X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamIndex.h;h=fd41f6912b0fd6006be53ef5bce55d715ca05056;hb=1dd0e1cb8a8557dfb463bf4323f121614cb6fcb2;hp=a52922e76b6d3f0bc4272ba142b7215a02b9c765;hpb=c1fc1c5423ca73a1b5bcbe790650821d73e5959c;p=bamtools.git

diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h
index a52922e..fd41f69 100644
--- a/src/api/BamIndex.h
+++ b/src/api/BamIndex.h
@@ -2,7 +2,7 @@
 // BamIndex.h (c) 2009 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 5 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides basic BAM index interface
 // ***************************************************************************
@@ -10,8 +10,8 @@
 #ifndef BAM_INDEX_H
 #define BAM_INDEX_H
 
-#include <api/api_global.h>
-#include <api/BamAux.h>
+#include "api/api_global.h"
+#include "api/BamAux.h"
 #include <string>
 
 namespace BamTools {
@@ -29,19 +29,12 @@ namespace Internal {
 
     It is exposed to the public API to allow advanced users to implement
     their own custom indexing schemes.
-
-    More documentation on methods & enums coming soon.
 */
 
 class API_EXPORT BamIndex {
 
     // enums
     public:
-        // specify index-caching behavior
-        enum IndexCacheMode { FullIndexCaching = 0 // store entire index file contents in memory
-                            , LimitedIndexCaching  // store only index data for current reference
-                            , NoIndexCaching       // do not store any index data between jumps
-                            };
 
         // list of supported BamIndex types
         enum IndexType { BAMTOOLS = 0
@@ -56,22 +49,40 @@ class API_EXPORT BamIndex {
     // index interface
     public:
         // builds index from associated BAM file & writes out to index file
-        virtual bool Create(void) =0; // creates index file from BAM file
+        virtual bool Create(void) =0;
+
+        // returns a human-readable description of the last error encountered
+        std::string GetErrorString(void) { return m_errorString; }
+
         // returns whether reference has alignments or no
         virtual bool HasAlignments(const int& referenceID) const =0;
+
         // attempts to use index data to jump to @region, returns success/fail
         // a "successful" jump indicates no error, but not whether this region has data
         //   * thus, the method sets a flag to indicate whether there are alignments
         //     available after the jump position
         virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0;
+
         // loads existing data from file into memory
         virtual bool Load(const std::string& filename) =0;
-        // change the index caching behavior
-        virtual void SetCacheMode(const BamIndex::IndexCacheMode& mode) =0;
+
+        // returns the 'type' enum for derived index format
+        virtual BamIndex::IndexType Type(void) const =0;
+
+    //! \cond
+
+    // internal methods
+    protected:
+        void SetErrorString(const std::string& where, const std::string& what) const {
+            m_errorString = where + ": " + what;
+        }
 
     // data members
     protected:
-        Internal::BamReaderPrivate* m_reader; // copy, not ownedprivate:
+        Internal::BamReaderPrivate* m_reader; // copy, not owned
+        mutable std::string m_errorString;
+
+    //! \endcond
 };
 
 } // namespace BamTools