Added SAM header-handling classes for read/write/validate.

[bamtools.git] / src / api / SamReadGroupDictionary.cpp

diff --git a/src/api/SamReadGroupDictionary.cpp b/src/api/SamReadGroupDictionary.cpp
new file mode 100644 (file)
index 0000000..fb03fac
--- /dev/null
+++ b/src/api/SamReadGroupDictionary.cpp
@@ -0,0 +1,168 @@
+// ***************************************************************************
+// SamReadGroupDictionary.cpp (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 23 December 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides container operations for collection of read group entries
+// *************************************************************************
+
+#include <api/SamReadGroupDictionary.h>
+using namespace BamTools;
+
+#include <algorithm>
+#include <iostream>
+using namespace std;
+
+// ctor
+SamReadGroupDictionary::SamReadGroupDictionary(void) { }
+
+// dtor
+SamReadGroupDictionary::~SamReadGroupDictionary(void) {
+    m_data.clear();
+}
+
+// adds read group if not already in container
+void SamReadGroupDictionary::Add(const SamReadGroup& readGroup) {
+    if ( IsEmpty() || !Contains(readGroup) )
+        m_data.push_back(readGroup);
+}
+
+// overload to support std::string
+void SamReadGroupDictionary::Add(const string& readGroupId) {
+    Add( SamReadGroup(readGroupId) );
+}
+
+// add multiple read groups
+void SamReadGroupDictionary::Add(const vector<SamReadGroup>& readGroups) {
+    vector<SamReadGroup>::const_iterator rgIter = readGroups.begin();
+    vector<SamReadGroup>::const_iterator rgEnd  = readGroups.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Add(*rgIter);
+}
+
+// overload to support std::string
+void SamReadGroupDictionary::Add(const vector<string>& readGroupIds) {
+    vector<string>::const_iterator rgIter = readGroupIds.begin();
+    vector<string>::const_iterator rgEnd  = readGroupIds.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Add(*rgIter);
+}
+
+// returns iterator to container begin
+SamReadGroupIterator SamReadGroupDictionary::Begin(void) {
+    return m_data.begin();
+}
+
+// returns const_iterator to container begin
+SamReadGroupConstIterator SamReadGroupDictionary::Begin(void) const {
+    return m_data.begin();
+}
+
+// clear read group container
+void SamReadGroupDictionary::Clear(void) {
+    m_data.clear();
+}
+
+// explicit request for const_iterator to container begin
+SamReadGroupConstIterator SamReadGroupDictionary::ConstBegin(void) const {
+    return m_data.begin();
+}
+
+// explicit request for const_iterator to container end
+SamReadGroupConstIterator SamReadGroupDictionary::ConstEnd(void) const {
+    return m_data.end();
+}
+
+// returns true if container contains a read group with this ID tag
+bool SamReadGroupDictionary::Contains(const string& readGroupId) const {
+    return ( IndexOf(readGroupId) != (int)m_data.size() );
+}
+
+bool SamReadGroupDictionary::Contains(const SamReadGroup& readGroup) const {
+    return ( IndexOf(readGroup) != (int)m_data.size() );
+}
+
+// returns iterator to container end
+SamReadGroupIterator SamReadGroupDictionary::End(void) {
+    return m_data.end();
+}
+
+// returns const_iterator to container begin
+SamReadGroupConstIterator SamReadGroupDictionary::End(void) const {
+    return m_data.end();
+}
+
+// returns vector index of read group if found
+// returns vector::size() (invalid index) if not found
+int SamReadGroupDictionary::IndexOf(const SamReadGroup& readGroup) const {
+    SamReadGroupConstIterator begin = ConstBegin();
+    SamReadGroupConstIterator iter  = begin;
+    SamReadGroupConstIterator end   = ConstEnd();
+    for ( ; iter != end; ++iter )
+        if ( *iter == readGroup ) break;
+    return distance( begin, iter );
+}
+
+// overload to support std::string
+int SamReadGroupDictionary::IndexOf(const string& readGroupId) const {
+    return IndexOf( SamReadGroup(readGroupId) );
+}
+
+// returns true if container is empty
+bool SamReadGroupDictionary::IsEmpty(void) const {
+    return m_data.empty();
+}
+
+// removes read group (if it exists)
+void SamReadGroupDictionary::Remove(const SamReadGroup& readGroup) {
+    if ( Contains(readGroup) )
+        m_data.erase( m_data.begin() + IndexOf(readGroup) );
+}
+
+// overlaod to support std::string
+void SamReadGroupDictionary::Remove(const string& readGroupId) {
+    Remove( SamReadGroup(readGroupId) );
+}
+
+// remove multiple read groups
+void SamReadGroupDictionary::Remove(const vector<SamReadGroup>& readGroups) {
+    vector<SamReadGroup>::const_iterator rgIter = readGroups.begin();
+    vector<SamReadGroup>::const_iterator rgEnd  = readGroups.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Remove(*rgIter);
+}
+
+// overload to support std::string
+void SamReadGroupDictionary::Remove(const vector<string>& readGroupIds) {
+    vector<string>::const_iterator rgIter = readGroupIds.begin();
+    vector<string>::const_iterator rgEnd  = readGroupIds.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Remove(*rgIter);
+}
+
+// returns size of container (number of current read groups)
+int SamReadGroupDictionary::Size(void) const {
+    return m_data.size();
+}
+
+// retrieves the SamReadGroup object associated with this ID
+// if readGroupId is unknown, a new SamReadGroup is created with this ID
+// and a reference to this new read group entry is returned (like std::map)
+SamReadGroup& SamReadGroupDictionary::operator[](const std::string& readGroupId) {
+
+    // look up read group ID
+    int index = IndexOf(readGroupId);
+
+    // if found, return read group at index
+    if ( index != (int)m_data.size() )
+        return m_data[index];
+
+    // otherwise, append new read group and return reference
+    else {
+        SamReadGroup rg(readGroupId);
+        m_data.push_back(rg);
+        return m_data.back();
+    }
+}