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 4f6928b6832fb9a3b2299626fed22b40e5611b56..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: 2 June 2010
+// Last modified: 8 September 2011
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
@@ -11,25 +10,54 @@
 #ifndef BAMTOOLS_UTILITIES_H
 #define BAMTOOLS_UTILITIES_H
 
+#include <api/BamAux.h>
+#include <utils/utils_global.h>
 #include <string>
-#include "BamAux.h"
+#include <vector>
+
+#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:                          
+    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);
 
-        // check if a file exists
-        static bool FileExists(const std::string& fname); 
+        // 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