X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FSamSequence.h;h=c1a8792065df16bdd1a10ba46f90b540ba7b6c95;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=fea09d39b4148526e639784af9b509e4f5a30569;hpb=8c80d760637f8df39262683cd2570f0589423d36;p=bamtools.git

diff --git a/src/api/SamSequence.h b/src/api/SamSequence.h
index fea09d3..c1a8792 100644
--- a/src/api/SamSequence.h
+++ b/src/api/SamSequence.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // SamSequence.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 4 March 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides direct read/write access to the SAM sequence data fields.
 // ***************************************************************************
@@ -11,7 +10,7 @@
 #ifndef SAM_SEQUENCE_H
 #define SAM_SEQUENCE_H
 
-#include <api/api_global.h>
+#include "api/api_global.h"
 #include <string>
 
 namespace BamTools {
@@ -21,27 +20,28 @@ struct API_EXPORT SamSequence {
     // ctor & dtor
     SamSequence(void);
     SamSequence(const std::string& name, const int& length);
+    SamSequence(const std::string& name, const std::string& length);
     SamSequence(const SamSequence& other);
     ~SamSequence(void);
 
     // query/modify entire sequence
-    void Clear(void);                           // clears all contents
+    void Clear(void);                // clears all contents
 
     // convenience query methods
-    bool HasName(void) const;                   // returns true if sequence has a name
-    bool HasLength(void) const;                 // returns true if sequence has a length
-    bool HasAssemblyID(void) const;             // returns true if sequence has an assembly ID
-    bool HasChecksum(void) const;               // returns true if sequence has an MD5 checksum
-    bool HasURI(void) const;                    // returns true if sequence has a URI
-    bool HasSpecies(void) const;                // returns true if sequence has a species ID
+    bool HasAssemblyID(void) const;  // returns true if sequence has an assembly ID
+    bool HasChecksum(void) const;    // returns true if sequence has an MD5 checksum
+    bool HasLength(void) const;      // returns true if sequence has a length
+    bool HasName(void) const;        // returns true if sequence has a name
+    bool HasSpecies(void) const;     // returns true if sequence has a species ID
+    bool HasURI(void) const;         // returns true if sequence has a URI
 
     // data members
-    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>
+    std::string AssemblyID;          // AS:<AssemblyID>
+    std::string Checksum;            // M5:<Checksum>
+    std::string Length;              // LN:<Length>      *Required for valid SAM header*
+    std::string Name;                // SN:<Name>        *Required for valid SAM header*
+    std::string Species;             // SP:<Species>
+    std::string URI;                 // UR:<URI>
 };
 
 /*! \fn bool operator==(const SamSequence& lhs, const SamSequence& rhs)