Major speedup in SamSequenceDictionary & SamReadGroupDictionary classes

[bamtools.git] / src / api / internal / SamFormatPrinter_p.cpp

diff --git a/src/api/internal/SamFormatPrinter_p.cpp b/src/api/internal/SamFormatPrinter_p.cpp
index 1e670b0155be479d88d9ed6d21b1c406600313af..a5b61a017bbdf4bcaa63d26b2e489a8078f31e5a 100644 (file)
--- a/src/api/internal/SamFormatPrinter_p.cpp
+++ b/src/api/internal/SamFormatPrinter_p.cpp
@@ -1,16 +1,15 @@
 // ***************************************************************************
 // SamFormatPrinter.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 19 April 2011 (DB)
+// Last modified: 12 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides functionality for printing formatted SAM header to string
 // ***************************************************************************
 
-#include <api/SamConstants.h>
-#include <api/SamHeader.h>
-#include <api/internal/SamFormatPrinter_p.h>
+#include "api/SamConstants.h"
+#include "api/SamHeader.h"
+#include "api/internal/SamFormatPrinter_p.h"
 using namespace BamTools;
 using namespace BamTools::Internal;
 
@@ -19,16 +18,25 @@ using namespace BamTools::Internal;
 #include <vector>
 using namespace std;
 
+// ------------------------
+// static utility methods
+// ------------------------
+
+static inline
+const string FormatTag(const string& tag, const string& value) {
+    return string(Constants::SAM_TAB + tag + Constants::SAM_COLON + value);
+}
+
+// ---------------------------------
+// SamFormatPrinter implementation
+// ---------------------------------
+
 SamFormatPrinter::SamFormatPrinter(const SamHeader& header)
     : m_header(header)
 { }
 
 SamFormatPrinter::~SamFormatPrinter(void) { }
 
-const string SamFormatPrinter::FormatTag(const string &tag, const string &value) const {
-    return string(Constants::SAM_TAB + tag + Constants::SAM_COLON + value);
-}
-
 const string SamFormatPrinter::ToString(void) const {
 
     // clear out stream
@@ -73,7 +81,7 @@ void SamFormatPrinter::PrintSQ(std::stringstream& out) const {
     SamSequenceConstIterator seqIter = m_header.Sequences.ConstBegin();
     SamSequenceConstIterator seqEnd  = m_header.Sequences.ConstEnd();
     for ( ; seqIter != seqEnd; ++seqIter ) {
-        const SamSequence& seq = (*seqIter);
+        const SamSequence& seq = seqIter->second;
 
         // @SQ SN:<Name> LN:<Length>
         out << Constants::SAM_SQ_BEGIN_TOKEN
@@ -107,7 +115,7 @@ void SamFormatPrinter::PrintRG(std::stringstream& out) const {
     SamReadGroupConstIterator rgIter = m_header.ReadGroups.ConstBegin();
     SamReadGroupConstIterator rgEnd  = m_header.ReadGroups.ConstEnd();
     for ( ; rgIter != rgEnd; ++rgIter ) {
-        const SamReadGroup& rg = (*rgIter);
+        const SamReadGroup& rg = rgIter->second;
 
         // @RG ID:<ID>
         out << Constants::SAM_RG_BEGIN_TOKEN