// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 23 September 2010
+// Last modified: 9 June 2011
// ---------------------------------------------------------------------------
// Provides general utilities used by BamTools sub-tools.
// ***************************************************************************
#ifndef BAMTOOLS_UTILITIES_H
#define BAMTOOLS_UTILITIES_H
+#include <api/BamAux.h>
+#include <utils/utils_global.h>
#include <cassert>
#include <stdexcept>
#include <string>
-#include "BamAux.h"
+#include <vector>
#define BAMTOOLS_ASSERT_UNREACHABLE assert( false )
#define BAMTOOLS_ASSERT_MESSAGE( condition, message ) if (!( condition )) throw std::runtime_error( message );
class BamReader;
class BamMultiReader;
-class Utilities {
+class UTILS_EXPORT Utilities {
public:
+ // returns true if 'source' contains 'pattern' or 'c'
+ static bool Contains(const std::string& source, const std::string& pattern);
+ static bool Contains(const std::string& source, const char c);
+
+ // returns true if 'source' ends with 'pattern' or 'c'
+ static bool EndsWith(const std::string& source, const std::string& pattern);
+ static bool EndsWith(const std::string& source, const char c);
+
// check if a file exists
static bool FileExists(const std::string& fname);
// Parses a region string, uses reader to do validation (valid ID's, positions), stores in Region struct
// Returns success (true/false)
- static bool ParseRegionString(const std::string& regionString, const BamReader& reader, BamRegion& region);
+ static bool ParseRegionString(const std::string& regionString,
+ const BamReader& reader,
+ BamRegion& region);
// Same as above, but accepts a BamMultiReader
- static bool ParseRegionString(const std::string& regionString, const BamMultiReader& reader, BamRegion& region);
+ static bool ParseRegionString(const std::string& regionString,
+ const BamMultiReader& reader,
+ BamRegion& region);
// sequence utilities
static void Reverse(std::string& sequence);
static void ReverseComplement(std::string& sequence);
+
+ // split string on delimiter character (or string of allowed delimiters)
+ static std::vector<std::string> Split(const std::string& source, const char delim);
+ static std::vector<std::string> Split(const std::string& source, const std::string& delims);
+
+ // returns true if 'source' starts with 'pattern' or 'c'
+ static bool StartsWith(const std::string& source, const std::string& pattern);
+ static bool StartsWith(const std::string &source, const char c);
};
} // namespace BamTools