Minor cleanup

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

diff --git a/src/utils/bamtools_utilities.h b/src/utils/bamtools_utilities.h
index f72897a9112876121da2054e154e0720763ea3a2..52098d0c4811c2977c360e573cd16c587b210551 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: 30 August 2010
+// Last modified: 9 June 2011
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
@@ -11,10 +10,12 @@
 #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 );
@@ -24,19 +25,41 @@ 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