Added SAM header-handling classes for read/write/validate.

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

diff --git a/src/api/SamSequence.h b/src/api/SamSequence.h
new file mode 100644 (file)
index 0000000..db6891d
--- /dev/null
+++ b/src/api/SamSequence.h
@@ -0,0 +1,64 @@
+// ***************************************************************************
+// SamSequence.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 23 December 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides functionality for querying/manipulating sequence data
+// **************************************************************************
+
+#ifndef SAM_SEQUENCE_H
+#define SAM_SEQUENCE_H
+
+#include <api/api_global.h>
+#include <string>
+
+namespace BamTools {
+
+class API_EXPORT SamSequence {
+
+    // ctor & dtor
+    public:
+        SamSequence(const std::string& name = "");
+        ~SamSequence(void);
+
+    // public methods
+    public:
+
+        // clear all contents
+        void Clear(void);
+
+        // convenience methods to check if SamSequence contains these values:
+        bool HasName(void) const;
+        bool HasLength(void) const;
+        bool HasAssemblyID(void) const;
+        bool HasChecksum(void) const;
+        bool HasURI(void) const;
+        bool HasSpecies(void) const;
+
+    // data members
+    public:
+        std::string Name;       // SN:<Name>
+        std::string Length;     // LN:<Length>
+        std::string AssemblyID; // AS:<AssemblyID>
+        std::string Checksum;   // M5:<Checksum>
+        std::string URI;        // UR:<URI>
+        std::string Species;    // SP:<Species>
+};
+
+// ---------------------------------------------------
+// comparison operators
+
+// for equality: compare Name, Length, & Checksum (if it exists for both)
+inline bool operator==(const SamSequence& lhs, const SamSequence& rhs) {
+    if ( lhs.Name   != rhs.Name   ) return false;
+    if ( lhs.Length != rhs.Length ) return false;
+    if ( lhs.HasChecksum() && rhs.HasChecksum() )
+        return (lhs.Checksum == rhs.Checksum);
+    else return true;
+}
+
+} // namespace BamTools
+
+#endif // SAM_SEQUENCE_H