Added UTILS_EXPORT macro to classes in BamTools utility library

diff --git a/src/utils/bamtools_fasta.cpp b/src/utils/bamtools_fasta.cpp
index ef1c742e57073fe95b5343257bfc14c8922c4c94..3a72d7d4ebe5612331befefe74f6865e045f9606 100644 (file)
--- a/src/utils/bamtools_fasta.cpp
+++ b/src/utils/bamtools_fasta.cpp
@@ -8,6 +8,9 @@
 // Provides FASTA reading/indexing functionality.
 // ***************************************************************************
 
+#include <utils/bamtools_fasta.h>
+using namespace BamTools;
+
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
@@ -15,9 +18,7 @@
 #include <iostream>
 #include <sstream>
 #include <vector>
-#include "bamtools_fasta.h"
 using namespace std;
-using namespace BamTools;
 
 struct Fasta::FastaPrivate {
   

diff --git a/src/utils/bamtools_fasta.h b/src/utils/bamtools_fasta.h
index f64a0876a0913721a58791411bf86764dd43c46b..d0ae8e4a38a5173a65fa08475865c06a7b899485 100644 (file)
--- a/src/utils/bamtools_fasta.h
+++ b/src/utils/bamtools_fasta.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 13 July 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Provides FASTA reading/indexing functionality.
 // ***************************************************************************
@@ -11,11 +11,12 @@
 #ifndef BAMTOOLS_FASTA_H
 #define BAMTOOLS_FASTA_H
 
+#include <utils/utils_global.h>
 #include <string>
 
 namespace BamTools {
 
-class Fasta {  
+class UTILS_EXPORT Fasta {
   
     // ctor & dtor
     public:
@@ -44,4 +45,4 @@ class Fasta {
   
 } // BAMTOOLS_FASTA_H
   
-#endif // BAMTOOLS_FASTA_H
\ No newline at end of file
+#endif // BAMTOOLS_FASTA_H

diff --git a/src/utils/bamtools_filter_engine.h b/src/utils/bamtools_filter_engine.h
index cc9312081ab03d98c8b2644c9e12060a1fe41f51..9ea1e8d2138823cf22363a54f7ff6f0206d04721 100644 (file)
--- a/src/utils/bamtools_filter_engine.h
+++ b/src/utils/bamtools_filter_engine.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 29 September 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Provides a generic filter engine based on filter-sets of properties,
 // with possible "rules" (compound logical expressions) to create more complex
@@ -42,23 +42,23 @@
 #ifndef BAMTOOLS_FILTER_ENGINE_H
 #define BAMTOOLS_FILTER_ENGINE_H
 
+#include <utils/bamtools_filter_properties.h>
+#include <utils/bamtools_filter_ruleparser.h>
+#include <utils/bamtools_utilities.h>
+#include <utils/utils_global.h>
 #include <algorithm>
 #include <iostream>
 #include <map>
 #include <queue>
 #include <sstream>
 #include <stack>
-#include <sstream>
 #include <string>
 #include <utility>
 #include <vector>
-#include "bamtools_filter_properties.h"
-#include "bamtools_filter_ruleparser.h"
-#include "bamtools_utilities.h"
 
 namespace BamTools {
 
-struct FilterCompareType {    
+struct UTILS_EXPORT FilterCompareType {
     enum Type { AND = 0
               , NOT
               , OR
@@ -69,7 +69,7 @@ struct FilterCompareType {
 // FilterEngine
   
 template <typename FilterChecker>
-class FilterEngine {
+class UTILS_EXPORT FilterEngine {
   
     // ctor & dtor
     public:
@@ -550,4 +550,4 @@ inline void FilterEngine<FilterChecker>::setRule(const std::string& ruleString)
 
 } // namespace BamTools
 
-#endif // BAMTOOLS_FILTER_ENGINE_H
\ No newline at end of file
+#endif // BAMTOOLS_FILTER_ENGINE_H

diff --git a/src/utils/bamtools_filter_properties.h b/src/utils/bamtools_filter_properties.h
index 119da060df00e96239fddd1451a58dc0da16b473..9de3e275fe9055d42a6508167c996783fd5ac235 100644 (file)
--- a/src/utils/bamtools_filter_properties.h
+++ b/src/utils/bamtools_filter_properties.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 30 August 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Provides support data structures & methods for FilterEngine
 //
@@ -40,18 +40,19 @@
 #ifndef BAMTOOLS_FILTER_PROPERTIES_H
 #define BAMTOOLS_FILTER_PROPERTIES_H
 
+#include <utils/bamtools_utilities.h>
+#include <utils/bamtools_variant.h>
+#include <utils/utils_global.h>
 #include <iostream>
 #include <map>
 #include <string>
-#include "bamtools_utilities.h"
-#include "bamtools_variant.h"
 
 namespace BamTools {
 
 // ----------------------------------------------------------
 // PropertyFilterValue
   
-struct PropertyFilterValue {
+struct UTILS_EXPORT PropertyFilterValue {
   
     // define valid ValueCompareTypes
     enum ValueCompareType { CONTAINS = 0
@@ -165,7 +166,7 @@ typedef std::map<std::string, PropertyFilterValue> PropertyMap;
 // ----------------------------------------------------------
 // PropertyFilter
 
-struct PropertyFilter {  
+struct UTILS_EXPORT PropertyFilter {
     // data members
     PropertyMap Properties;
 };
@@ -178,7 +179,7 @@ typedef std::map<std::string, PropertyFilter> FilterMap;
 // Property
   
 // used to store properties known to engine & keep track of enabled state
-struct Property {
+struct UTILS_EXPORT Property {
     std::string Name;
     bool IsEnabled;
     Property(const std::string& name, bool isEnabled = false) 

diff --git a/src/utils/bamtools_filter_ruleparser.h b/src/utils/bamtools_filter_ruleparser.h
index 7e3b1fdc36758971b1de9fc947d43432250af4db..b0ec0ab741f8a98d502735337dab9ee382f95ac7 100644 (file)
--- a/src/utils/bamtools_filter_ruleparser.h
+++ b/src/utils/bamtools_filter_ruleparser.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 21 September 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Provides a compound rule parser for FilterEngine.
 // ***************************************************************************
@@ -11,10 +11,10 @@
 #ifndef BAMTOOLS_FILTER_RULEPARSER_H
 #define BAMTOOLS_FILTER_RULEPARSER_H
 
+#include <utils/bamtools_utilities.h>
 #include <queue>
 #include <stack>
 #include <string>
-#include "bamtools_utilities.h"
 
 namespace BamTools {
 
@@ -315,4 +315,4 @@ void RuleParser::skipSpaces(void) {
 
 } // namespace BamTools
 
-#endif // BAMTOOLS_FILTER_RULEPARSER_H
\ No newline at end of file
+#endif // BAMTOOLS_FILTER_RULEPARSER_H

diff --git a/src/utils/bamtools_options.cpp b/src/utils/bamtools_options.cpp
index 71aa2ebd4507fa5ecd7800d66090c11b90f5f67d..c46d0049c2b244046a58c88d18af48b63a5911d2 100644 (file)
--- a/src/utils/bamtools_options.cpp
+++ b/src/utils/bamtools_options.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 7 September 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Parses command line arguments and creates a help menu
 // ---------------------------------------------------------------------------
@@ -17,14 +17,15 @@
 // *  (BamTools namespace, added stdin/stdout) (DB)
 // ***************************************************************************
 
-#include "bamtools_options.h"
+#include <utils/bamtools_options.h>
+using namespace BamTools;
+
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
 #include <iomanip>
 #include <sstream>
 using namespace std;
-using namespace BamTools;
 
 string Options::m_programName;                   // the program name
 string Options::m_description;                   // the main description

diff --git a/src/utils/bamtools_options.h b/src/utils/bamtools_options.h
index 668ac522c977c6419993330d2b21c206ea6f3a74..7b9073dad6f335b905ec9bf33a09c1fd039b7ed0 100644 (file)
--- a/src/utils/bamtools_options.h
+++ b/src/utils/bamtools_options.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 7 September 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Parses command line arguments and creates a help menu
 // ---------------------------------------------------------------------------
@@ -20,10 +20,12 @@
 #ifndef BAMTOOLS_OPTIONS_H
 #define BAMTOOLS_OPTIONS_H
 
+#include <utils/bamtools_variant.h>
+#include <utils/utils_global.h>
+
 #include <map>
 #include <string>
 #include <vector>
-#include "bamtools_variant.h"
 
 #ifndef WIN32
     #include <stdint.h>
@@ -45,7 +47,7 @@ namespace BamTools {
   #define strtoui64 strtoull
 #endif
 
-struct Option {
+struct UTILS_EXPORT Option {
   
     // data members
     std::string Argument;
@@ -62,7 +64,7 @@ struct Option {
     { }
 };
 
-struct OptionValue {
+struct UTILS_EXPORT OptionValue {
   
     // data members
     bool* pFoundArgument;
@@ -83,12 +85,12 @@ struct OptionValue {
     { } 
 };
 
-struct OptionGroup {
+struct UTILS_EXPORT OptionGroup {
     std::string Name;
     std::vector<Option> Options;
 };
 
-class Options {
+class UTILS_EXPORT Options {
   
     // add option/argument rules
     public:
@@ -207,4 +209,4 @@ void Options::AddValueOption(const std::string& argument,
 
 } // namespace BamTools
 
-#endif // BAMTOOLS_OPTIONS_H
\ No newline at end of file
+#endif // BAMTOOLS_OPTIONS_H

diff --git a/src/utils/bamtools_pileup_engine.cpp b/src/utils/bamtools_pileup_engine.cpp
index 70bace8f87e3625046142a55a4135172f0deea3c..bc0e7c85e832b0bfa49c703fe6e09e45df74ca12 100644 (file)
--- a/src/utils/bamtools_pileup_engine.cpp
+++ b/src/utils/bamtools_pileup_engine.cpp
@@ -3,15 +3,16 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 16 September 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Provides pileup at position functionality for various tools.
 // ***************************************************************************
 
+#include <utils/bamtools_pileup_engine.h>
+using namespace BamTools;
+
 #include <iostream>
-#include "bamtools_pileup_engine.h"
 using namespace std;
-using namespace BamTools;
 
 // ---------------------------------------------
 // PileupEnginePrivate implementation

diff --git a/src/utils/bamtools_pileup_engine.h b/src/utils/bamtools_pileup_engine.h
index bbfd102b523179f52d6e6e2cca33dc9b230ac482..6900dc94cb6f86d071dc9f0b76655e93e9a38184 100644 (file)
--- a/src/utils/bamtools_pileup_engine.h
+++ b/src/utils/bamtools_pileup_engine.h
@@ -11,14 +11,15 @@
 #ifndef BAMTOOLS_PILEUP_ENGINE_H
 #define BAMTOOLS_PILEUP_ENGINE_H
 
+#include <api/BamAlignment.h>
+#include <utils/utils_global.h>
 #include <vector>
-#include "BamAlignment.h"
 
 namespace BamTools {
 
 // contains auxiliary data about a single BamAlignment
 // at current position considered
-struct PileupAlignment {
+struct UTILS_EXPORT PileupAlignment {
   
     // data members
     BamAlignment Alignment;
@@ -46,7 +47,7 @@ struct PileupAlignment {
 };
   
 // contains all data at a position
-struct PileupPosition {
+struct UTILS_EXPORT PileupPosition {
   
     // data members
     int RefId;
@@ -63,7 +64,7 @@ struct PileupPosition {
     { }
 };
   
-class PileupVisitor {
+class UTILS_EXPORT PileupVisitor {
   
     public:
         PileupVisitor(void) { }
@@ -73,7 +74,7 @@ class PileupVisitor {
         virtual void Visit(const PileupPosition& pileupData) =0;
 };
 
-class PileupEngine {
+class UTILS_EXPORT PileupEngine {
   
     public:
         PileupEngine(void);

diff --git a/src/utils/bamtools_utilities.cpp b/src/utils/bamtools_utilities.cpp
index 559fc8fd2c1028881fbdd4147384e0be71428eba..6f3c0cb43bd2db01dd23f55f18cb909cc1768b7b 100644 (file)
--- a/src/utils/bamtools_utilities.cpp
+++ b/src/utils/bamtools_utilities.cpp
@@ -3,20 +3,21 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 23 September 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
 
+#include <api/BamMultiReader.h>
+#include <api/BamReader.h>
+#include <utils/bamtools_utilities.h>
+using namespace BamTools;
+
 #include <algorithm>
 #include <cstdlib>
 #include <fstream>
 #include <iostream>
-#include "bamtools_utilities.h"
-#include "BamReader.h"
-#include "BamMultiReader.h"
 using namespace std;
-using namespace BamTools;
 
 namespace BamTools {
   

diff --git a/src/utils/bamtools_utilities.h b/src/utils/bamtools_utilities.h
index e31f63a59f0882a9464b5cef84a1921db3ab616d..73604fbff5f4812800e280450be967d8a4f74b3d 100644 (file)
--- a/src/utils/bamtools_utilities.h
+++ b/src/utils/bamtools_utilities.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 23 September 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
@@ -11,10 +11,11 @@
 #ifndef BAMTOOLS_UTILITIES_H
 #define BAMTOOLS_UTILITIES_H
 
+#include <api/BamAux.h>
+#include <utils/utils_global.h>
 #include <cassert>
 #include <stdexcept>
 #include <string>
-#include "BamAux.h"
 
 #define BAMTOOLS_ASSERT_UNREACHABLE assert( false )
 #define BAMTOOLS_ASSERT_MESSAGE( condition, message ) if (!( condition )) throw std::runtime_error( message );
@@ -24,7 +25,7 @@ namespace BamTools {
 class BamReader;
 class BamMultiReader;
 
-class Utilities {
+class UTILS_EXPORT Utilities {
   
     public: 
         // check if a file exists

diff --git a/src/utils/bamtools_variant.h b/src/utils/bamtools_variant.h
index 93ef8ab472004cc2836d04a116dd2f8fcb5980e8..116a2c0addf6c06ff48cddfc62ef795e69e3d8ca 100644 (file)
--- a/src/utils/bamtools_variant.h
+++ b/src/utils/bamtools_variant.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 19 November 2010
 // ---------------------------------------------------------------------------
 // Provides a template-based variant type
 // ---------------------------------------------------------------------------
@@ -18,13 +18,14 @@
 #ifndef BAMTOOLS_VARIANT_H
 #define BAMTOOLS_VARIANT_H
 
+#include <utils/utils_global.h>
 #include <stdexcept>
-#include <typeinfo>
 #include <string>
+#include <typeinfo>
 
 namespace BamTools {
 
-class Variant {
+class UTILS_EXPORT Variant {
   
     public:
         Variant(void) : data(NULL) { }