SortedChunkList Class Reference

Public Member Functions
Chunk	pop ()
bool	insert (const Chunk &chunkToInsert)
void	clear ()
bool	empty ()
bool	mergeOverlapping ()

Detailed Description

Definition at line 48 of file IndexBase.h.

Member Function Documentation

clear()

void SortedChunkList::clear

(

)

Definition at line 55 of file IndexBase.cpp.

{
    chunkList.clear();
}

empty()

bool SortedChunkList::empty

(

)

Definition at line 60 of file IndexBase.cpp.

{
    return(chunkList.empty());
}

insert()

bool SortedChunkList::insert

(

const Chunk &

chunkToInsert

)

Definition at line 29 of file IndexBase.cpp.

{
    std::pair<std::map<uint64_t, Chunk>::iterator, bool> insertRes;
    // Insert the passed in chunk.
    insertRes = 
        chunkList.insert(std::pair<uint64_t, Chunk>(chunkToInsert.chunk_beg,
                                                    chunkToInsert));
 
    if(!insertRes.second)
    {
        // Failed to insert the chunk.
        std::cerr << "Failed to insert into the SortedChunkList.\n";
        std::cerr << "\tpreviously found chunk:\tbeg = " << std::hex
                  << insertRes.first->second.chunk_beg 
                  << "\tend = "
                  << insertRes.first->second.chunk_end
                  << "\nnew chunk:\tbeg = " << std::hex
                  << chunkToInsert.chunk_beg 
                  << "\tend = "
                  << chunkToInsert.chunk_end
                  << std::endl;
    }
    // return the result that comes from insertRes.
    return(insertRes.second);
}

mergeOverlapping()

bool SortedChunkList::mergeOverlapping

(

)

Definition at line 67 of file IndexBase.cpp.

{
    // Start at the beginning of the list and iterate through.
    std::map<uint64_t, Chunk>::iterator currentPos = chunkList.begin();
    std::map<uint64_t, Chunk>::iterator nextPos = chunkList.begin();
    if(nextPos != chunkList.end())
    {
        ++nextPos;
    }
    
    // Loop until the end is reached.
    while(nextPos != chunkList.end())
    {
        // If the next chunk is completely contained within the current 
        // chunk (its end is less than the current chunk's end), 
        // delete it since its position is already covered.
        if(nextPos->second.chunk_end < currentPos->second.chunk_end)
        {
            chunkList.erase(nextPos);
            nextPos = currentPos;
            ++nextPos;
            continue;
        }
        
        // If the next chunk's start position's BGZF block is less than or
        // equal to the BGZF block of the current chunk's end position,
        // combine the two chunks into the current chunk.
        if((nextPos->second.chunk_beg >> 16) <= 
           (currentPos->second.chunk_end >> 16))
        {
            currentPos->second.chunk_end = nextPos->second.chunk_end;
            // nextPos has now been included in the current pos, so
            // remove it.
            chunkList.erase(nextPos);
            nextPos = currentPos;
            ++nextPos;
            continue;
        }
        else
        {
            // Nothing to combine.  So try combining at the next 
            currentPos = nextPos;
            ++nextPos;
        }
    }
    return(true);
}

pop()

Chunk SortedChunkList::pop

(

)

Definition at line 21 of file IndexBase.cpp.

{
    Chunk newChunk = chunkList.begin()->second;
    chunkList.erase(chunkList.begin());
    return(newChunk);
}

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

• general/IndexBase.h
• general/IndexBase.cpp