--- /dev/null
+// ***************************************************************************
+// BamRandomAccessController_p.h (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 10 October 2011(DB)
+// ---------------------------------------------------------------------------
+// Manages random access operations in a BAM file
+// ***************************************************************************
+
+#ifndef BAMRACONTROLLER_P_H
+#define BAMRACONTROLLER_P_H
+
+// -------------
+// W A R N I N G
+// -------------
+//
+// This file is not part of the BamTools API. It exists purely as an
+// implementation detail. This header file may change from version to version
+// without notice, or even be removed.
+//
+// We mean it.
+
+#include "api/BamAux.h"
+#include "api/BamIndex.h"
+
+namespace BamTools {
+
+class BamAlignment;
+
+namespace Internal {
+
+class BamReaderPrivate;
+
+class BamRandomAccessController {
+
+ // enums
+ public: enum RegionState { BeforeRegion = 0
+ , OverlapsRegion
+ , AfterRegion
+ };
+
+ // ctor & dtor
+ public:
+ BamRandomAccessController(void);
+ ~BamRandomAccessController(void);
+
+ // BamRandomAccessController interface
+ public:
+
+ // index methods
+ void ClearIndex(void);
+ bool CreateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& type);
+ bool HasIndex(void) const;
+ bool IndexHasAlignmentsForReference(const int& refId);
+ bool LocateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& preferredType);
+ bool OpenIndex(const std::string& indexFilename, BamReaderPrivate* reader);
+ void SetIndex(BamIndex* index);
+
+ // region methods
+ void ClearRegion(void);
+ bool HasRegion(void) const;
+ RegionState AlignmentState(const BamAlignment& alignment) const;
+ bool RegionHasAlignments(void) const;
+ bool SetRegion(const BamRegion& region, const int& referenceCount);
+
+ // general methods
+ void Close(void);
+ std::string GetErrorString(void) const;
+
+ // internal methods
+ private:
+ // adjusts requested region if necessary (depending on where data actually begins)
+ void AdjustRegion(const int& referenceCount);
+ // error-string handling
+ void SetErrorString(const std::string& where, const std::string& what);
+
+ // data members
+ private:
+
+ // index data
+ BamIndex* m_index; // owns the index, not a copy - responsible for deleting
+
+ // region data
+ BamRegion m_region;
+ bool m_hasAlignmentsInRegion;
+
+ // general data
+ std::string m_errorString;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // BAMRACONTROLLER_P_H