void makeCactusTree_terminalNode(Flower *flower, FILE *fileHandle, const char *parentNodeName, const char *parentEdgeColour) { char *groupNameString = cactusMisc_nameToString(flower_getName(flower)); double scalingFactor = flower_getTotalBaseLength(flower) / totalProblemSize; assert(scalingFactor <= 1.001); assert(scalingFactor >= -0.001); addNodeToGraph(groupNameString, fileHandle, scalingFactor, "triangle", groupNameString); //Write in the parent edge. if (parentNodeName != NULL) { graphViz_addEdgeToGraph(parentNodeName, groupNameString, fileHandle, "", parentEdgeColour, 10, 1, "forward"); } free(groupNameString); }
int main(int argc, char *argv[]) { st_setLogLevelFromString(argv[1]); st_logDebug("Set up logging\n"); stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(argv[2]); CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, 0); stKVDatabaseConf_destruct(kvDatabaseConf); st_logDebug("Set up the flower disk\n"); Name flowerName = cactusMisc_stringToName(argv[3]); Flower *flower = cactusDisk_getFlower(cactusDisk, flowerName); int64_t totalBases = flower_getTotalBaseLength(flower); int64_t totalEnds = flower_getEndNumber(flower); int64_t totalFreeEnds = flower_getFreeStubEndNumber(flower); int64_t totalAttachedEnds = flower_getAttachedStubEndNumber(flower); int64_t totalCaps = flower_getCapNumber(flower); int64_t totalBlocks = flower_getBlockNumber(flower); int64_t totalGroups = flower_getGroupNumber(flower); int64_t totalChains = flower_getChainNumber(flower); int64_t totalLinkGroups = 0; int64_t maxEndDegree = 0; int64_t maxAdjacencyLength = 0; int64_t totalEdges = 0; Flower_EndIterator *endIt = flower_getEndIterator(flower); End *end; while((end = flower_getNextEnd(endIt)) != NULL) { assert(end_getOrientation(end)); if(end_getInstanceNumber(end) > maxEndDegree) { maxEndDegree = end_getInstanceNumber(end); } stSortedSet *ends = stSortedSet_construct(); End_InstanceIterator *capIt = end_getInstanceIterator(end); Cap *cap; while((cap = end_getNext(capIt)) != NULL) { if(cap_getSequence(cap) != NULL) { Cap *adjacentCap = cap_getAdjacency(cap); assert(adjacentCap != NULL); End *adjacentEnd = end_getPositiveOrientation(cap_getEnd(adjacentCap)); stSortedSet_insert(ends, adjacentEnd); int64_t adjacencyLength = cap_getCoordinate(cap) - cap_getCoordinate(adjacentCap); if(adjacencyLength < 0) { adjacencyLength *= -1; } assert(adjacencyLength >= 1); if(adjacencyLength >= maxAdjacencyLength) { maxAdjacencyLength = adjacencyLength; } } } end_destructInstanceIterator(capIt); totalEdges += stSortedSet_size(ends); if(stSortedSet_search(ends, end) != NULL) { //This ensures we count self edges twice, so that the division works. totalEdges += 1; } stSortedSet_destruct(ends); } assert(totalEdges % 2 == 0); flower_destructEndIterator(endIt); Flower_GroupIterator *groupIt = flower_getGroupIterator(flower); Group *group; while((group = flower_getNextGroup(groupIt)) != NULL) { if(group_getLink(group) != NULL) { totalLinkGroups++; } } flower_destructGroupIterator(groupIt); printf("flower name: %" PRIi64 " total bases: %" PRIi64 " total-ends: %" PRIi64 " total-caps: %" PRIi64 " max-end-degree: %" PRIi64 " max-adjacency-length: %" PRIi64 " total-blocks: %" PRIi64 " total-groups: %" PRIi64 " total-edges: %" PRIi64 " total-free-ends: %" PRIi64 " total-attached-ends: %" PRIi64 " total-chains: %" PRIi64 " total-link groups: %" PRIi64 "\n", flower_getName(flower), totalBases, totalEnds, totalCaps, maxEndDegree, maxAdjacencyLength, totalBlocks, totalGroups, totalEdges/2, totalFreeEnds, totalAttachedEnds, totalChains, totalLinkGroups); return 0; }
int main(int argc, char *argv[]) { Flower *flower; FILE *fileHandle; /* * Arguments/options */ char * logLevelString = NULL; char * cactusDiskDatabaseString = NULL; char * flowerName = NULL; char * outputFile = NULL; /////////////////////////////////////////////////////////////////////////// // (0) Parse the inputs handed by genomeCactus.py / setup stuff. /////////////////////////////////////////////////////////////////////////// while (1) { static struct option long_options[] = { { "logLevel", required_argument, 0, 'a' }, { "cactusDisk", required_argument, 0, 'c' }, { "flowerName", required_argument, 0, 'd' }, { "outputFile", required_argument, 0, 'e' }, { "scaleNodeSizes", no_argument, 0, 'f' }, { "nameLabels", no_argument, 0, 'g' }, { "help", no_argument, 0, 'h' }, { 0, 0, 0, 0 } }; int option_index = 0; int key = getopt_long(argc, argv, "a:c:d:e:fgh", long_options, &option_index); if (key == -1) { break; } switch (key) { case 'a': logLevelString = stString_copy(optarg); break; case 'c': cactusDiskDatabaseString = stString_copy(optarg); break; case 'd': flowerName = stString_copy(optarg); break; case 'e': outputFile = stString_copy(optarg); break; case 'f': scaleNodeSizes = !scaleNodeSizes; break; case 'g': nameLabels = !nameLabels; break; case 'h': usage(); return 0; default: usage(); return 1; } } /////////////////////////////////////////////////////////////////////////// // (0) Check the inputs. /////////////////////////////////////////////////////////////////////////// assert(cactusDiskDatabaseString != NULL); assert(flowerName != NULL); assert(outputFile != NULL); ////////////////////////////////////////////// //Set up logging ////////////////////////////////////////////// st_setLogLevelFromString(logLevelString); ////////////////////////////////////////////// //Log (some of) the inputs ////////////////////////////////////////////// st_logInfo("Flower name : %s\n", flowerName); st_logInfo("Output graph file : %s\n", outputFile); ////////////////////////////////////////////// //Load the database ////////////////////////////////////////////// stKVDatabaseConf *kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskDatabaseString); CactusDisk *cactusDisk = cactusDisk_construct(kvDatabaseConf, 0); st_logInfo("Set up the flower disk\n"); /////////////////////////////////////////////////////////////////////////// // Parse the basic reconstruction problem /////////////////////////////////////////////////////////////////////////// flower = cactusDisk_getFlower(cactusDisk, cactusMisc_stringToName(flowerName)); st_logInfo("Parsed the top level flower of the cactus tree to build\n"); /////////////////////////////////////////////////////////////////////////// // Build the graph. /////////////////////////////////////////////////////////////////////////// totalProblemSize = flower_getTotalBaseLength(flower); fileHandle = fopen(outputFile, "w"); graphViz_setupGraphFile(fileHandle); makeCactusTree_flower(flower, fileHandle, NULL, NULL); graphViz_finishGraphFile(fileHandle); fclose(fileHandle); st_logInfo("Written the tree to file\n"); /////////////////////////////////////////////////////////////////////////// // Clean up. /////////////////////////////////////////////////////////////////////////// cactusDisk_destruct(cactusDisk); stKVDatabaseConf_destruct(kvDatabaseConf); return 0; }
void makeCactusTree_flower(Flower *flower, FILE *fileHandle, const char *parentNodeName, const char *parentEdgeColour) { if(flower_isTerminal(flower)) { makeCactusTree_terminalNode(flower, fileHandle, parentNodeName, parentEdgeColour); } else { //Write the flower nodes. char *flowerNameString = cactusMisc_nameToString(flower_getName(flower)); const char *edgeColour = graphViz_getColour(); addNodeToGraph(flowerNameString, fileHandle, flower_getTotalBaseLength(flower) / totalProblemSize, "ellipse", flowerNameString); //Write in the parent edge. if (parentNodeName != NULL) { graphViz_addEdgeToGraph(parentNodeName, flowerNameString, fileHandle, "", parentEdgeColour, 10, 1, "forward"); } //Create the chains. Flower_ChainIterator *chainIterator = flower_getChainIterator(flower); Chain *chain; while ((chain = flower_getNextChain(chainIterator)) != NULL) { makeCactusTree_chain(chain, fileHandle, flowerNameString, edgeColour); } flower_destructChainIterator(chainIterator); //Create the diamond node char *diamondNodeNameString = st_malloc(sizeof(char) * (strlen( flowerNameString) + 2)); sprintf(diamondNodeNameString, "z%s", flowerNameString); const char *diamondEdgeColour = graphViz_getColour(); //Create all the groups linked to the diamond. Flower_GroupIterator *groupIterator = flower_getGroupIterator(flower); Group *group; double size = 0.0; //get the size of the group organising node.. int64_t nonTrivialGroupCount = 0; while ((group = flower_getNextGroup(groupIterator)) != NULL) { assert(!group_isLeaf(group)); if (group_isTangle(group)) { size += group_getTotalBaseLength(group); nonTrivialGroupCount++; } } flower_destructGroupIterator(groupIterator); if(nonTrivialGroupCount == 0) { assert(flower_getParentGroup(flower) == 0); } else { //assert(nonTrivialGroupCount > 0); addNodeToGraph(diamondNodeNameString, fileHandle, size / totalProblemSize, "diamond", ""); graphViz_addEdgeToGraph(flowerNameString, diamondNodeNameString, fileHandle, "", edgeColour, 10, 1, "forward"); groupIterator = flower_getGroupIterator(flower); while ((group = flower_getNextGroup(groupIterator)) != NULL) { if (group_isTangle(group)) { assert(!group_isLeaf(group)); makeCactusTree_flower(group_getNestedFlower(group), fileHandle, diamondNodeNameString, diamondEdgeColour); } } flower_destructGroupIterator(groupIterator); } free(flowerNameString); free(diamondNodeNameString); } }