示例#1
0
static stList *getSubstringsForFlowerSegments(stList *flowers) {
    /*
     * Get the set of substrings representing the strings in the segments of the given flowers.
     */
    stList *substrings = stList_construct3(0, (void (*)(void *)) substring_destruct);
    for (int64_t i = 0; i < stList_length(flowers); i++) {
        Flower *flower = stList_get(flowers, i);
        Flower_EndIterator *blockIt = flower_getBlockIterator(flower);
        Block *block;
        while ((block = flower_getNextBlock(blockIt)) != NULL) {
            Block_InstanceIterator *instanceIt = block_getInstanceIterator(block);
            Segment *segment;
            while ((segment = block_getNext(instanceIt)) != NULL) {
                Sequence *sequence;
                if ((sequence = segment_getSequence(segment)) != NULL) {
                    segment = segment_getStrand(segment) ? segment : segment_getReverse(segment);
                    assert(segment_getLength(segment) > 0);
                    stList_append(substrings,
                            substring_construct(sequence_getMetaSequence(sequence)->stringName,
                                    segment_getStart(segment) - sequence_getStart(sequence),
                                    segment_getLength(segment)));
                }
            }
            block_destructInstanceIterator(instanceIt);
        }
        flower_destructBlockIterator(blockIt);
    }
    return substrings;
}
示例#2
0
void flower_check(Flower *flower) {
    eventTree_check(flower_getEventTree(flower));

    Flower_GroupIterator *groupIterator = flower_getGroupIterator(flower);
    Group *group;
    while ((group = flower_getNextGroup(groupIterator)) != NULL) {
        group_check(group);
    }
    flower_destructGroupIterator(groupIterator);

    Flower_ChainIterator *chainIterator = flower_getChainIterator(flower);
    Chain *chain;
    while ((chain = flower_getNextChain(chainIterator)) != NULL) {
        chain_check(chain);
    }
    flower_destructCapIterator(chainIterator);

    //We check built trees in here.
    Flower_EndIterator *endIterator = flower_getEndIterator(flower);
    End *end;
    while ((end = flower_getNextEnd(endIterator)) != NULL) {
        end_check(end);
        end_check(end_getReverse(end)); //We will test everything backwards also.
    }
    flower_destructEndIterator(endIterator);

    if (flower_builtFaces(flower)) {
        Flower_FaceIterator *faceIterator = flower_getFaceIterator(flower);
        Face *face;
        while ((face = flower_getNextFace(faceIterator)) != NULL) {
            face_check(face);
        }
        flower_destructFaceIterator(faceIterator);
        face_checkFaces(flower);
    } else {
        cactusCheck(flower_getFaceNumber(flower) == 0);
    }

    if (flower_builtBlocks(flower)) { //Note that a flower for which the blocks are not yet built must be a leaf.
        Flower_BlockIterator *blockIterator = flower_getBlockIterator(flower);
        Block *block;
        while ((block = flower_getNextBlock(blockIterator)) != NULL) {
            block_check(block);
            block_check(block_getReverse(block)); //We will test everything backwards also.
        }
        flower_destructBlockIterator(blockIterator);
    } else {
        cactusCheck(flower_isLeaf(flower)); //Defensive
        cactusCheck(flower_isTerminal(flower)); //Checks that a flower without built blocks is a leaf and does not
        //contain any blocks.
    }

    Flower_SequenceIterator *sequenceIterator = flower_getSequenceIterator(flower);
    Sequence *sequence;
    while ((sequence = flower_getNextSequence(sequenceIterator)) != NULL) {
        sequence_check(sequence);
    }
    flower_destructSequenceIterator(sequenceIterator);
}
示例#3
0
void flower_writeBinaryRepresentation(Flower *flower, void(*writeFn)(const void * ptr, size_t size, size_t count)) {
    Flower_SequenceIterator *sequenceIterator;
    Flower_EndIterator *endIterator;
    Flower_BlockIterator *blockIterator;
    Flower_GroupIterator *groupIterator;
    Flower_ChainIterator *chainIterator;
    Sequence *sequence;
    End *end;
    Block *block;
    Group *group;
    Chain *chain;

    binaryRepresentation_writeElementType(CODE_FLOWER, writeFn);
    binaryRepresentation_writeName(flower_getName(flower), writeFn);
    binaryRepresentation_writeBool(flower_builtBlocks(flower), writeFn);
    binaryRepresentation_writeBool(flower_builtTrees(flower), writeFn);
    binaryRepresentation_writeBool(flower_builtFaces(flower), writeFn);
    binaryRepresentation_writeName(flower->parentFlowerName, writeFn);

    if (flower_getEventTree(flower) != NULL) {
        eventTree_writeBinaryRepresentation(flower_getEventTree(flower), writeFn);
    }

    sequenceIterator = flower_getSequenceIterator(flower);
    while ((sequence = flower_getNextSequence(sequenceIterator)) != NULL) {
        sequence_writeBinaryRepresentation(sequence, writeFn);
    }
    flower_destructSequenceIterator(sequenceIterator);

    endIterator = flower_getEndIterator(flower);
    while ((end = flower_getNextEnd(endIterator)) != NULL) {
        end_writeBinaryRepresentation(end, writeFn);
    }
    flower_destructEndIterator(endIterator);

    blockIterator = flower_getBlockIterator(flower);
    while ((block = flower_getNextBlock(blockIterator)) != NULL) {
        block_writeBinaryRepresentation(block, writeFn);
    }
    flower_destructBlockIterator(blockIterator);

    groupIterator = flower_getGroupIterator(flower);
    while ((group = flower_getNextGroup(groupIterator)) != NULL) {
        group_writeBinaryRepresentation(group, writeFn);
    }
    flower_destructGroupIterator(groupIterator);

    chainIterator = flower_getChainIterator(flower);
    while ((chain = flower_getNextChain(chainIterator)) != NULL) {
        chain_writeBinaryRepresentation(chain, writeFn);
    }
    flower_destructChainIterator(chainIterator);

    binaryRepresentation_writeElementType(CODE_FLOWER, writeFn); //this avoids interpretting things wrong.
}
示例#4
0
int64_t flower_getTrivialChainNumber(Flower *flower) {
    int64_t i = 0;
    Flower_BlockIterator *blockIt = flower_getBlockIterator(flower);
    Block *block;
    while ((block = flower_getNextBlock(blockIt)) != NULL) {
        if (block_isTrivialChain(block)) {
            i++;
        }
    }
    flower_destructBlockIterator(blockIt);
    return i;
}