SamReferenceInfo Class Reference

Class for tracking the reference information mapping between the reference ids and the reference names. More...

#include <SamReferenceInfo.h>

Collaboration diagram for SamReferenceInfo:

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List of all members.

Public Member Functions
	SamReferenceInfo ()
	Constructor.
	~SamReferenceInfo ()
	Destructor.
void	add (const char *referenceSequenceName, int32_t referenceSequenceLength)
	Add reference sequence name and reference sequence length.
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 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.
const String &	getReferenceLabel (int id) const
	Get the reference name for the specified id, if the id is not found, return "*".
int32_t	getNumEntries () const
	Get the number of entries contained here.
const char *	getReferenceName (int index) const
	Return the reference name at the specified index, returning "" if the index is out of bounds.
int32_t	getReferenceLength (int index) const
	Return the reference length at the specified index, returning 0 if the index is out of bounds.
void	clear ()
	Reset this reference info.
SamReferenceInfo &	operator= (const SamReferenceInfo &rhs)
	Copy the reference information.
bool	operator== (const SamReferenceInfo &rhs) const
bool	operator!= (const SamReferenceInfo &rhs) const
Static Public Attributes
static const int	NO_REF_ID = -3
	Constant for the value returned if a reference id does not exist for a queried reference name.

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Detailed Description

Class for tracking the reference information mapping between the reference ids and the reference names.

Definition at line 27 of file SamReferenceInfo.h.

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Member Function Documentation

int SamReferenceInfo::getReferenceID	(	const char *	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.

Definition at line 71 of file SamReferenceInfo.cpp.

References getReferenceID().

{
    String referenceNameString = referenceName;

    return(getReferenceID(referenceNameString, addID));
}

int SamReferenceInfo::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.

Definition at line 45 of file SamReferenceInfo.cpp.

References NO_REF_ID.

Referenced by getReferenceID(), and SamFileHeader::getReferenceID().

{
    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;
}

const String & SamReferenceInfo::getReferenceLabel

(

int

id

)

const

Get the reference name for the specified id, if the id is not found, return "*".

Definition at line 80 of file SamReferenceInfo.cpp.

Referenced by SamFileHeader::getReferenceLabel().

{
    static String noname("*");

    if ((id < 0) || (id >= myReferenceContigs.Length()))
    {
        return noname;
    }

    return myReferenceContigs[id];
}

int32_t SamReferenceInfo::getReferenceLength

(

int

index

)

const

Return the reference length at the specified index, returning 0 if the index is out of bounds.

Definition at line 112 of file SamReferenceInfo.cpp.

References getNumEntries().

{
    if((index >= 0) && (index < getNumEntries()))
    {
        return(myReferenceLengths[index]);
    }
    
    // Out of bounds, return 0
    return(0);
}

const char * SamReferenceInfo::getReferenceName

(

int

index

)

const

Return the reference name at the specified index, returning "" if the index is out of bounds.

Definition at line 100 of file SamReferenceInfo.cpp.

References getNumEntries().

{
    if((index >= 0) && (index < getNumEntries()))
    {
        return(myReferenceContigs[index].c_str());
    }
    
    // Out of range, return blank
    return("");
}

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Member Data Documentation

const int SamReferenceInfo::NO_REF_ID = -3 [static]

Constant for the value returned if a reference id does not exist for a queried reference name.

Definition at line 77 of file SamReferenceInfo.h.

Referenced by getReferenceID().

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The documentation for this class was generated from the following files:

• bam/SamReferenceInfo.h
• bam/SamReferenceInfo.cpp