| libMems/Backbone.cpp | 2 +- |
| libMems/Files.h | 64 +++++++++++++++++++++--------------------- |
| libMems/ProgressiveAligner.cpp | 2 +- |
| 3 files changed, 34 insertions(+), 34 deletions(-) |
| |
| diff --git a/libMems/Backbone.cpp b/libMems/Backbone.cpp |
| index 86698a9..0025cd8 100644 |
| --- a/libMems/Backbone.cpp |
| +++ b/libMems/Backbone.cpp |
| @@ -15,7 +15,7 @@ |
| #include "libMems/Islands.h"
|
| #include "libMems/CompactGappedAlignment.h"
|
|
|
| -#include <boost/property_map.hpp>
|
| +#include <boost/property_map/property_map.hpp>
|
| #include <boost/graph/graph_traits.hpp>
|
| #include <boost/graph/adjacency_list.hpp>
|
| #include <boost/graph/topological_sort.hpp>
|
| diff --git a/libMems/Files.h b/libMems/Files.h |
| index 8d6e9be..8191065 100644 |
| --- a/libMems/Files.h |
| +++ b/libMems/Files.h |
| @@ -22,44 +22,44 @@ |
| |
| #include "boost/filesystem/operations.hpp" |
| #include "boost/filesystem/exception.hpp" |
| -#include "boost/algorithm/string.hpp"
|
| +#include "boost/algorithm/string.hpp" |
| #include <string> |
| #include <sstream> |
| #include <iostream> |
| #include <iomanip> |
| |
| |
| -/**
|
| - * Register a file name to be deleted before the process exits
|
| - * When passed an empty string, it does not add to the list of files to delete
|
| - * @param fname The name of a file to delete, empty strings are ignored
|
| - * @return A vector of file names registered for deletion
|
| - */
|
| -std::vector< std::string >& registerFileToDelete( std::string fname = "" );
|
| -
|
| -inline
|
| -std::vector< std::string >& registerFileToDelete( std::string fname ) {
|
| - // since this vector is needed when atexit() is called we allocate it
|
| - // on the heap so its destructor won't get called
|
| - static std::vector< std::string >* files = new std::vector< std::string >();
|
| -#pragma omp critical
|
| -{
|
| - if( fname != "" )
|
| - files->push_back( fname );
|
| -}
|
| - return *files;
|
| -}
|
| +/** |
| + * Register a file name to be deleted before the process exits |
| + * When passed an empty string, it does not add to the list of files to delete |
| + * @param fname The name of a file to delete, empty strings are ignored |
| + * @return A vector of file names registered for deletion |
| + */ |
| +std::vector< std::string >& registerFileToDelete( std::string fname = "" ); |
| |
| -void deleteRegisteredFiles();
|
| -inline
|
| -void deleteRegisteredFiles() {
|
| - // don't be a slob, clean up after yourself:
|
| - // delete any files that are laying around
|
| - std::vector< std::string >& del_files = registerFileToDelete();
|
| - for( int fileI = 0; fileI < del_files.size(); fileI++ )
|
| - boost::filesystem::remove( del_files[ fileI ] );
|
| - del_files.clear(); // clear the deleted files from the list
|
| -}
|
| +inline |
| +std::vector< std::string >& registerFileToDelete( std::string fname ) { |
| + // since this vector is needed when atexit() is called we allocate it |
| + // on the heap so its destructor won't get called |
| + static std::vector< std::string >* files = new std::vector< std::string >(); |
| +#pragma omp critical |
| +{ |
| + if( fname != "" ) |
| + files->push_back( fname ); |
| +} |
| + return *files; |
| +} |
| + |
| +void deleteRegisteredFiles(); |
| +inline |
| +void deleteRegisteredFiles() { |
| + // don't be a slob, clean up after yourself: |
| + // delete any files that are laying around |
| + std::vector< std::string >& del_files = registerFileToDelete(); |
| + for( int fileI = 0; fileI < del_files.size(); fileI++ ) |
| + boost::filesystem::remove( del_files[ fileI ] ); |
| + del_files.clear(); // clear the deleted files from the list |
| +} |
| |
| |
| /** |
| @@ -80,7 +80,7 @@ std::string CreateTempFileName(const std::string& prefix) |
| #endif |
| boost::filesystem::path path( prefix ); |
| dir = path.branch_path().string(); |
| - name = path.leaf(); |
| + name = path.filename().string(); |
| if( name == "/" ) |
| { |
| dir += name; |
| diff --git a/libMems/ProgressiveAligner.cpp b/libMems/ProgressiveAligner.cpp |
| index 3be5fe0..5667a9e 100644 |
| --- a/libMems/ProgressiveAligner.cpp |
| +++ b/libMems/ProgressiveAligner.cpp |
| @@ -27,7 +27,7 @@ |
|
|
| #include <boost/dynamic_bitset.hpp>
|
| #include <boost/tuple/tuple.hpp>
|
| -#include <boost/property_map.hpp>
|
| +#include <boost/property_map/property_map.hpp>
|
| #include <boost/graph/graph_traits.hpp>
|
| #include <boost/graph/adjacency_list.hpp>
|
| #include <boost/graph/johnson_all_pairs_shortest.hpp>
|