Merge branches 'master' and 'iodevice' into iodevice

[bamtools.git] / src / utils / bamtools_utilities.h

diff --git a/src/utils/bamtools_utilities.h b/src/utils/bamtools_utilities.h
index e31f63a59f0882a9464b5cef84a1921db3ab616d..d9a319271c1da6e856325cacc7371e20cc0a978a 100644 (file)
--- a/src/utils/bamtools_utilities.h
+++ b/src/utils/bamtools_utilities.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // bamtools_utilities.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 23 September 2010
+// Last modified: 8 September 2011
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
@@ -11,34 +10,54 @@
 #ifndef BAMTOOLS_UTILITIES_H
 #define BAMTOOLS_UTILITIES_H
 
-#include <cassert>
-#include <stdexcept>
+#include <api/BamAux.h>
+#include <utils/utils_global.h>
 #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 );
+#define BAMTOOLS_ASSERT_UNREACHABLE BT_ASSERT_UNREACHABLE
+#define BAMTOOLS_ASSERT_MESSAGE( condition, message ) BT_ASSERT_X( condition, message )
 
 namespace BamTools {
 
 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