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/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __SAM_REFERENCE_INFO_H__
#define __SAM_REFERENCE_INFO_H__
#include "StringArray.h"
#include "StringHash.h"
#include "IntArray.h"
/// Class for tracking the reference information mapping between the
/// reference ids and the reference names.
class SamReferenceInfo
{
public:
/// Constructor.
SamReferenceInfo();
/// Destructor.
~SamReferenceInfo();
/// Add reference sequence name and reference sequence length.
void add(const char* referenceSequenceName,
int32_t referenceSequenceLength);
/// Get the reference ID for the specified name, if addID is set to true,
/// a reference id will be created for the referenceName if one does not
/// already exist, while if addID is set to false (default), it will return
/// NO_REF_ID if the reference name does not exist.
int getReferenceID(const String & referenceName, bool addID = false);
/// Get the reference ID for the specified name, if addID is set to true,
/// a reference id will be created for the referenceName if one does not
/// already exist, while if addID is set to false (default), it will return
/// NO_REF_ID if the reference name does not exist.
int getReferenceID(const char* referenceName, bool addID = false);
/// Get the reference name for the specified id, if the id is not found,
/// return "*".
const String & getReferenceLabel(int id) const;
/// Get the number of entries contained here.
int32_t getNumEntries() const;
/// Return the reference name at the specified index, returning "" if the
/// index is out of bounds.
const char* getReferenceName(int index) const;
/// Return the reference length at the specified index, returning 0 if the
/// index is out of bounds.
int32_t getReferenceLength(int index) const;
/// Reset this reference info.
void clear();
/// Copy the reference information.
SamReferenceInfo & operator = (const SamReferenceInfo & rhs);
bool operator== (const SamReferenceInfo& rhs) const;
bool operator!= (const SamReferenceInfo& rhs) const
{
return(!operator==(rhs));
}
/// Constant for the value returned if a reference id does not exist
/// for a queried reference name.
static const int NO_REF_ID = -3;
private:
// Reference Name information
StringArray myReferenceContigs;
StringIntHash myReferenceHash;
IntArray myReferenceLengths;
};
#endif
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