static void assignEventsAndSequences(Event *parentEvent, stTree *tree,
stSet *outgroupNameSet,
char *argv[], int64_t *j) {
Event *myEvent = NULL; // To distinguish from the global "event" variable.
assert(tree != NULL);
totalEventNumber++;
if (stTree_getChildNumber(tree) > 0) {
myEvent = event_construct3(stTree_getLabel(tree),
stTree_getBranchLength(tree), parentEvent,
eventTree);
for (int64_t i = 0; i < stTree_getChildNumber(tree); i++) {
assignEventsAndSequences(myEvent, stTree_getChild(tree, i),
outgroupNameSet, argv, j);
}
}
if (stTree_getChildNumber(tree) == 0 || (stTree_getLabel(tree) != NULL && (stSet_search(outgroupNameSet, (char *)stTree_getLabel(tree)) != NULL))) {
// This event is a leaf and/or an outgroup, so it has
// associated sequence.
assert(stTree_getLabel(tree) != NULL);
assert(stTree_getBranchLength(tree) != INFINITY);
if (stTree_getChildNumber(tree) == 0) {
// Construct the leaf event
myEvent = event_construct3(stTree_getLabel(tree), stTree_getBranchLength(tree), parentEvent, eventTree);
}
char *fileName = argv[*j];
if (!stFile_exists(fileName)) {
st_errAbort("File does not exist: %s\n", fileName);
}
// Set the global "event" variable, which is needed for the
// function provided to fastaReadToFunction.
event = myEvent;
if (stFile_isDir(fileName)) {
st_logInfo("Processing directory: %s\n", fileName);
stList *filesInDir = stFile_getFileNamesInDirectory(fileName);
for (int64_t i = 0; i < stList_length(filesInDir); i++) {
char *absChildFileName = stFile_pathJoin(fileName, stList_get(filesInDir, i));
assert(stFile_exists(absChildFileName));
setCompleteStatus(absChildFileName); //decide if the sequences in the file should be free or attached.
FILE *fileHandle = fopen(absChildFileName, "r");
fastaReadToFunction(fileHandle, processSequence);
fclose(fileHandle);
free(absChildFileName);
}
stList_destruct(filesInDir);
} else {
st_logInfo("Processing file: %s\n", fileName);
setCompleteStatus(fileName); //decide if the sequences in the file should be free or attached.
FILE *fileHandle = fopen(fileName, "r");
fastaReadToFunction(fileHandle, processSequence);
fclose(fileHandle);
}
(*j)++;
}
}
static void cactusEventTreeTestSetup() {
if(!nestedTest) {
cactusEventTreeTestTeardown();
cactusDisk = testCommon_getTemporaryCactusDisk();
flower = flower_construct(cactusDisk);
eventTree = eventTree_construct2(flower);
rootEvent = eventTree_getRootEvent(eventTree);
internalEvent = event_construct3("INTERNAL", 0.5, rootEvent, eventTree);
leafEvent1 = event_construct3("LEAF1", 0.2, internalEvent, eventTree);
leafEvent2 = event_construct3("LEAF2", 1.3, internalEvent, eventTree);
event_setOutgroupStatus(leafEvent1, 1);
}
}
