From 369e2de20a6d939d07ffc09462167a3b688bbdde Mon Sep 17 00:00:00 2001 From: derek Date: Mon, 22 Nov 2010 13:02:38 -0500 Subject: [PATCH] Moved private implementation API files to internal directory for clearer separation. These should not be included by client code --- src/api/BamIndex.cpp | 6 +++--- src/api/BamReader.cpp | 4 ++-- src/api/BamWriter.cpp | 4 ++-- src/api/CMakeLists.txt | 11 ++++++----- src/api/{ => internal}/BamReader_p.cpp | 9 ++++----- src/api/{ => internal}/BamReader_p.h | 0 .../BamStandardIndex_p.cpp} | 4 ++-- .../BamStandardIndex_p.h} | 0 .../BamToolsIndex_p.cpp} | 4 ++-- .../{BamToolsIndex.h => internal/BamToolsIndex_p.h} | 0 src/api/{ => internal}/BamWriter_p.cpp | 4 ++-- src/api/{ => internal}/BamWriter_p.h | 0 12 files changed, 23 insertions(+), 23 deletions(-) rename src/api/{ => internal}/BamReader_p.cpp (99%) rename src/api/{ => internal}/BamReader_p.h (100%) rename src/api/{BamStandardIndex.cpp => internal/BamStandardIndex_p.cpp} (99%) rename src/api/{BamStandardIndex.h => internal/BamStandardIndex_p.h} (100%) rename src/api/{BamToolsIndex.cpp => internal/BamToolsIndex_p.cpp} (99%) rename src/api/{BamToolsIndex.h => internal/BamToolsIndex_p.h} (100%) rename src/api/{ => internal}/BamWriter_p.cpp (99%) rename src/api/{ => internal}/BamWriter_p.h (100%) diff --git a/src/api/BamIndex.cpp b/src/api/BamIndex.cpp index 053f8e9..d0230b7 100644 --- a/src/api/BamIndex.cpp +++ b/src/api/BamIndex.cpp @@ -3,7 +3,7 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 19 November 2010 (DB) +// Last modified: 22 November 2010 (DB) // --------------------------------------------------------------------------- // Provides index functionality - both for the default (standardized) BAM // index format (.bai) as well as a BamTools-specific (nonstandard) index @@ -13,8 +13,8 @@ #include #include #include -#include -#include +#include +#include using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp index 2650045..bd4bff9 100644 --- a/src/api/BamReader.cpp +++ b/src/api/BamReader.cpp @@ -3,13 +3,13 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 19 November 2010 (DB) +// Last modified: 22 November 2010 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for reading BAM files // *************************************************************************** #include -#include +#include using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp index 2af45cb..08ec3fe 100644 --- a/src/api/BamWriter.cpp +++ b/src/api/BamWriter.cpp @@ -3,13 +3,13 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 19 November 2010 (DB) +// Last modified: 22 November 2010 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for producing BAM files // *************************************************************************** #include -#include +#include using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt index 7c1b8ff..fb2d485 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt @@ -17,12 +17,12 @@ add_library ( BamTools SHARED BamIndex.cpp BamMultiReader.cpp BamReader.cpp - BamReader_p.cpp - BamStandardIndex.cpp - BamToolsIndex.cpp BamWriter.cpp - BamWriter_p.cpp - BGZF.cpp + BGZF.cpp + internal/BamReader_p.cpp + internal/BamStandardIndex_p.cpp + internal/BamToolsIndex_p.cpp + internal/BamWriter_p.cpp ) # link BamTools library with zlib automatically @@ -33,3 +33,4 @@ set_target_properties( BamTools PROPERTIES SOVERSION 0.9.0 OUTPUT_NAME bamtools ) + diff --git a/src/api/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp similarity index 99% rename from src/api/BamReader_p.cpp rename to src/api/internal/BamReader_p.cpp index 792be22..bffbfba 100644 --- a/src/api/BamReader_p.cpp +++ b/src/api/internal/BamReader_p.cpp @@ -3,17 +3,16 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 19 November 2010 (DB) +// Last modified: 22 November 2010 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for reading BAM files // *************************************************************************** #include -#include -#include -#include #include - +#include +#include +#include using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/BamReader_p.h b/src/api/internal/BamReader_p.h similarity index 100% rename from src/api/BamReader_p.h rename to src/api/internal/BamReader_p.h diff --git a/src/api/BamStandardIndex.cpp b/src/api/internal/BamStandardIndex_p.cpp similarity index 99% rename from src/api/BamStandardIndex.cpp rename to src/api/internal/BamStandardIndex_p.cpp index 28db076..c90aef6 100644 --- a/src/api/BamStandardIndex.cpp +++ b/src/api/internal/BamStandardIndex_p.cpp @@ -3,15 +3,15 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 19 November 2010 (DB) +// Last modified: 22 November 2010 (DB) // --------------------------------------------------------------------------- // Provides index operations for the standardized BAM index format (".bai") // *************************************************************************** #include #include -#include #include +#include using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/BamStandardIndex.h b/src/api/internal/BamStandardIndex_p.h similarity index 100% rename from src/api/BamStandardIndex.h rename to src/api/internal/BamStandardIndex_p.h diff --git a/src/api/BamToolsIndex.cpp b/src/api/internal/BamToolsIndex_p.cpp similarity index 99% rename from src/api/BamToolsIndex.cpp rename to src/api/internal/BamToolsIndex_p.cpp index 3bb314b..5590e8e 100644 --- a/src/api/BamToolsIndex.cpp +++ b/src/api/internal/BamToolsIndex_p.cpp @@ -3,15 +3,15 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 19 November 2010 (DB) +// Last modified: 22 November 2010 (DB) // --------------------------------------------------------------------------- // Provides index operations for the BamTools index format (".bti") // *************************************************************************** #include #include -#include #include +#include using namespace BamTools; using namespace BamTools::Internal; diff --git a/src/api/BamToolsIndex.h b/src/api/internal/BamToolsIndex_p.h similarity index 100% rename from src/api/BamToolsIndex.h rename to src/api/internal/BamToolsIndex_p.h diff --git a/src/api/BamWriter_p.cpp b/src/api/internal/BamWriter_p.cpp similarity index 99% rename from src/api/BamWriter_p.cpp rename to src/api/internal/BamWriter_p.cpp index 9887d56..a75eb44 100644 --- a/src/api/BamWriter_p.cpp +++ b/src/api/internal/BamWriter_p.cpp @@ -3,13 +3,13 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 19 November 2010 (DB) +// Last modified: 22 November 2010 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for producing BAM files // *************************************************************************** #include -#include +#include using namespace BamTools; using namespace BamTools::Internal; using namespace std; diff --git a/src/api/BamWriter_p.h b/src/api/internal/BamWriter_p.h similarity index 100% rename from src/api/BamWriter_p.h rename to src/api/internal/BamWriter_p.h -- 2.39.5