This class encapsulates the tag value pairs contained with a SAM Header line with accessors for getting and setting the tags within this header. More...

#include <SamHeaderRecord.h>

Inheritance diagram for SamHeaderRecord:

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Collaboration diagram for SamHeaderRecord:

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List of all members.

Public Types
enum	SamHeaderRecordType { HD, SQ, RG, PG }
	Specifies the Type for the sam header record (line). More...
Public Member Functions
	SamHeaderRecord ()
	Constructor.
virtual	~SamHeaderRecord ()
	Destructor.
virtual SamHeaderRecord *	createCopy () const =0
	Return a pointer to a newly created header record of the appropriate type that is a copy of this record.
bool	setFields (const StringArray &tokens)
	Set the fields from the passed in line.
bool	isValid ()
	Check to see if the record is valid.
const char *	getTagValue (const char *tag) const
	Return the value associated with the specified tag.
bool	setTag (const char tag, const char value)
	Set the value of the specified tag to the specified value, deletes the tag when value is NULL.
void	reset ()
	Reset this header record to an empty state with no tags.
bool	appendString (std::string &header)
	Appends the string representation of this header record to the passed in string.
bool	addKey (const char *value)
	Add the key tag with the specified value (not for HD headers).
const char *	getKeyValue () const
	Get the value associated with the key tag. Returns "" if it is not set.
bool	isActiveHeaderRecord ()
	This record is active (true) if there is at least one tag set.
const char *	getTypeString ()
	Return the type of this header record (HD, SQ, RG, or PG) as a string.
SamHeaderRecordType	getType ()
	Return the type of this header record (HD, SQ, RG, or PG) as an enum.
Protected Member Functions
void	addRequiredTag (const char *requiredTag)
virtual void	internalCopy (SamHeaderRecord &newRec) const
Protected Attributes
std::string	myTypeString
SamHeaderRecordType	myType
std::string	myKeyTag

Detailed Description

This class encapsulates the tag value pairs contained with a SAM Header line with accessors for getting and setting the tags within this header.

Definition at line 27 of file SamHeaderRecord.h.

Member Enumeration Documentation

enum SamHeaderRecord::SamHeaderRecordType

Specifies the Type for the sam header record (line).

Enumerator:

HD	Header.
SQ	Sequence Dictionary.
RG	Read Group.
PG	Program.

Definition at line 31 of file SamHeaderRecord.h.

                             {
        HD, ///< Header
        SQ, ///< Sequence Dictionary
        RG, ///< Read Group
        PG  ///< Program
    };

Member Function Documentation

bool SamHeaderRecord::appendString ( std::string & header )

Appends the string representation of this header record to the passed in string.

Definition at line 234 of file SamHeaderRecord.cpp.

References isActiveHeaderRecord(), and isValid().

{
    // Track whether or not the header type has been written.
    // Only write the header type if at least one of the tags has
    // an associated value.
    bool writtenHeader = false;

    if(isActiveHeaderRecord() && isValid())
    {
        // Loop through all the entries in the tag vector.
        for(unsigned int vectorIndex = 0; 
            vectorIndex < myTags.size(); 
            vectorIndex++)
        {
            if(!writtenHeader && (myTags[vectorIndex]->hasValue()))
            {
                // The tag has a value and the header type has not yet been written,
                // so write it.
                header += "@";
                header += myTypeString;
                writtenHeader = true;
            }
            myTags[vectorIndex]->getTagString(header);
        }

        // If a header has been written, add a new line character.
        if(writtenHeader)
        {
            header += "\n";
            return(true);
        }
    }

    // Nothing was written, return false.
    return(false);
}

virtual SamHeaderRecord* SamHeaderRecord::createCopy ( ) const [pure virtual]

Return a pointer to a newly created header record of the appropriate type that is a copy of this record.

The newly created record will not be deleted by this class and it is the responsibility of the calling method to handle the deletion. Returns NULL on failure to copy.

Implemented in SamHeaderHD, SamHeaderPG, SamHeaderRG, and SamHeaderSQ.

Referenced by SamFileHeader::addRecordCopy().

const char * SamHeaderRecord::getTagValue ( const char * tag ) const

Return the value associated with the specified tag.

Returns "" if it is not set.

Definition at line 100 of file SamHeaderRecord.cpp.

Referenced by SamFileHeader::addPG(), SamFileHeader::addRG(), SamFileHeader::addSQ(), SamFileHeader::getHDTagValue(), SamFileHeader::getPGTagValue(), SamFileHeader::getRGTagValue(), and SamFileHeader::getSQTagValue().

{
    // Look up the tag in myTags.
    int index = myTagHash.Integer(tag);
    if(index < 0)
    {
        // The tag was not found in the hash, so return "".
        return("");
    }

    // The tag was found in the hash, so return the tag value found at the 
    // index associated with the tag.
    return(myTags[index]->getValue());
}

bool SamHeaderRecord::setFields ( const StringArray & tokens )

Set the fields from the passed in line.

Return true if successfully set.

Definition at line 38 of file SamHeaderRecord.cpp.

References isValid(), and setTag().

{
    bool status = true;
   
    // Loop through the tags for this type.
    // The tags start in column 1 since column 0 contains the type.
    for(int columnIndex = 1; columnIndex < tokens.Length(); columnIndex++)
    {
        // Validate that the tag is at least 3 characters. Two for the token,
        // one for the ':'.
        if((tokens[columnIndex].Length() < 3) || 
           (tokens[columnIndex][2] != ':'))
        {
            // Continue to the next tag, this one is too small/invalid.
            status = false;
            std::cerr << "ERROR: Poorly formatted tag in header: " 
                      << tokens[columnIndex] << std::endl;
            continue;
        }
      
        // Get the tag from the token.
        char tag[3];
        tag[0] = tokens[columnIndex][0];
        tag[1] = tokens[columnIndex][1];
        tag[2] = 0;

        // The tag value is the rest of the substring.
        String tagValue = (tokens[columnIndex]).SubStr(3);

        // Set the tag.      
        status &= setTag(tag, tagValue.c_str());
    }

    status &= isValid();

    return(status);
}

bool SamHeaderRecord::setTag	(	const char *	tag,
		const char *	value
	)

Set the value of the specified tag to the specified value, deletes the tag when value is NULL.

Returns whether or not it was successful, fails if tag is the key tag and the key tag already exists.

Definition at line 119 of file SamHeaderRecord.cpp.

Referenced by addKey(), setFields(), SamFileHeader::setHDTag(), SamFileHeader::setPGTag(), SamFileHeader::setRGTag(), and SamFileHeader::setSQTag().

{
    // Lookup the tag in the hash.
    int vectorIndex = myTagHash.Integer(tag);
    if(vectorIndex < 0)
    {
        // The tag was not found in the hash, so create a new one.
        SamHeaderTag* tagPtr = new SamHeaderTag(tag, value);
      
        if(tagPtr == NULL)
        {
            // Failed to allocate the tag, return false.
            std::cerr << "Failed to allocate space (new) for a SamHeaderTag.\n";
            return(false);
        }

        // Add the new tag to the back of the tag values.
        vectorIndex = myTags.size();
        myTags.push_back(tagPtr);

        // If the value is not null, increment the number of active tags.
        if(value[0] != 0)
        {
            ++myNumActiveTags;
        }

        // Add the tag to the hash.
        int hashIndex = myTagHash.Add(tag, vectorIndex);
      
        if((myTagHash.Integer(hashIndex) != vectorIndex) ||
           (myTagHash[hashIndex] != tag))
        {
            // Failed to add the tag, so return false.
            std::cerr << "Failed to add tag, " << tag
                      << ", to the hash." << std::endl;
            return(false);
        }
        return(true);
    }
    else if((unsigned int)vectorIndex < myTags.size())
    {
        // Found the tag in the hash.  So, update the tag if it
        // is not the key.
        if(myKeyTag != tag)
        {
            // Not the key, so update the tag.
            // If the new value is null and the old one is not, decrement the
            // number of active tags.
            if((value[0] == 0) && ((myTags[vectorIndex]->getValue())[0] != 0))
            {
                // Tag was deleted since the new value is blank but the old
                // value was not.
                --myNumActiveTags;
            }
            else if((value[0] != 0) && 
                    ((myTags[vectorIndex]->getValue())[0] == 0))
            {
                // Tag was added since the old value was blank and the new value
                // is not.
                ++myNumActiveTags;
            }

            // Just modifying a tag, so this does not affect the number 
            // of active tags.
            return(myTags[vectorIndex]->setValue(value));
        }
        else if(strcmp(value, myTags[vectorIndex]->getValue()) == 0)
        {
            // The new key value is the same as the previous value, so
            // it is not a change, return true.
            return(true);
        }
        else
        {
            // Can't modify the key tag's value since that will
            // screw up the hash.
            std::cerr << "Can't modify the key tag, " << tag << " from "
                      << myTags[vectorIndex]->getValue() << " to " 
                      << value << std::endl;
            return(false);
        }
    }

    // Got an invalid index from the hash.  This is not supposed to happen.
    // so return false.
    std::cerr << "Invalid tag index found: " << vectorIndex 
              << ", but max index is " << myTags.size() << " for tag: " 
              << tag << std::endl;
    return(false);
}

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

bam/SamHeaderRecord.h
bam/SamHeaderRecord.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

Member Function Documentation