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SamReferenceInfo.cpp
/*
* 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/>.
*/
#include "SamReferenceInfo.h"
SamReferenceInfo::SamReferenceInfo()
: myReferenceContigs(),
myReferenceHash(),
myReferenceLengths()
{
clear();
}
SamReferenceInfo::~SamReferenceInfo()
{
clear();
}
// Add reference sequence name and reference sequence length.
void SamReferenceInfo::add(const char* referenceSequenceName,
int32_t referenceSequenceLength)
{
myReferenceHash.Add(referenceSequenceName,
myReferenceContigs.Length());
myReferenceContigs.Push(referenceSequenceName);
myReferenceLengths.Push(referenceSequenceLength);
}
int SamReferenceInfo::getReferenceID(const String & referenceName,
bool addID)
{
if (referenceName == "*")
return -1;
int id = myReferenceHash.Find(referenceName);
if (id >= 0)
return myReferenceHash.Integer(id);
if(!addID)
{
// Don't add the id, so return NO_REF_ID
return(NO_REF_ID);
}
id = myReferenceContigs.Length();
myReferenceContigs.Push(referenceName);
myReferenceLengths.Push(0);
myReferenceHash.Add(referenceName, id);
return id;
}
int SamReferenceInfo::getReferenceID(const char* referenceName,
bool addID)
{
String referenceNameString = referenceName;
return(getReferenceID(referenceNameString, addID));
}
const String & SamReferenceInfo::getReferenceLabel(int id) const
{
static String noname("*");
if ((id < 0) || (id >= myReferenceContigs.Length()))
{
return noname;
}
return myReferenceContigs[id];
}
int32_t SamReferenceInfo::getNumEntries() const
{
// The number of entries is the size of referenceLengths.
return(myReferenceLengths.Length());
}
const char* SamReferenceInfo::getReferenceName(int index) const
{
if((index >= 0) && (index < getNumEntries()))
{
return(myReferenceContigs[index].c_str());
}
// Out of range, return blank
return("");
}
int32_t SamReferenceInfo::getReferenceLength(int index) const
{
if((index >= 0) && (index < getNumEntries()))
{
return(myReferenceLengths[index]);
}
// Out of bounds, return 0
return(0);
}
void SamReferenceInfo::clear()
{
myReferenceContigs.Clear();
myReferenceHash.Clear();
myReferenceLengths.Clear();
}
SamReferenceInfo& SamReferenceInfo::operator = (const SamReferenceInfo &newInfo)
{
clear();
// Copy Reference contigs, hash, lengths.
myReferenceContigs = newInfo.myReferenceContigs;
myReferenceHash = newInfo.myReferenceHash;
myReferenceLengths = newInfo.myReferenceLengths;
return(*this);
}
bool SamReferenceInfo::operator== (const SamReferenceInfo& rhs) const
{
// Hash may be different, but if Contigs are the same, the hashes will
// contain the same basic info (maybe just at different indices.
return((myReferenceContigs == rhs.myReferenceContigs) &&
(myReferenceLengths == rhs.myReferenceLengths));
}
SamReferenceInfo
Class for tracking the reference information mapping between the reference ids and the reference name...
Definition SamReferenceInfo.h:28
SamReferenceInfo::clear
void clear()
Reset this reference info.
Definition SamReferenceInfo.cpp:123
SamReferenceInfo::getReferenceID
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 ...
Definition SamReferenceInfo.cpp:45
SamReferenceInfo::getNumEntries
int32_t getNumEntries() const
Get the number of entries contained here.
Definition SamReferenceInfo.cpp:93
SamReferenceInfo::operator=
SamReferenceInfo & operator=(const SamReferenceInfo &rhs)
Copy the reference information.
Definition SamReferenceInfo.cpp:131
SamReferenceInfo::NO_REF_ID
static const int NO_REF_ID
Constant for the value returned if a reference id does not exist for a queried reference name.
Definition SamReferenceInfo.h:77
SamReferenceInfo::SamReferenceInfo
SamReferenceInfo()
Constructor.
Definition SamReferenceInfo.cpp:20
SamReferenceInfo::getReferenceName
const char * getReferenceName(int index) const
Return the reference name at the specified index, returning "" if the index is out of bounds.
Definition SamReferenceInfo.cpp:100
SamReferenceInfo::getReferenceLabel
const String & getReferenceLabel(int id) const
Get the reference name for the specified id, if the id is not found, return "*".
Definition SamReferenceInfo.cpp:80
SamReferenceInfo::add
void add(const char *referenceSequenceName, int32_t referenceSequenceLength)
Add reference sequence name and reference sequence length.
Definition SamReferenceInfo.cpp:35
SamReferenceInfo::~SamReferenceInfo
~SamReferenceInfo()
Destructor.
Definition SamReferenceInfo.cpp:29
SamReferenceInfo::getReferenceLength
int32_t getReferenceLength(int index) const
Return the reference length at the specified index, returning 0 if the index is out of bounds.
Definition SamReferenceInfo.cpp:112
String
Definition StringBasics.h:39