<TGuideTree, DfsPreorder>::Type
TDfsPreorderIterator;
if(isLeaf(tree, root)) {
_buildLeafString(g, root, alignSeq);
@@ -458,7 +458,7 @@ progressiveMatching(Graph<Alignment<TStringSet, TCargo,
TSpec> >& g,
TEdgeMap& edgeMapOut)
{
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
- typedef typename Size<TGraph>::Type TSize;
+ // typedef typename Size<TGraph>::Type TSize;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef String<TVertexDescriptor> TVertexString;
typedef String<TVertexString> TSegmentString;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_refinement.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_refinement.h
index 4144c42..cd848d8 100644
---
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_refinement.h
+++
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_refinement.h
@@ -123,7 +123,7 @@ scoreGapExtendHorizontal(
{
typedef typename Size<TSeq1>::Type TSize;
typedef typename Value<TSeq1>::Type TAlphabet1;
- typedef typename Value<TSeq2>::Type TAlphabet2;
+ // typedef typename Value<TSeq2>::Type TAlphabet2;
typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
// Last character is a gap
@@ -149,7 +149,7 @@ scoreGapOpenHorizontal(
{
typedef typename Size<TSeq1>::Type TSize;
typedef typename Value<TSeq1>::Type TAlphabet1;
- typedef typename Value<TSeq2>::Type TAlphabet2;
+ // typedef typename Value<TSeq2>::Type TAlphabet2;
typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
TSize alph_size = ValueSize<TSourceValue>::VALUE;
@@ -177,7 +177,7 @@ scoreGapExtendVertical(
{
typedef typename Size<TSeq1>::Type TSize;
typedef typename Value<TSeq1>::Type TAlphabet1;
- typedef typename Value<TSeq2>::Type TAlphabet2;
+ // typedef typename Value<TSeq2>::Type TAlphabet2;
typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
// Last character is a gap
@@ -203,7 +203,7 @@ scoreGapOpenVertical(
{
typedef typename Size<TSeq1>::Type TSize;
typedef typename Value<TSeq1>::Type TAlphabet1;
- typedef typename Value<TSeq2>::Type TAlphabet2;
+ // typedef typename Value<TSeq2>::Type TAlphabet2;
typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
TSize alph_size = ValueSize<TSourceValue>::VALUE;
@@ -230,7 +230,7 @@ score(Score<TValue, ProfileProfileScore<TScoreMember> >
const & me,
{
typedef typename Size<TSeq1>::Type TSize;
typedef typename Value<TSeq1>::Type TAlphabet1;
- typedef typename Value<TSeq2>::Type TAlphabet2;
+ // typedef typename Value<TSeq2>::Type TAlphabet2;
typedef typename SourceValue<TAlphabet1>::Type TSourceValue;
// Last character is a gap
diff --git a/mugsy-seqan/projects/library/seqan/graph_types/graph_drawing.h
b/mugsy-seqan/projects/library/seqan/graph_types/graph_drawing.h
index 8bab7e6..750c652 100644
--- a/mugsy-seqan/projects/library/seqan/graph_types/graph_drawing.h
+++ b/mugsy-seqan/projects/library/seqan/graph_types/graph_drawing.h
@@ -142,7 +142,7 @@ _createNodeAttributes(Graph<TSpec> const& g,
{
SEQAN_CHECKPOINT
typedef Graph<TSpec> TGraph;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
resizeVertexMap(g, nodeMap);
typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
@@ -168,7 +168,7 @@ _createNodeAttributes(Graph<TSpec> const& g,
TNameMap const& nameMap)
{
typedef Graph<TSpec> TGraph;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
resizeVertexMap(g, nodeMap);
typedef typename Iterator<TGraph, VertexIterator>::Type TConstIter;
@@ -193,7 +193,7 @@ _createEmptyEdgeAttributes(Graph<TSpec> const& g,
{
SEQAN_CHECKPOINT
typedef Graph<TSpec> TGraph;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
resizeEdgeMap(g, edgeMap);
typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
@@ -244,7 +244,7 @@ _createEdgeAttributes(Graph<Tree<TCargo, TSpec> > const& g,
TEdgeAttributes& edgeMap)
{
typedef Graph<Tree<TCargo, TSpec> > TGraph;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
resizeEdgeMap(g, edgeMap);
typedef typename Iterator<TGraph, EdgeIterator>::Type TConstEdIter;
@@ -469,7 +469,7 @@ write(TFile & file,
SEQAN_CHECKPOINT
typedef Graph<TSpec> TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
_writeGraphType(file,g,DotDrawing());
_streamWrite(file, " G {\n");
diff --git
a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_automaton.h
b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_automaton.h
index 73277a4..8e3eed2 100644
--- a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_automaton.h
+++ b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_automaton.h
@@ -161,7 +161,7 @@ _copyGraph(Graph<Automaton<TAlphabet, TCargo, TSpec> >
const& source,
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename EdgeType<TGraph>::Type TEdge;
- typedef typename Cargo<TEdge>::Type TCargoType;
+ // typedef typename Cargo<TEdge>::Type TCargoType;
typedef typename Size<TAlphabet>::Type TSize;
typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet> >
const, Standard>::Type TIterConst;
@@ -421,7 +421,7 @@ addEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
SEQAN_CHECKPOINT
typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename Size<TGraph>::Type TSize;
+ // typedef typename Size<TGraph>::Type TSize;
typedef typename Id<TGraph>::Type TId;
TEdgeDescriptor e = addEdge(g,source,target, (TAlphabet) label);
assignCargo(e,cargo);
@@ -474,7 +474,7 @@ removeOutEdges(Graph<Automaton<TAlphabet, TCargo, TSpec> >&
g,
typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename Size<TGraph>::Type TSize;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
for(TSize i=0;i< (TSize) ValueSize<TAlphabet>::VALUE;++i) {
TEdgeDescriptor ed = &g.data_vertex[vertex].data_edge[i];
@@ -498,7 +498,7 @@ removeInEdges(Graph<Automaton<TAlphabet, TCargo, TSpec> >&
g,
typedef typename EdgeType<TGraph>::Type TEdge;
typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename Size<TGraph>::Type TSize;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
typedef typename Iterator<String<AutomatonEdgeArray<TEdge, TAlphabet>
>, Standard>::Type TIter;
TIter it = begin(g.data_vertex, Standard());
@@ -607,7 +607,7 @@ findEdge(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
{
SEQAN_CHECKPOINT
SEQAN_ASSERT(idInUse(g.data_id_managerV, v) == true)
- typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
+ // typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
return &g.data_vertex[v].data_edge[ordValue((TAlphabet) c)];
}
diff --git a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_hmm.h
b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_hmm.h
index 15721e3..c0dc42f 100644
--- a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_hmm.h
+++ b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_hmm.h
@@ -247,9 +247,9 @@ inline void
clearVertices(Graph<Hmm<TAlphabet, TCargo, TSpec> >& g)
{
SEQAN_CHECKPOINT
- typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
- typedef typename Size<TGraph>::Type TSize;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+ // typedef typename Size<TGraph>::Type TSize;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
g.data_begin = 0;
g.data_end = 0;
@@ -519,7 +519,7 @@ write(TFile & target,
TSize alph_size = ValueSize<TAlphabet>::VALUE;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename Iterator<String<TCargo> const, Standard>::Type
TEmisIter;
@@ -884,7 +884,7 @@ getEmissionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec>
> const& g,
{
SEQAN_CHECKPOINT
- typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+ // typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename Size<TAlphabet>::Type TSize;
return g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE +
ordValue(symbol)];
}
@@ -912,7 +912,7 @@ emissionProbability(Graph<Hmm<TAlphabet, TCargo, TSpec> >&
g,
{
SEQAN_CHECKPOINT
- typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+ // typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename Size<TAlphabet>::Type TSize;
return g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE +
ordValue(symbol)];
}
@@ -942,7 +942,7 @@ assignEmissionProbability(Graph<Hmm<TAlphabet, TCargo,
TSpec> >& g,
{
SEQAN_CHECKPOINT
- typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
+ // typedef Graph<Hmm<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename Size<TAlphabet>::Type TSize;
g.data_emission[state * (TSize) ValueSize<TAlphabet>::VALUE +
ordValue(symbol)] = (TCargo) eProb;
}
diff --git a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_oracle.h
b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_oracle.h
index a5d1b4d..ea0df18 100644
--- a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_oracle.h
+++ b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_oracle.h
@@ -68,8 +68,8 @@ _addLetterToOracle(Graph<Automaton<TAlphabet, TCargo, TSpec>
>& g,
SEQAN_CHECKPOINT
typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename Size<TGraph>::Type TSize;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename Size<TGraph>::Type TSize;
TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
TVertexDescriptor newState = addVertex(g);
TVertexDescriptor pred = newState - 1;
@@ -171,11 +171,11 @@ createSetOracle(Graph<Automaton<TAlphabet, TCargo, TSpec>
>& g,
SEQAN_CHECKPOINT
typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename Position<TKeywords>::Type TPos;
typedef typename Value<TKeywords>::Type TKeyword;
typedef typename Iterator<TKeyword, Standard>::Type TIterator;
- typedef typename Value<TKeywords>::Type TValue;
+ // typedef typename Value<TKeywords>::Type TValue;
createTrie(g, terminalStateMap, keywords);
diff --git a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_tree.h
b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_tree.h
index 56e3936..3463e39 100644
--- a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_tree.h
+++ b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_tree.h
@@ -463,7 +463,7 @@ addEdge(Graph<Tree<TCargo, TSpec> >& g,
typedef Graph<Tree<TCargo, TSpec> > TGraph;
typedef typename EdgeType<TGraph>::Type TEdgeStump;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Id<TGraph>::Type TId;
TEdgeStump* edge_ptr;
allocate(g.data_allocator, edge_ptr, 1);
@@ -748,7 +748,7 @@ assignRoot(Graph<Tree<TCargo, TSpec> >& g,
SEQAN_CHECKPOINT
SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex) == true)
- typedef Graph<Tree<TCargo, TSpec> > TGraph;
+ // typedef Graph<Tree<TCargo, TSpec> > TGraph;
g.data_root = vertex;
g.data_parent[vertex] = getNil<TVertexDescriptor>();
@@ -1060,8 +1060,8 @@ collectLeaves(Graph<Tree<TCargo, TSpec> > const& g,
{
SEQAN_CHECKPOINT
typedef Graph<Tree<TCargo, TSpec> > TGraph;
- typedef typename Size<TGraph>::Type TSize;
- typedef typename Id<TGraph>::Type TId;
+ // typedef typename Size<TGraph>::Type TSize;
+ // typedef typename Id<TGraph>::Type TId;
typedef typename Iterator<TGraph, AdjacencyIterator>::Type
TAdjacencyIterator;
if (isLeaf(g, root)) appendValue(group, root, Generous());
diff --git a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_trie.h
b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_trie.h
index b6c033c..2bf3322 100644
--- a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_trie.h
+++ b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_trie.h
@@ -72,8 +72,8 @@ _addStringToTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >&
g,
SEQAN_CHECKPOINT
typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
- typedef typename Size<TKeyword>::Type TSize;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename Size<TKeyword>::Type TSize;
TVertexDescriptor current = getRoot(g);
TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
@@ -127,7 +127,7 @@ createTrie(Graph<Automaton<TAlphabet, TCargo, TSpec> >& g,
SEQAN_CHECKPOINT
typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename Position<TKeywords>::Type TPos;
TVertexDescriptor root = addVertex(g);
assignRoot(g,root);
@@ -165,7 +165,7 @@ createTrieOnReverse(Graph<Automaton<TAlphabet, TCargo,
TSpec> >& g,
SEQAN_CHECKPOINT
typedef Graph<Automaton<TAlphabet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename Position<TKeywords>::Type TPos;
TVertexDescriptor root = addVertex(g);
assignRoot(g,root);
diff --git
a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_wordgraph.h
b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_wordgraph.h
index c21874f..5583c3a 100644
--- a/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_wordgraph.h
+++ b/mugsy-seqan/projects/library/seqan/graph_types/graph_impl_wordgraph.h
@@ -173,7 +173,7 @@ write(TFile & target,
{
typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec>
> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
+ // typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
typedef typename EdgeType<TGraph>::Type TEdge;
typedef typename Size<TAlphabet>::Type TSize;
TSize table_length = ValueSize<TAlphabet>::VALUE;
@@ -212,7 +212,7 @@ getSuccessor(Graph<Automaton<TAlphabet, String<TAlphabet>,
WordGraph<TSpec> > >
SEQAN_ASSERT(idInUse(g.data_id_managerV, vertex) == true)
typedef Graph<Automaton<TAlphabet, String<TAlphabet>, WordGraph<TSpec>
> > TGraph;
typedef typename EdgeType<TGraph>::Type TEdgeStump;
- typedef typename Size<TAlphabet>::Type TSize;
+ // typedef typename Size<TAlphabet>::Type TSize;
TEdgeStump* ed = findEdge(g, vertex, getValue(chars, 0));
if (getCargo(ed) == suffix(chars, 1)) {
return getTarget(ed);
diff --git a/mugsy-seqan/projects/library/seqan/map/map_skiplist.h
b/mugsy-seqan/projects/library/seqan/map/map_skiplist.h
index 498dbcb..2dced48 100644
--- a/mugsy-seqan/projects/library/seqan/map/map_skiplist.h
+++ b/mugsy-seqan/projects/library/seqan/map/map_skiplist.h
@@ -272,7 +272,7 @@ assign(Map<TValue, Skiplist<TSpec> > & target,
typedef SkiplistPath<TValue, TSpec> TPath;
typedef SkiplistElement<TValue, TSpec> TElement;
typedef typename Iterator<TSkiplist>::Type TIterator;
- typedef typename Value<TSkiplist>::Type TValue2;
+ // typedef typename Value<TSkiplist>::Type TValue2;
clear(target);
@@ -589,7 +589,7 @@ _skiplistInsertElement(Map<TValue, Skiplist<TSpec> > & me,
SkiplistElement<TValue, TSpec> & el,
unsigned char height)
{
- typedef SkiplistElement<TValue, TSpec> TElement;
+ // typedef SkiplistElement<TValue, TSpec> TElement;
typedef SkiplistPath<TValue, TSpec> TPath;
TPath path;
@@ -739,7 +739,7 @@ inline void
add(Map<TValue, Skiplist<TSpec> > & me,
TValue2 const & _value)
{
- typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
+ // typedef Map<TValue, Skiplist<TSpec> > TSkiplist;
typedef SkiplistElement<TValue, TSpec> TElement;
unsigned char height = _skiplistCreateHeight(me);
diff --git a/mugsy-seqan/projects/library/seqan/map/sumlist_skip.h
b/mugsy-seqan/projects/library/seqan/map/sumlist_skip.h
index 3360388..c8a67c0 100644
--- a/mugsy-seqan/projects/library/seqan/map/sumlist_skip.h
+++ b/mugsy-seqan/projects/library/seqan/map/sumlist_skip.h
@@ -149,7 +149,7 @@ template <typename TValue, unsigned int DIM, typename
TSpec, typename TSkiplist>
void goNext(SkiplistPath<TValue, _SkipSumList<DIM, TSpec> > & path,
TSkiplist const & skiplist)
{
- typedef SkiplistPath<TValue, _SkipSumList<DIM, TSpec> > TPath;
+ // typedef SkiplistPath<TValue, _SkipSumList<DIM, TSpec> > TPath;
typedef SkiplistElement<TValue, _SkipSumList<DIM, TSpec> > TElement;
TElement * next = path.data_elements[0]->data_next[0].data_element;
@@ -213,12 +213,12 @@ _skipsumlistFind(Map<TValue, Skiplist<_SkipSumList<DIM,
TSpec> > > & me,
unsigned int dim,
/*OUT*/ SkiplistPath<TValue, _SkipSumList<DIM,
TSpec> > & path)
{
- typedef Map<TValue, Skiplist<_SkipSumList<DIM, TSpec> > > TMap;
+ // typedef Map<TValue, Skiplist<_SkipSumList<DIM, TSpec> > > TMap;
typedef SkiplistElement<TValue, _SkipSumList<DIM, TSpec> > TElement;
typedef SkiplistNext<TValue, _SkipSumList<DIM, TSpec> > TNext;
typedef SumListValues<DIM, TValue> TValues;
- typedef typename Size<TMap>::Type TSize;
+ // typedef typename Size<TMap>::Type TSize;
TElement * here = & me.data_border;
@@ -490,8 +490,8 @@ appendValues(SumList<DIM, TValue, SkipSumList<TSpec> > & me,
{
typedef SkiplistPath<TValue, _SkipSumList<DIM, TSpec> > TPath;
typedef SkiplistElement<TValue, _SkipSumList<DIM, TSpec> > TElement;
- typedef Pair<TValue, TElement *> TPair;
- typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
+ // typedef Pair<TValue, TElement *> TPair;
+ // typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
//find end of skip list
TPath path;
@@ -721,8 +721,8 @@ inline void
goBeforeEnd(Iter<SumList<DIM, TValue, SkipSumList<TSpec> >,
SkipSumListIterator > & it)
{
typedef SkiplistPath<TValue, _SkipSumList<DIM, TSpec> > TPath;
- typedef SkiplistElement<TValue, _SkipSumList<DIM, TSpec> > TElement;
- typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
+ // typedef SkiplistElement<TValue, _SkipSumList<DIM, TSpec> > TElement;
+ // typedef SumList<DIM, TValue, MiniSumList< > > TMiniSumList;
//find end of skip list
TPath path;
diff --git
a/mugsy-seqan/projects/library/seqan/modifier/modifier_alphabet_expansion.h
b/mugsy-seqan/projects/library/seqan/modifier/modifier_alphabet_expansion.h
index 8a0021f..2da2537 100644
--- a/mugsy-seqan/projects/library/seqan/modifier/modifier_alphabet_expansion.h
+++ b/mugsy-seqan/projects/library/seqan/modifier/modifier_alphabet_expansion.h
@@ -180,7 +180,7 @@ inline void
_initializeAlphabetConversionTable(ModifiedAlphabet<THost, ModExpand<CHAR,
TSpec> > * buf,
TSource
const &)
{
- typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
+ // typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
//assure that the conversion from TSource to THost is possible
// _AlphabetConversionTable<THost, TSource>::initialize();
@@ -272,7 +272,7 @@ inline void
_initializeAlphabetConversionTable(TTarget * buf,
ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > const &)
{
- typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TSource;
+ // typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TSource;
//assure that the conversion from THost to TTarget is possible
_AlphabetConversionTable<TTarget, THost>::initialize();
diff --git
a/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_exact_iterative.h
b/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_exact_iterative.h
index 09dc556..d829f3d 100644
---
a/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_exact_iterative.h
+++
b/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_exact_iterative.h
@@ -181,11 +181,11 @@ createTreesForAllSequences(String<TGraph> & gs,
TValue numSequences)
{
SEQAN_CHECKPOINT
- typedef typename Value<TAlignmentString>::Type TAlignment;
+ // typedef typename Value<TAlignmentString>::Type TAlignment;
// typedef TAlignment* TCargo;
typedef TValue TCargo;
typedef IntervalAndCargo<int,TCargo> TInterval;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
//std::cout <<"create interval trees..." <<std::flush;
clock_t start, finish1;
@@ -454,7 +454,7 @@ SEQAN_CHECKPOINT
_makeRefinedGraphNodes(all_nodes,seqs,ali_g);
//add annotation to nodes
- typedef typename Value<TAnnoString>::Type TAnnotation;
+ // typedef typename Value<TAnnoString>::Type TAnnotation;
//typedef typename Value<TAnnotation>::Type TLabel;
typedef char TLabel;
String<String<TLabel> > pm;
@@ -497,8 +497,8 @@ matchRefinement(TAlignmentString & alis,
typedef Graph<Directed<void,WithoutEdgeId> > TGraph;
typedef IntervalTreeNode<TInterval> TNode;
typedef String<TNode> TPropertyMap;
- typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef String<TCargo> TList;
+ // typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef String<TCargo> TList;
typedef typename std::set<TValue>::iterator TSetIterator;
typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type
TAlignmentPointer;
typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type
TSegmentIterator;
diff --git
a/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_inexact.h
b/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_inexact.h
index cfa6e29..b878103 100644
---
a/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_inexact.h
+++
b/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_inexact.h
@@ -146,8 +146,8 @@ SEQAN_CHECKPOINT
typedef typename Value<TAlign>::Type TValue;
typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
- typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
- typedef typename Cargo<TAliGraph>::Type TCargo;
+ // typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
+ // typedef typename Cargo<TAliGraph>::Type TCargo;
//make edges
TAliIterator ali_it = begin(alis);
TAliIterator ali_end = end(alis);
diff --git a/mugsy-seqan/projects/library/seqan/refinement/graph_impl_align.h
b/mugsy-seqan/projects/library/seqan/refinement/graph_impl_align.h
index 6a8d1ca..6447d03 100644
--- a/mugsy-seqan/projects/library/seqan/refinement/graph_impl_align.h
+++ b/mugsy-seqan/projects/library/seqan/refinement/graph_impl_align.h
@@ -555,10 +555,10 @@ removeVertex(Graph<Alignment<TStringSet, TCargo, TSpec>
>& g,
{
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
- typedef typename Id<TGraph>::Type TIdType;
+ // typedef typename Id<TGraph>::Type TIdType;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename TGraph::TKey TKey;
- typedef typename TGraph::TPosToVertexMap TPosToVertexMap;
+ // typedef typename TGraph::TPosToVertexMap TPosToVertexMap;
// Clear the interval
(g.data_pvMap.lower_bound(TKey(sequenceId(g,v), fragmentBegin(g,v) +
fragmentLength(g,v))))->second = getNil<TVertexDescriptor>();
@@ -693,7 +693,7 @@ write(TFile & target,
{
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
- typedef typename Id<TGraph>::Type TIdType;
+ // typedef typename Id<TGraph>::Type TIdType;
typedef typename Size<TGraph>::Type TSize;
typedef typename TGraph::TFragmentInfo TSegment;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
@@ -1174,7 +1174,7 @@ write(TFile & file,
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename Size<TGraph>::Type TSize;
typedef typename Id<TGraph>::Type TId;
- typedef FragmentInfo<TId, TSize> TSegment;
+ // typedef FragmentInfo<TId, TSize> TSegment;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename EdgeType<TGraph>::Type TEdgeStump;
typedef typename Iterator<String<TEdgeStump*> const, Rooted>::Type
TIterConst;
@@ -1401,8 +1401,8 @@ label(Graph<Alignment<TStringSet, TCargo, TSpec> > const&
g,
{
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
- typedef typename Id<TGraph>::Type TIdType;
- typedef typename Size<TGraph>::Type TSize;
+ // typedef typename Id<TGraph>::Type TIdType;
+ // typedef typename Size<TGraph>::Type TSize;
typedef typename TGraph::TFragmentInfo TSegment;
TSegment seg = getProperty(g.data_fragment, v);
//std::cout << seg.data_seq_id << ",";
@@ -1583,9 +1583,9 @@ getFirstCoveredPosition(Graph<Alignment<TStringSet,
TCargo, TSpec> > const& g,
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename Id<TGraph>::Type TIdType;
- typedef typename Size<TGraph>::Type TSize;
- typedef typename EdgeType<TGraph>::Type TEdgeStump;
+ // typedef typename Id<TGraph>::Type TIdType;
+ // typedef typename Size<TGraph>::Type TSize;
+ // typedef typename EdgeType<TGraph>::Type TEdgeStump;
typedef typename TGraph::TPosToVertexMap TPosToVertexMap;
@@ -1626,9 +1626,9 @@ getLastCoveredPosition(Graph<Alignment<TStringSet,
TCargo, TSpec> >& g,
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
- typedef typename Id<TGraph>::Type TIdType;
- typedef typename Size<TGraph>::Type TSize;
- typedef typename EdgeType<TGraph>::Type TEdgeStump;
+ // typedef typename Id<TGraph>::Type TIdType;
+ // typedef typename Size<TGraph>::Type TSize;
+ // typedef typename EdgeType<TGraph>::Type TEdgeStump;
typedef typename TGraph::TPosToVertexMap TPosToVertexMap;
TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
@@ -1771,7 +1771,7 @@ convertAlignment(Graph<Alignment<TStringSet, TCargo,
TSpec> > const& g,
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename Value<TMatrix>::Type TValue;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename Size<TGraph>::Type TSize;
typedef typename Id<TGraph>::Type TIdType;
typedef typename TGraph::TPosToVertexMap TPosToVertexMap;
@@ -1839,8 +1839,8 @@ convertAlignment(String<TValue, TSpec1> const& mat,
typedef String<TValue, TSpec1> TMatrix;
typedef Graph<Alignment<TStringSet, TCargo, TSpec2> > TGraph;
typedef typename Size<TGraph>::Type TSize;
- typedef typename Value<TStringSet>::Type TSequence;
- typedef typename Value<TSequence>::Type TAlphabet;
+ // typedef typename Value<TStringSet>::Type TSequence;
+ // typedef typename Value<TSequence>::Type TAlphabet;
typedef typename Iterator<TMatrix, Standard>::Type TMatIter;
clearVertices(g);
TValue gapChar = gapValue<TValue>();
@@ -1892,7 +1892,7 @@ rebuildGraph(Graph<Alignment<TStringSet, TCargo, TSpec>
>& g)
// Initialization
typedef Fragment<> TFragment;
typedef String<TFragment> TFragmentString;
- typedef typename Iterator<TFragmentString>::Type TFragmentStringIter;
+ // typedef typename Iterator<TFragmentString>::Type TFragmentStringIter;
TFragmentString matches;
TSize nseq = length(stringSet(g));
@@ -1994,7 +1994,7 @@ __heaviestCommonSubsequence(Graph<Alignment<TStringSet,
TCargo, TSpec> > const&
typedef typename Iterator<TString const, Standard>::Type TStringIter;
typedef typename Iterator<TString, Standard>::Type TSIter;
typedef typename Iterator<TVertexSet const, Standard>::Type
TVertexSetIter;
- typedef typename Iterator<TVertexSet, Standard>::Type TIter;
+ // typedef typename Iterator<TVertexSet, Standard>::Type TIter;
// Create the alignment sequence
TSize numMatches = length(positions);
@@ -2121,7 +2121,7 @@ heaviestCommonSubsequence(Graph<Alignment<TStringSet,
TCargo, TSpec> > const& g,
SEQAN_CHECKPOINT
typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
typedef typename Size<TGraph>::Type TSize;
- typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
+ // typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
typedef typename Iterator<TGraph, OutEdgeIterator>::Type
TOutEdgeIterator;
typedef typename Value<TString>::Type TVertexSet;
@@ -2191,7 +2191,7 @@ heaviestCommonSubsequence(Graph<Alignment<TStringSet,
TCargo, TSpec> > const& g,
// Walk through str2 and fill in the weights of the actual edges
typedef String<TCargo> TWeights;
- typedef typename Iterator<TWeights>::Type TWeightsIter;
+ // typedef typename Iterator<TWeights>::Type TWeightsIter;
TWeights weights;
fill(weights, length(slotToPos), 0);
itStr2 = begin(str2, Standard());
diff --git a/mugsy-seqan/projects/library/seqan/sequence/lexical.h
b/mugsy-seqan/projects/library/seqan/sequence/lexical.h
index 9312876..668d776 100644
--- a/mugsy-seqan/projects/library/seqan/sequence/lexical.h
+++ b/mugsy-seqan/projects/library/seqan/sequence/lexical.h
@@ -236,8 +236,8 @@ compare_(Lexical<TSpec> & lexical,
TRight & right)
{
SEQAN_CHECKPOINT
- typedef typename Value<TLeft>::Type TLeftValue;
- typedef typename Value<TRight>::Type TRightValue;
+ // typedef typename Value<TLeft>::Type TLeftValue;
+ // typedef typename Value<TRight>::Type TRightValue;
typename Iterator<TLeft, Standard>::Type left_it = begin(left,
Standard());
typename Size<TLeft>::Type left_length = length(left);
diff --git a/mugsy-seqan/projects/library/seqan/sequence/sequence_multiple.h
b/mugsy-seqan/projects/library/seqan/sequence/sequence_multiple.h
index 2aa8b34..1e452b7 100644
--- a/mugsy-seqan/projects/library/seqan/sequence/sequence_multiple.h
+++ b/mugsy-seqan/projects/library/seqan/sequence/sequence_multiple.h
@@ -1501,7 +1501,7 @@ end(StringSet< TString, TSpec > const & me,
SEQAN_CHECKPOINT
typedef StringSet<TString, Dependent<Tight> > TStringSet;
typedef typename TStringSet::TIdPosMap::const_iterator TIter;
- typedef typename Size<TStringSet>::Type TSize;
+ // typedef typename Size<TStringSet>::Type TSize;
typedef typename Id<TStringSet>::Type TId;
if (me.lastId < (TId) id) me.lastId = (TId) (id + 1);
diff --git a/mugsy-seqan/projects/library/seqan/sequence/string_base.h
b/mugsy-seqan/projects/library/seqan/sequence/string_base.h
index 27722ee..5fc3e07 100644
--- a/mugsy-seqan/projects/library/seqan/sequence/string_base.h
+++ b/mugsy-seqan/projects/library/seqan/sequence/string_base.h
@@ -808,7 +808,7 @@ assign(String<TTargetValue, TTargetSpec> & target,
TSource const & source,
Tag<TExpand> const)
{
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Assign_String<Tag<TExpand> const>::assign_(target, source);
}
template<typename TTargetValue, typename TTargetSpec, typename TSource,
typename TSize, typename TExpand>
@@ -818,7 +818,7 @@ assign(String<TTargetValue, TTargetSpec> & target,
TSize limit,
Tag<TExpand> const)
{
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Assign_String<Tag<TExpand> const>::assign_(target, source, limit);
}
@@ -831,7 +831,7 @@ assign(String<TTargetValue, TTargetSpec> & target,
TSourceValue const * source,
Tag<TExpand> const)
{
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Assign_String<Tag<TExpand> const>::assign_(target, source);
}
template<typename TTargetValue, typename TTargetSpec, typename TSourceValue,
typename TSize, typename TExpand>
@@ -841,7 +841,7 @@ assign(String<TTargetValue, TTargetSpec> & target,
TSize limit,
Tag<TExpand> const)
{
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Assign_String<Tag<TExpand> const>::assign_(target, source, limit);
}
@@ -1041,7 +1041,7 @@ append(String<TTargetValue, TTargetSpec> & target,
Tag<TExpand> const)
{
SEQAN_CHECKPOINT
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Append_String<Tag<TExpand> const>::append_(target, source);
}
@@ -1053,7 +1053,7 @@ append(String<TTargetValue, TTargetSpec> & target,
Tag<TExpand> const)
{
SEQAN_CHECKPOINT
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Append_String<Tag<TExpand> const>::append_(target, source, limit);
}
@@ -1067,7 +1067,7 @@ append(String<TTargetValue, TTargetSpec> & target,
Tag<TExpand> const)
{
SEQAN_CHECKPOINT
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Append_String<Tag<TExpand> const>::append_(target, source);
}
@@ -1079,7 +1079,7 @@ append(String<TTargetValue, TTargetSpec> & target,
Tag<TExpand> const)
{
SEQAN_CHECKPOINT
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Append_String<Tag<TExpand> const>::append_(target, source, limit);
}
@@ -1246,7 +1246,7 @@ replace(String<TTargetValue, TTargetSpec> & target,
Tag<TExpand> const)
{
SEQAN_CHECKPOINT
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Replace_String<Tag<TExpand> const>::replace_(target, pos_begin,
pos_end, source);
}
@@ -1260,7 +1260,7 @@ replace(String<TTargetValue, TTargetSpec> & target,
Tag<TExpand> const)
{
SEQAN_CHECKPOINT
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Replace_String<Tag<TExpand> const>::replace_(target, pos_begin,
pos_end, source, limit);
}
@@ -1276,7 +1276,7 @@ replace(String<TTargetValue, TTargetSpec> & target,
Tag<TExpand> const)
{
SEQAN_CHECKPOINT
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Replace_String<Tag<TExpand> const>::replace_(target, pos_begin,
pos_end, source);
}
@@ -1290,7 +1290,7 @@ replace(String<TTargetValue, TTargetSpec> & target,
Tag<TExpand> const)
{
SEQAN_CHECKPOINT
- typedef String<TTargetValue, TTargetSpec> TTarget;
+ // typedef String<TTargetValue, TTargetSpec> TTarget;
_Replace_String<Tag<TExpand> const>::replace_(target, pos_begin,
pos_end, source, limit);
}
diff --git a/mugsy-seqan/projects/library/seqan/sequence/string_packed.h
b/mugsy-seqan/projects/library/seqan/sequence/string_packed.h
index 0d9c158..e6176ec 100644
--- a/mugsy-seqan/projects/library/seqan/sequence/string_packed.h
+++ b/mugsy-seqan/projects/library/seqan/sequence/string_packed.h
@@ -599,7 +599,7 @@ SEQAN_CHECKPOINT
// - avoid double moving of the rest-part if
"resize" allocates a new block
typedef typename Size<T>::Type TSize;
- typedef typename Iterator<T, Standard>::Type TIterator;
+ // typedef typename Iterator<T, Standard>::Type TIterator;
TSize old_length = length(seq);
TSize old_size = end - start;
--
2.3.5
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