Cleaned up intra-API includes & moved version numbers to 2.0.0

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

diff --git a/src/api/BamAlgorithms.h b/src/api/BamAlgorithms.h
index c62e68e57c24efb281999588ed89f152d41014be..61094123a734b527f709a6c7ea62e012b7330e93 100644 (file)
--- a/src/api/BamAlgorithms.h
+++ b/src/api/BamAlgorithms.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 29 September 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides generic algorithms that are intended to work with BamTools data
 // structures. Where possible, these are intended to be STL-compatible.
@@ -12,133 +12,10 @@
 #ifndef BAMALGORITHMS_H
 #define BAMALGORITHMS_H
 
-#include <api/api_global.h>
-#include <api/BamAlignment.h>
-#include <api/BamReader.h>
-#include <api/BamMultiReader.h>
-#include <algorithm>
-#include <functional>
-#include <string>
-#include <vector>
+#include "api/algorithms/Sort.h"
 
-namespace BamTools {
-namespace Algorithms {
-
-// -------------------------------------------------------
-// Built-in function objects for comparing BamAlignments
-
-typedef std::binary_function<BamAlignment, BamAlignment, bool> BamAlignmentComparer;
-
-// Algorithms::SortByName<Compare>
-// compare alignments by name (default comparison is std::less<std::string> )
-template<template <typename> class Compare = std::less>
-struct API_EXPORT SortByName : public BamAlignmentComparer {
-    bool operator()(const BamTools::BamAlignment& lhs,
-                    const BamTools::BamAlignment& rhs)
-    {
-        Compare<std::string> comp;
-        return comp(lhs.Name, rhs.Name);
-    }
-};
-
-// Algorithms::SortByPosition<Compare>
-// compare alignments by position (default comparison is std::less<int>)
-template<template <typename> class Compare = std::less>
-struct API_EXPORT SortByPosition : public BamAlignmentComparer {
-    bool operator()(const BamTools::BamAlignment& lhs,
-                    const BamTools::BamAlignment& rhs)
-    {
-        // force unmapped aligmnents to end
-        if ( lhs.RefID == -1 ) return false;
-        if ( rhs.RefID == -1 ) return true;
-
-        // otherwise compare first on RefID, then position
-        Compare<int32_t> comp;
-        if ( lhs.RefID == rhs.RefID )
-            return comp(lhs.Position, rhs.Position);
-        return comp(lhs.RefID, rhs.RefID);
-    }
-};
-
-// Algorithms::SortByTag<Compare>("XY")
-// compare alignments by tag value (default comparison is std::less<T>)
-// where T is the expected tag type (e.g. RG -> string, NM -> int, etc.)
-template<typename T, template <typename> class Compare = std::less>
-struct API_EXPORT SortByTag : public BamAlignmentComparer {
-
-    // ctor - needed to provide the tag name ("RG", "NM", "Aq", etc)
-    explicit SortByTag(const std::string& tag) : m_tag(tag) { }
-
-    bool operator()(const BamTools::BamAlignment& lhs,
-                    const BamTools::BamAlignment& rhs)
-    {
-        // force alignments without tag to end
-        T lhsTagValue;
-        T rhsTagValue;
-        if ( !lhs.GetTag(m_tag, lhsTagValue) ) return false;
-        if ( !rhs.GetTag(m_tag, rhsTagValue) ) return true;
-
-        // otherwise compare tag values
-        Compare<T> comp;
-        return comp(lhsTagValue, rhsTagValue);
-    }
-
-    private:
-        std::string m_tag;
-};
-
-// Algorithms::Unsorted
-// placeholder comparison object, ignores the alignments' data
-// N.B. - returning false typically retains initial insertion order
-struct API_EXPORT Unsorted : public BamAlignmentComparer {
-    bool operator()(const BamTools::BamAlignment& /*lhs*/,
-                    const BamTools::BamAlignment& /*rhs*/)
-    {
-        return false;
-    }
-};
-
-API_EXPORT template<typename Compare>
-std::vector<BamAlignment> SortReaderRegion(BamReader& reader,
-                                           const BamRegion& region,
-                                           const Compare& comp = Compare())
-{
-    // return empty container if unable to find region
-    if ( !reader.IsOpen() )          return std::vector<BamAlignment>();
-    if ( !reader.SetRegion(region) ) return std::vector<BamAlignment>();
-
-    // iterate through region, grabbing alignments
-    BamAlignment al;
-    std::vector<BamAlignment> results;
-    while ( reader.GetNextAlignment(al) )
-        results.push_back(al);
-
-    // sort & return alignments
-    std::sort(results.begin(), results.end(), comp);
-    return results;
-}
-
-API_EXPORT template<typename Compare>
-std::vector<BamAlignment> SortReaderRegion(BamMultiReader& reader,
-                                           const BamRegion& region,
-                                           const Compare& comp = Compare())
-{
-    // return empty container if unable to find region
-    if ( !reader.HasOpenReaders() )  return std::vector<BamAlignment>();
-    if ( !reader.SetRegion(region) ) return std::vector<BamAlignment>();
-
-    // iterate through region, grabbing alignments
-    BamAlignment al;
-    std::vector<BamAlignment> results;
-    while ( reader.GetNextAlignment(al) )
-        results.push_back(al);
-
-    // sort & return alignments
-    std::sort(results.begin(), results.end(), comp);
-    return results;
-}
-
-} // namespace Algorithms
-} // namespace BamTools
+/*! \namespace BamTools::Algorithms
+    \brief Provides convenient classes & methods for working with BAM data
+*/
 
 #endif // BAM_ALGORITHMS_H