X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamIndex.h;h=5e40d87eb517d4fbc8797e8f5d874eb520602f56;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=00a8f0174458f542268944d30aa39997400d0338;hpb=a15dba1bdfe5a1a61e175cb18b1e2694cfcd1746;p=bamtools.git

diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h
index 00a8f01..5e40d87 100644
--- a/src/api/BamIndex.h
+++ b/src/api/BamIndex.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // BamIndex.h (c) 2009 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 5 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides basic BAM index interface
 // ***************************************************************************
@@ -11,8 +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 {
@@ -30,8 +29,6 @@ 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 {
@@ -57,22 +54,40 @@ 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;
 
+    //! \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