Major update to BamTools version 1.0

[bamtools.git] / src / api / internal / BamRandomAccessController_p.h

diff --git a/src/api/internal/BamRandomAccessController_p.h b/src/api/internal/BamRandomAccessController_p.h
new file mode 100644 (file)
index 0000000..e541cdf
--- /dev/null
+++ b/src/api/internal/BamRandomAccessController_p.h
@@ -0,0 +1,94 @@
+// ***************************************************************************
+// BamRandomAccessController_p.h (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 24 February 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);
+
+    // general interface
+    public:
+        void Close(void);
+
+    // index operations
+    public:
+        //
+        void ClearIndex(void);
+        bool CreateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& type);
+        bool HasIndex(void) const;
+        bool IndexHasAlignmentsForReference(const int& refId);
+        bool LocateIndex(const std::string& bamFilename, const BamIndex::IndexType& preferredType);
+        bool OpenIndex(const std::string& indexFilename);
+        void SetIndex(BamIndex* index);
+        void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
+
+    // region operations
+    public:
+        void ClearRegion(void);
+        bool HasRegion(void) const;
+        RegionState AlignmentState(const BamAlignment& alignment) const;
+        bool RegionHasAlignments(void) const;
+        bool SetRegion(BamReaderPrivate* reader,
+                       const BamRegion& region,
+                       const int& referenceCount);
+
+    // 'internal' methods
+    public:
+        // adjusts requested region if necessary (depending on where data actually begins)
+        void AdjustRegion(const int& referenceCount);
+
+    // data members
+    private:
+
+        // index data
+        BamIndex* m_index;  // owns index, not a copy - responsible for deleting
+        BamIndex::IndexCacheMode m_indexCacheMode;
+
+        // region data
+        BamRegion m_region;
+        bool m_hasAlignmentsInRegion;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // BAMRACONTROLLER_P_H