X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBamToolsIndex_p.h;h=1e9ec18c62e02021b01c6fec3a6c943e95dcb658;hb=a50400c186a05160e1164bf544571b739ff6fac8;hp=269792ed979152e09131a232d512b83dd35aa523;hpb=c1fc1c5423ca73a1b5bcbe790650821d73e5959c;p=bamtools.git

diff --git a/src/api/internal/BamToolsIndex_p.h b/src/api/internal/BamToolsIndex_p.h
index 269792e..1e9ec18 100644
--- a/src/api/internal/BamToolsIndex_p.h
+++ b/src/api/internal/BamToolsIndex_p.h
@@ -2,7 +2,7 @@
 // BamToolsIndex.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 5 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides index operations for the BamTools index format (".bti")
 // ***************************************************************************
@@ -20,8 +20,8 @@
 //
 // We mean it.
 
-#include <api/BamAux.h>
-#include <api/BamIndex.h>
+#include "api/BamAux.h"
+#include "api/BamIndex.h"
 #include <map>
 #include <string>
 #include <vector>
@@ -87,7 +87,7 @@ class BamToolsIndex : public BamIndex {
     // (might be useful later to handle any 'legacy' versions if the format changes)
     // listed for example like: BTI_1_0 = 1, BTI_1_1 = 2, BTI_1_2 = 3, BTI_2_0 = 4, and so on
     //
-    // so a change introduced in (hypothetical) BTI_1_2 would be handled from then on by:
+    // so a change introduced in BTI_1_2 may be handled from then on by:
     //
     // if ( indexVersion >= BTI_1_2 )
     //   do something new
@@ -96,6 +96,7 @@ class BamToolsIndex : public BamIndex {
     enum Version { BTI_1_0 = 1
                  , BTI_1_1
                  , BTI_1_2
+                 , BTI_2_0
                  };
 
     // ctor & dtor
@@ -116,66 +117,63 @@ class BamToolsIndex : public BamIndex {
         bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion);
         // loads existing data from file into memory
         bool Load(const std::string& filename);
-        // change the index caching behavior
-        void SetCacheMode(const BamIndex::IndexCacheMode& mode);
+        BamIndex::IndexType Type(void) const { return BamIndex::BAMTOOLS; }
     public:
         // returns format's file extension
         static const std::string Extension(void);
 
-    // internal file ops
+    // internal methods
     private:
-        bool CheckMagicNumber(void);
-        bool CheckVersion(void);
+
+        // index file ops
+        void CheckMagicNumber(void);
+        void CheckVersion(void);
         void CloseFile(void);
         bool IsFileOpen(void) const;
-        bool OpenFile(const std::string& filename, const char* mode);
-        bool Seek(const int64_t& position, const int& origin);
+        void OpenFile(const std::string& filename, const char* mode);
+        void Seek(const int64_t& position, const int& origin);
         int64_t Tell(void) const;
 
-    // internal BTI index building methods
-    private:
+        // index-creation methods
         void ClearReferenceEntry(BtiReferenceEntry& refEntry);
-
-    // internal random-access methods
-    private:
-        bool GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion);
-
-    // internal BTI summary data methods
-    private:
+        void WriteBlock(const BtiBlock& block);
+        void WriteBlocks(const BtiBlockVector& blocks);
+        void WriteHeader(void);
+        void WriteReferenceEntry(const BtiReferenceEntry& refEntry);
+
+        // random-access methods
+        void GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion);
+        void ReadBlock(BtiBlock& block);
+        void ReadBlocks(const BtiReferenceSummary& refSummary, BtiBlockVector& blocks);
+        void ReadReferenceEntry(BtiReferenceEntry& refEntry);
+
+        // BTI summary data methods
         void InitializeFileSummary(const int& numReferences);
-        bool LoadFileSummary(void);
-        bool LoadHeader(void);
-        bool LoadNumBlocks(int& numBlocks);
-        bool LoadNumReferences(int& numReferences);
-        bool LoadReferenceSummary(BtiReferenceSummary& refSummary);
-        bool SkipBlocks(const int& numBlocks);
-
-    // internal BTI full index input methods
-    private:
-        bool ReadBlock(BtiBlock& block);
-        bool ReadBlocks(const BtiReferenceSummary& refSummary, BtiBlockVector& blocks);
-        bool ReadReferenceEntry(BtiReferenceEntry& refEntry);
-
-    // internal BTI full index output methods
-    private:
-        bool WriteBlock(const BtiBlock& block);
-        bool WriteBlocks(const BtiBlockVector& blocks);
-        bool WriteHeader(void);
-        bool WriteReferenceEntry(const BtiReferenceEntry& refEntry);
+        void LoadFileSummary(void);
+        void LoadHeader(void);
+        void LoadNumBlocks(int& numBlocks);
+        void LoadNumReferences(int& numReferences);
+        void LoadReferenceSummary(BtiReferenceSummary& refSummary);
+        void SkipBlocks(const int& numBlocks);
 
     // data members
     private:
-        FILE* m_indexStream;
         bool  m_isBigEndian;
-        BamIndex::IndexCacheMode m_cacheMode;
         BtiFileSummary m_indexFileSummary;
-        int m_blockSize;
+        uint32_t m_blockSize;
         int32_t m_inputVersion; // Version is serialized as int
         Version m_outputVersion;
 
+        struct RaiiWrapper {
+            FILE* IndexStream;
+            RaiiWrapper(void);
+            ~RaiiWrapper(void);
+        };
+        RaiiWrapper Resources;
+
     // static constants
     private:
-        static const int DEFAULT_BLOCK_LENGTH;
+        static const uint32_t DEFAULT_BLOCK_LENGTH;
         static const std::string BTI_EXTENSION;
         static const char* const BTI_MAGIC;
         static const int SIZEOF_BLOCK;