Added API_EXPORT macro to classes in BamTools API

[bamtools.git] / src / api / BamMultiReader.h

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index cc30326b59f0773750739dda999df6e89bb153f0..d30a0d37c5a23dcb4a3d6148f17b7416c086baf0 100644 (file)
--- a/src/api/BamMultiReader.h
+++ b/src/api/BamMultiReader.h
@@ -1,9 +1,9 @@
 // ***************************************************************************\r
-// BamMultiReader.h (c) 2010 Erik Garrison\r
+// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett\r
 // Marth Lab, Department of Biology, Boston College\r
 // All rights reserved.\r
 // ---------------------------------------------------------------------------\r
-// Last modified: 3 September 2010 (DB)\r
+// Last modified: 19 November 2010 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Functionality for simultaneously reading multiple BAM files\r
 // ***************************************************************************\r
@@ -11,25 +11,19 @@
 #ifndef BAMMULTIREADER_H\r
 #define BAMMULTIREADER_H\r
 \r
-// C++ includes\r
-#include <string>\r
+#include <api/api_global.h>\r
+#include <api/BamReader.h>\r
 #include <map>\r
-#include <utility> // for pair\r
 #include <sstream>\r
-\r
-using namespace std;\r
-\r
-// BamTools includes\r
-#include "BamAux.h"\r
-#include "BamReader.h"\r
+#include <string>\r
+#include <utility>\r
 \r
 namespace BamTools {\r
 \r
 // index mapping reference/position pairings to bamreaders and their alignments\r
-typedef multimap<pair<int, int>, pair<BamReader*, BamAlignment*> > AlignmentIndex;\r
-\r
+typedef std::multimap<std::pair<int, int>, std::pair<BamReader*, BamAlignment*> > AlignmentIndex;\r
 \r
-class BamMultiReader {\r
+class API_EXPORT BamMultiReader {\r
 \r
     // constructor / destructor\r
     public:\r
@@ -61,7 +55,7 @@ class BamMultiReader {
         // also useful for merging\r
         // @preferStandardIndex - look for standard BAM index ".bai" first.  If false, \r
         // will look for BamTools index ".bti".  \r
-        bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = true);\r
+        bool Open(const std::vector<std::string>& filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = false);\r
 \r
         // returns whether underlying BAM readers ALL have an index loaded\r
         // this is useful to indicate whether Jump() or SetRegion() are possible\r
@@ -97,7 +91,7 @@ class BamMultiReader {
         // ----------------------\r
 \r
         // returns unified SAM header text for all files\r
-        const string GetHeaderText(void) const;\r
+        const std::string GetHeaderText(void) const;\r
         // returns number of reference sequences\r
         const int GetReferenceCount(void) const;\r
         // returns vector of reference objects\r
@@ -112,7 +106,10 @@ class BamMultiReader {
         // ----------------------\r
 \r
         // creates index for BAM files which lack them, saves to files (default = bamFilename + ".bai")\r
-        bool CreateIndexes(bool useDefaultIndex = true);\r
+        bool CreateIndexes(bool useStandardIndex = true);\r
+\r
+        // sets the index caching mode for the readers\r
+        void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);\r
 \r
         //const int GetReferenceID(const string& refName) const;\r
 \r
@@ -125,13 +122,13 @@ class BamMultiReader {
     private:\r
 \r
         // the set of readers and alignments which we operate on, maintained throughout the life of this class\r
-        vector<pair<BamReader*, BamAlignment*> > readers;\r
+        std::vector<std::pair<BamReader*, BamAlignment*> > readers;\r
 \r
         // readers and alignments sorted by reference id and position, to keep track of the lowest (next) alignment\r
         // when a reader reaches EOF, its entry is removed from this index\r
         AlignmentIndex alignments;\r
 \r
-        vector<string> fileNames;\r
+        std::vector<std::string> fileNames;\r
 };\r
 \r
 } // namespace BamTools\r