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

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

diff --git a/src/api/SamSequenceDictionary.cpp b/src/api/SamSequenceDictionary.cpp
new file mode 100644 (file)
index 0000000..c023a39
--- /dev/null
+++ b/src/api/SamSequenceDictionary.cpp
@@ -0,0 +1,159 @@
+#include <api/SamSequenceDictionary.h>
+using namespace BamTools;
+
+#include <iostream>
+using namespace std;
+
+// ctor
+SamSequenceDictionary::SamSequenceDictionary(void) { }
+
+// dtor
+SamSequenceDictionary::~SamSequenceDictionary(void) {
+    m_data.clear();
+}
+
+// adds sequence if not already in container
+void SamSequenceDictionary::Add(const SamSequence& sequence) {
+    if ( IsEmpty() || !Contains(sequence) )
+        m_data.push_back(sequence);
+}
+
+// overload to support std::string
+void SamSequenceDictionary::Add(const string& sequenceName) {
+    Add( SamSequence(sequenceName) );
+}
+
+// add multiple sequences
+void SamSequenceDictionary::Add(const vector<SamSequence>& sequences) {
+    vector<SamSequence>::const_iterator rgIter = sequences.begin();
+    vector<SamSequence>::const_iterator rgEnd  = sequences.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Add(*rgIter);
+}
+
+// overload to support std::string
+void SamSequenceDictionary::Add(const vector<string>& sequenceNames) {
+    vector<string>::const_iterator rgIter = sequenceNames.begin();
+    vector<string>::const_iterator rgEnd  = sequenceNames.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Add(*rgIter);
+}
+
+// returns iterator to container begin
+SamSequenceIterator SamSequenceDictionary::Begin(void) {
+    return m_data.begin();
+}
+
+// returns const_iterator to container begin
+SamSequenceConstIterator SamSequenceDictionary::Begin(void) const {
+    return m_data.begin();
+}
+
+// clear sequence container
+void SamSequenceDictionary::Clear(void) {
+    m_data.clear();
+}
+
+// explicit request for const_iterator to container begin
+SamSequenceConstIterator SamSequenceDictionary::ConstBegin(void) const {
+    return m_data.begin();
+}
+
+// explicit request for const_iterator to container end
+SamSequenceConstIterator SamSequenceDictionary::ConstEnd(void) const {
+    return m_data.end();
+}
+
+// returns true if container contains a sequence with this ID tag
+bool SamSequenceDictionary::Contains(const string& sequenceName) const {
+    return ( IndexOf(sequenceName) != (int)m_data.size() );
+}
+
+bool SamSequenceDictionary::Contains(const SamSequence& seq) const {
+    return ( IndexOf(seq) != (int)m_data.size() );
+}
+
+// returns iterator to container end
+SamSequenceIterator SamSequenceDictionary::End(void) {
+    return m_data.end();
+}
+
+// returns const_iterator to container begin
+SamSequenceConstIterator SamSequenceDictionary::End(void) const {
+    return m_data.end();
+}
+
+// returns vector index of sequence if found
+// returns vector::size() (invalid index) if not found
+int SamSequenceDictionary::IndexOf(const SamSequence& sequence) const {
+    SamSequenceConstIterator begin = ConstBegin();
+    SamSequenceConstIterator iter  = begin;
+    SamSequenceConstIterator end   = ConstEnd();
+    for ( ; iter != end; ++iter )
+        if ( *iter == sequence ) break;
+    return distance( begin, iter );
+}
+
+// overload to support std::string
+int SamSequenceDictionary::IndexOf(const string& sequenceName) const {
+    return IndexOf( SamSequence(sequenceName) );
+}
+
+// returns true if container is empty
+bool SamSequenceDictionary::IsEmpty(void) const {
+    return m_data.empty();
+}
+
+// removes sequence (if it exists)
+void SamSequenceDictionary::Remove(const SamSequence& sequence) {
+    if ( Contains(sequence) )
+        m_data.erase( m_data.begin() + IndexOf(sequence) );
+}
+
+// overlaod to support std::string
+void SamSequenceDictionary::Remove(const string& sequenceName) {
+    Remove( SamSequence(sequenceName) );
+}
+
+// remove multiple sequences
+void SamSequenceDictionary::Remove(const vector<SamSequence>& sequences) {
+    vector<SamSequence>::const_iterator rgIter = sequences.begin();
+    vector<SamSequence>::const_iterator rgEnd  = sequences.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Remove(*rgIter);
+}
+
+// overload to support std::string
+void SamSequenceDictionary::Remove(const vector<string>& sequenceNames) {
+    vector<string>::const_iterator rgIter = sequenceNames.begin();
+    vector<string>::const_iterator rgEnd  = sequenceNames.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Remove(*rgIter);
+}
+
+// returns size of container (number of current sequences)
+int SamSequenceDictionary::Size(void) const {
+    return m_data.size();
+}
+
+// retrieves the SamSequence object associated with this name
+// if sequenceName is unknown, a new SamSequence is created with this name (and invalid length 0)
+// and a reference to this new sequence entry is returned (like std::map)
+SamSequence& SamSequenceDictionary::operator[](const std::string& sequenceName) {
+
+    // look up sequence ID
+    int index = IndexOf(sequenceName);
+
+    // if found, return sequence at index
+    if ( index != (int)m_data.size() )
+        return m_data[index];
+
+    // otherwise, append new sequence and return reference
+    else {
+        SamSequence seq(sequenceName);
+        seq.Length = "0";
+        m_data.push_back(seq);
+        return m_data.back();
+    }
+}
+