void test_2_create_tree_and_insert_root_with_int_data(){
Iterator* iterator;int result;
Tree tree = createTree(compareInt);
result = insertNode(&tree, NULL, &data[0]);
iterator = getChildren(&tree, &data[0]);
ASSERT(NULL == iterator->next(iterator));
ASSERT(result == 1);
DisposeTree((List*)(tree.root));
};
void DisposeTree(List *list){
TreeNode* temp;
Iterator it = getIterator(list);
while(it.hasNext(&it)){
temp = it.next(&it);
if(NULL != temp->children->head){
DisposeTree(temp->children);
}
dispose(temp->children);
}
}
int main(int argc, char **argv)
{
int i, j, k, treeNo, sumLength;
char ch;
TTree **treeSet;
FILE *text_fv;
clock_t totalStart;
double totalSecs, scale, sum;
char *ancestor;
totalStart = clock();
ReadParams(argc, argv);
if (rateHetero == CodonRates && invariableSites) {
fprintf(stderr, "Invariable sites model cannot be used with codon rate heterogeneity.\n");
exit(4);
}
if (writeAncestors && fileFormat == NEXUSFormat) {
fprintf(stderr, "Warning - When writing ancestral sequences, relaxed PHYLIP format is used.\n");
}
if (writeAncestors && maxPartitions > 1) {
fprintf(stderr, "Writing ancestral sequences can only be used for a single partition.\n");
exit(4);
}
if (!userSeed)
randomSeed = CreateSeed();
SetSeed(randomSeed);
if (!quiet)
PrintTitle();
numTrees = OpenTreeFile();
/* if (!treeFile) { */
ReadFileParams();
/*} */
if ((ancestorSeq>0 && !hasAlignment) || ancestorSeq>numSequences) {
fprintf(stderr, "Bad ancestral sequence number: %d (%d sequences loaded)\n", ancestorSeq, numSequences);
exit(4);
}
if (textFile) {
if ( (text_fv=fopen(textFileName, "rt"))==NULL ) {
fprintf(stderr, "Error opening text file for insertion into output: '%s'\n", textFileName);
exit(4);
}
}
ancestor=NULL;
if (hasAlignment) {
AllocateMemory();
ReadFile();
if (numSites<0)
numSites=numAlignmentSites;
if (ancestorSeq>0) {
if (numSites!=numAlignmentSites) {
fprintf(stderr, "Ancestral sequence is of a different length to the simulated sequences (%d)\n", numAlignmentSites);
exit(4);
}
ancestor=sequences[ancestorSeq-1];
}
} else if (numSites<0)
numSites=1000;
SetModel(model);
numTaxa=-1;
scale=1.0;
treeSet = (TTree **)malloc(sizeof(TTree **) * maxPartitions);
if (treeSet==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
partitionLengths = (int *)malloc(sizeof(int) * maxPartitions);
if (partitionLengths==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
partitionRates = (double *)malloc(sizeof(double) * maxPartitions);
if (partitionRates==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
for (i = 0; i < maxPartitions; i++) {
if ((treeSet[i]=NewTree())==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
}
CreateRates();
treeNo=0;
do {
partitionLengths[0] = -1;
ReadTree(tree_fv, treeSet[0], treeNo+1, 0, NULL, &partitionLengths[0], &partitionRates[0]);
if (treeNo==0) {
numTaxa=treeSet[0]->numTips;
if (!quiet)
fprintf(stderr, "Random number generator seed: %ld\n\n", randomSeed);
if (fileFormat == NEXUSFormat) {
fprintf(stdout, "#NEXUS\n");
fprintf(stdout, "[\nGenerated by %s %s\n\n", PROGRAM_NAME, VERSION_NUMBER);
PrintVerbose(stdout);
fprintf(stdout, "]\n\n");
}
} else if (treeSet[0]->numTips != numTaxa) {
fprintf(stderr, "All trees must have the same number of tips.\n");
exit(4);
}
if (maxPartitions == 1) {
if (partitionLengths[0] != -1) {
fprintf(stderr, "\nWARNING: The treefile contained partion lengths but only one partition\n");
fprintf(stderr, "was specified.\n");
}
partitionLengths[0] = numSites;
}
sumLength = partitionLengths[0];
i = 1;
while (sumLength < numSites && i <= maxPartitions) {
if (!IsTreeAvail(tree_fv)) {
fprintf(stderr, "\nA set of trees number %d had less partition length (%d) than\n", treeNo + 1, sumLength);
fprintf(stderr, "was required to make a sequence of length %d.\n", numSites);
exit(4);
}
ReadTree(tree_fv, treeSet[i], treeNo+1, treeSet[0]->numTips, treeSet[0]->names,
&partitionLengths[i], &partitionRates[i]);
if (treeSet[i]->numTips != numTaxa) {
fprintf(stderr, "All trees must have the same number of tips.\n");
exit(4);
}
sumLength += partitionLengths[i];
i++;
}
if (i > maxPartitions) {
fprintf(stderr, "\nA set of trees number %d had more partitions (%d) than\n", treeNo + 1, i);
fprintf(stderr, "was specified in the user options (%d).\n", maxPartitions);
}
numPartitions = i;
if (sumLength != numSites) {
fprintf(stderr, "The sum of the partition lengths in the treefile does not equal\n");
fprintf(stderr, "the specified number of sites.\n");
exit(4);
}
for (i = 0; i < numPartitions; i++)
CreateSequences(treeSet[i], partitionLengths[i]);
if (numPartitions > 1) {
sum = 0.0;
for (i = 0; i < numPartitions; i++)
sum += partitionRates[i] * partitionLengths[i];
for (i = 0; i < numPartitions; i++)
partitionRates[i] *= numSites / sum;
}
if (treeNo==0 && verbose && !quiet) {
PrintVerbose(stderr);
InitProgressBar(numTrees*numDatasets);
DrawProgressBar();
}
for (i=0; i<numDatasets; i++) {
SetCategories();
k = 0;
for (j = 0; j < numPartitions; j++) {
scale = partitionRates[j];
if (scaleTrees) {
if (!treeSet[j]->rooted) {
fprintf(stderr, "To scale tree length, they must be rooted and ultrametric.\n");
exit(4);
}
scale *= treeScale/treeSet[j]->totalLength;
} else if (scaleBranches)
scale *= branchScale;
EvolveSequences(treeSet[j], k, partitionLengths[j], scale, ancestor);
k += partitionLengths[j];
}
if (writeAncestors)
WriteAncestralSequences(stdout, treeSet[0]);
else
WriteSequences(stdout, (numTrees > 1 ? treeNo+1 : -1), (numDatasets > 1 ? i+1 : -1), treeSet, partitionLengths);
if (writeRates) {
WriteRates(stderr);
}
if (textFile) {
while (!feof(text_fv)) {
ch = fgetc(text_fv);
if (!feof(text_fv))
fputc(ch, stdout);
}
fputc('\n', stdout);
rewind(text_fv);
}
if (verbose && !quiet)
ProgressBar();
}
for (i = 0; i < numPartitions; i++)
DisposeTree(treeSet[i]);
treeNo++;
} while (IsTreeAvail(tree_fv));
/* for (i = 0; i < maxPartitions; i++)
FreeTree(treeSet[i]); */
if (treeFile)
fclose(tree_fv);
if (textFile)
fclose(text_fv);
totalSecs = (double)(clock() - totalStart) / CLOCKS_PER_SEC;
if (!quiet) {
fprintf(stderr, "Time taken: %G seconds\n", totalSecs);
if (verboseMemory)
fprintf(stderr, "Total memory used: %ld\n", totalMem);
}
return 0;
}
void tearDown(){
DisposeTree((List*)(tree.root));
}
