void CAMdataHandler::initialize(long size, int dType)
{
destroyData();
allocateData(size,dType);
setTypeFlag(dType);
temporaryFlag = 0;
}
Boolean List_destroyListAndData(List * list, void (*destroyData)(void * data))
{
ListNode * currentNode;
if(list == NULL)
return false;
destroyData(NULL);
while ((currentNode = detachFront(list)) != NULL) {
destroyData(currentNode->data);
if(!destroyNode(currentNode))
return false;
}
free(list);
return true;
}
void CThreadPoolJob::perform()
{
if (mPerformer)
{
mPerformer(mpJobData);
}
destroyData();
}
void CAMdataHandler::initialize()
{
destroyData();
dataType = 0;
dataPointer = 0;
dataSize = 0;
temporaryFlag = 0;
referenceCount = 0;
}
void destroyGame() {
destroyTimer();
destroyData();
inGame = 0;
pthread_mutex_destroy(&resourceMutex);
return;
}
static void destroySubTree(TreeNode * node, void (*destroyData)(void * data))
{
if(node == NULL)
return;
destroySubTree(node->left, destroyData);
destroySubTree(node->right, destroyData);
if(destroyData != NULL)
destroyData(node->data);
destroyNode(node);
}
bool DrawProfiler::loadSystemProperties() {
bool changed = false;
ProfileType newType = loadRequestedProfileType();
if (newType != mType) {
mType = newType;
if (mType == kNone) {
destroyData();
} else {
createData();
}
changed = true;
}
bool showDirty = property_get_bool(PROPERTY_DEBUG_SHOW_DIRTY_REGIONS, false);
if (showDirty != mShowDirtyRegions) {
mShowDirtyRegions = showDirty;
changed = true;
}
return changed;
}
void CAMdataHandler::initialize(const CAMdataHandler& A)
{
if(A.temporaryFlag == 1)
{
dataType = A.dataType;
dataSize = A.dataSize;
dataPointer = A.dataPointer;
temporaryFlag = 0;
}
else
{
destroyData();
allocateData(A.dataSize,A.dataType);
setTypeFlag(A.dataType);
copyData(A.dataSize,A.dataPointer);
temporaryFlag = 0;
}
}
bool FrameInfoVisualizer::consumeProperties() {
bool changed = false;
ProfileType newType = Properties::getProfileType();
if (newType != mType) {
mType = newType;
if (mType == ProfileType::None) {
destroyData();
} else {
createData();
}
changed = true;
}
bool showDirty = Properties::showDirtyRegions;
if (showDirty != mShowDirtyRegions) {
mShowDirtyRegions = showDirty;
changed = true;
}
return changed;
}
//
//********************************************************************************
// ASSIGNMENT
//********************************************************************************
//
CAMdataHandler& CAMdataHandler::operator =( const CAMdataHandler& A)
{
if(A.temporaryFlag == 1)
{
dataType = A.dataType;
dataSize = A.dataSize;
dataPointer = A.dataPointer;
temporaryFlag = 0;
referenceCount = 0;
}
else
{
destroyData();
allocateData(A.dataSize,A.dataType);
setTypeFlag(A.dataType);
copyData(A.dataSize,A.dataPointer);
temporaryFlag = 0;
referenceCount = 0;
}
return *this;
}
CollisionModel::~CollisionModel()
{
destroyData();
}
//
//********************************************************************************
// DESTRUCTOR
//********************************************************************************
//
CAMdataHandler::~CAMdataHandler()
{
if(temporaryFlag == 0) destroyData();
}
FrameInfoVisualizer::~FrameInfoVisualizer() {
destroyData();
}
int main(int argc, char* argv[]){
int a = 0, i = 0, j = 0, k = 0, l = 0, m = 0, n = 0, nN = 0, nK = 0;
int nNLen = 0, nKLen = 0;
t_Params tParams;
t_Data tSeqData, tRefData;
char *acTest = NULL;
int nTestMatch = -1, nTestLength = -1;
double dTest = 0.0;
int nParentD = 0;
int* anChi = NULL;
t_Result *atResult;
/*get command line params*/
getCommandLineParams(&tParams, argc, argv);
/*read sequences to chimera check*/
readData(tParams.szSeqInputFile, &tSeqData);
/*read sequences to compare too*/
readData(tParams.szRefInputFile, &tRefData);
/*set parameters for sequence distances*/
initLookUp(&tParams);
/*number of sequences*/
nN = tSeqData.nSeq;
/*number of reference sequences*/
nK = tRefData.nSeq;
atResult = (t_Result *) malloc(nN*sizeof(t_Result));
if(!atResult)
goto memoryError;
anChi = (int *) malloc(sizeof(int)*nN);
if(!anChi){
goto memoryError;
}
for(i = 0; i < nN; i++){
anChi[i] = FALSE;
atResult[i].dX = 0.0;
atResult[i].dY = 0.0;
atResult[i].dZ = 0.0;
atResult[i].dP = 0.0;
}
/*max length of sequences*/
nNLen = tSeqData.nMaxLen;
/*max length of references*/
nKLen = tRefData.nMaxLen;
sortByFreq(&tSeqData);
for(i = 0; i < nN; i++){
t_Align atAlign[nK];
double dBest = BIG_DBL, dBestChi = 0.0, dBestTri = 0.0;
int nBestJ = -1;
int nBest = BIG_INT, nBestChi = BIG_INT, nBestTri = BIG_INT;
int nSplit = -1, nSplit1 = -1, nSplit2 = -1, nP1 = -1, nP2 = -1, nT1 = -1, nT2 = -1, nT3 = -1;
int anRestrict[nK];
int nCompare = 0;
double dLoon = 0.0, dCIndex = 0.0, dP = 0.0, dR = 0.0;
int nI = tSeqData.anSort[i];
int nLenI = tSeqData.anLen[nI];
int anD[nLenI], anR[nLenI], anBestD[nLenI], anBestR[nLenI];
/*do pairwise alignments and get best hit for each sequence i*/
nCompare = alignAll(nI, nLenI, &nBest, &nBestJ, anRestrict, nK, &tSeqData, &tRefData, atAlign, &tParams, anChi);
if(nCompare >= 2){
nBestChi = getBestChimera(nK, &tRefData, &nP1, &nP2, &nSplit, anRestrict, nLenI, atAlign, anD, anR, anBestD, anBestR);
if(nBestChi >= 3 && nCompare >= 3){
nBestTri = getBestTrimera(nK, &tRefData, &nT1, &nT2, &nT3, &nSplit1, &nSplit2, anRestrict, nLenI, atAlign, anD, anR, anBestD, anBestR);
}
dBestChi = ((double) nBestChi)/((double) nLenI);
dBestTri = ((double) nBestTri)/((double) nLenI);
dBest = needlemanWunschN(&tSeqData.acSequences[nI*nNLen],&tRefData.acSequences[nBestJ*nKLen] , nLenI, tRefData.anLen[nBestJ], nKLen);
if(nBestChi - nBestTri >= 3){
nTestMatch = TRIMERA;
acTest = getTrimera(&nTestLength, &atAlign[nT1], &atAlign[nT2], &atAlign[nT3],nSplit1, nSplit2,nLenI);
/*Trimera*/
}
else{
/*Chimera*/
nTestMatch = CHIMERA;
acTest = getChimera(&nTestLength, &atAlign[nP1], &atAlign[nP2], nSplit, nLenI);
}
dTest = needlemanWunschN(&tSeqData.acSequences[nI*nNLen], acTest, nLenI, nTestLength, nKLen);
dCIndex = calcCIndex(nI, nP1, nP2, acTest, nTestLength, &tRefData, &tSeqData);
dLoon = calcLoonIndex(&tSeqData, &tRefData, nI, nP1, nP2, &nSplit, &nParentD, &tParams);
if(dCIndex >= 0.15 || dCIndex - dBest > 0.0){
dP = 0.0;
}
else{
dR = tParams.dAlpha + tParams.dBeta*dLoon;
dP = 1.0/(1.0 + exp(-dR));
}
if(dP > 0.5){
anChi[nI] = TRUE;
}
atResult[nI].dX = dCIndex;
atResult[nI].dY = dCIndex - dBest;
atResult[nI].dZ = dLoon;
atResult[nI].dP = dP;
switch(nTestMatch){
case GOOD:
//printf("Good\n");
break;
case CHIMERA:
//printf("Chimera\n");
break;
case TRIMERA:
//printf("Trimera\n");
break;
case QUAMERA:
//printf("Quamera\n");
break;
}
free(acTest);
}
else{
//printf("0 0 Null 0 0 0 Null Null 0.0 0.0 0.0 0.0 0 0 0 Null\n");
}
for(j = 0; j < nK; j++){
if(anRestrict[j] == FALSE){
free(atAlign[j].acA);
free(atAlign[j].acB);
free(atAlign[j].anD);
free(atAlign[j].anR);
free(atAlign[j].anMapD);
free(atAlign[j].anMapR);
}
}
}
for(i = 0; i < nN; i++){
printf("%s %f %f %f %f\n",tSeqData.aszID[i],atResult[i].dX, atResult[i].dY, atResult[i].dZ, atResult[i].dP);
}
/*free allocated memory*/
free(adLookUp);
free(anChi);
free(atResult);
destroyData(&tSeqData);
destroyData(&tRefData);
exit(EXIT_SUCCESS);
memoryError:
fprintf(stderr, "Failed allocating memory in main\n");
fflush(stderr);
exit(EXIT_FAILURE);
}
double calcLoonIndex(t_Data *ptSeqData, t_Data *ptRefData, int nI, int nP1, int nP2, int* pnSplit, int* pnParentD, t_Params *ptParams)
{
int i = 0, nLenI = ptSeqData->anLen[nI], nLenP1 = ptRefData->anLen[nP1], nLenP2 = ptRefData->anLen[nP2];
FILE *ofp = NULL;
char szCommand[MAX_LINE_LENGTH];
t_Data tAlign;
int nDiff1 = 0, anDiff1[MAX_DIFF + 1];
int nDiff2 = 0, anDiff2[MAX_DIFF + 1];
int anSplits[2*MAX_DIFF], s = 0, s1 = 0, s2 = 0;
int nSplit = -1, sMin = 0, nMinD = BIG_INT;
int anD[2*MAX_DIFF];
int nMaxLen = 0, nTLen = 0;
char* acSequences = NULL;
double dRet = 0;
char szTempFasta[MAX_LINE_LENGTH], szTempAlign[MAX_LINE_LENGTH];
int nTGap1 = 0, nTGap2 = 0, nTGap3 = 0,nMaxTGap = -1;
int nParentD = 0;
/*create sequence filenames*/
if(ptParams->bOutputAlignments == FALSE){
sprintf(szTempFasta, "Temp%s",FASTA_SUFFIX);
sprintf(szTempAlign, "Temp%s",ALIGN_SUFFIX);
}
else{
sprintf(szTempFasta, "Temp%d%s",nI,FASTA_SUFFIX);
sprintf(szTempAlign, "Temp%d%s",nI,ALIGN_SUFFIX);
}
/*write sequences*/
ofp = fopen(szTempFasta, "w");
if(ofp){
writeSequenceI(ofp, ptSeqData, nI);
writeSequenceI(ofp, ptRefData, nP1);
writeSequenceI(ofp, ptRefData, nP2);
fclose(ofp);
}
else{
fprintf(stderr, "Failed to open %s for writing ... abort\n",szTempFasta);
exit(EXIT_FAILURE);
}
/*run mafft remotely*/
sprintf(szCommand,"mafft-linsi %s > %s 2> %s",szTempFasta,szTempAlign, TEMP_ERROR_FILE);
system(szCommand);
/*read in mafft output - three sequence alignment*/
readData(szTempAlign, &tAlign);
acSequences = tAlign.acSequences; nMaxLen = tAlign.nMaxLen;
/*alignment length*/
nTLen = tAlign.nMaxLen;
/*find largest terminal gap*/
while(acSequences[nTLen - 1 - nTGap1] == GAP && nTLen - nTGap1> 1){
nTGap1++;
}
while(acSequences[nMaxLen + nTLen - 1 - nTGap2] == GAP && nTLen - nTGap2> 1){
nTGap2++;
}
while(acSequences[2*nMaxLen + nTLen - 1 - nTGap3] == GAP && nTLen - nTGap3> 1){
nTGap3++;
}
nMaxTGap = nTGap1 > nTGap2 ? nTGap1 : nTGap2;
nMaxTGap = nTGap3 > nMaxTGap ? nTGap3 : nMaxTGap;
/*remove from alignment*/
nTLen -= nMaxTGap;
/*find all differences between chimera and parents and positions*/
for(i = 0; i < nTLen; i++){
if(acSequences[i] != acSequences[nMaxLen + i]){
if(nDiff1 < MAX_DIFF){
anDiff1[nDiff1] = i;
nDiff1++;
}
else{
fprintf(stderr,"Max diff reached in calcLoon\n");
}
}
if(acSequences[i] != acSequences[2*nMaxLen + i]){
if(nDiff2 < MAX_DIFF){
anDiff2[nDiff2] = i;
nDiff2++;
}
else{
fprintf(stderr,"Max diff reached in calcLoon\n");
}
}
}
for(i = 0; i < nTLen; i++){
if(acSequences[nMaxLen + i] != acSequences[2*nMaxLen + i]){
nParentD++;
}
}
anDiff1[nDiff1] = nTLen;
anDiff2[nDiff2] = nTLen;
s = 0; s1 = 0; s2 = 0;
anSplits[s] = -1;
anD[s] = nDiff2;
s++;
/*loop differences to find optimal split point*/
while(s1 < nDiff1 || s2 < nDiff2){
if(anDiff1[s1] <= anDiff2[s2]){
anD[s] = anD[s - 1] + 1;
anSplits[s] = anDiff1[s1];
s++;
s1++;
}
else if(anDiff1[s1] > anDiff2[s2]){
anD[s] = anD[s - 1] - 1;
anSplits[s] = anDiff2[s2];
s++;
s2++;
}
}
for(i = 0; i < s; i++){
if(anD[i] < nMinD){
nMinD = anD[i];
sMin = i;
}
}
if(sMin < s - 1){
nSplit = (anSplits[sMin] + anSplits[sMin + 1])/2;
}
else{
nSplit = nTLen - 1;
}
/*dummy if, as we always do this*/
if(TRUE){
int nA = -1, nB = -1;
int nDLP1 = 0, nDRP1 = 0, nDLP2 = 0, nDRP2 = 0;
int nX = 0, nY = 0, nZ = 0, nXZ = 0;
int nXA = 0, nXB = 0, nYA = 0, nYB = 0;
char cC = '\0';
double pA = 0.0, pB = 0.0;
double dP = 0.0;
for(i = 0; i < nTLen; i++){
char cI = acSequences[i], cP1 = acSequences[nMaxLen + i], cP2 = acSequences[2*nMaxLen + i];
/*get consenus base*/
cC = getC(cI, cP1, cP2);
/*count number of differences between chimera and consensus*/
if(cI != cC){
nZ++;
}
/*count number of differences between chimera and parent 1*/
if(cP1 != cC){
/*count number to left*/
if(i <= nSplit){
nDLP1++;
}
/*count number to right*/
else{
nDRP1++;
}
}
/*count number of differences between chimera and parent 2*/
if(cP2 != cC){
if(i <= nSplit){
nDLP2++;
}
else{
nDRP2++;
}
}
}
/*if Parent1 is left*/
if(nDiff1 <= nDiff2){
nA = nP1;
nB = nP2;
nX = nDLP1 + nDRP1;
nXA = nDLP1; nXB = nDRP1;
nY = nDLP2 + nDRP2;
nYA = nDLP2; nYB = nDRP2;
pA = ((double) nSplit + 1)/((double) nTLen); /*probability of change to left*/
pB = ((double) nTLen - nSplit - 1)/((double) nTLen);/*prob. to right*/
}
else{
/*if parent 1 is right*/
nA = nP2;
nB = nP1;
nX = nDLP2 + nDRP2;
nXA = nDRP2; nXB = nDLP2;
nY = nDLP1 + nDRP1;
nYA = nDRP1; nYB = nDLP1;
pB = ((double) nSplit + 1)/((double) nTLen);
pA = ((double) nTLen - nSplit - 1)/((double) nTLen);
}
nXZ = nX + nZ;
dRet = 0.0;
dP = 0.0;
/*adds extra factor for tree imbalance - not generally used*/
if(ptParams->bImbalance){
if(nXZ > 0){
for(i = nX; i <= nXZ; i++){
dP += gsl_ran_binomial_pdf (i, 0.5, nXZ);
}
dRet += -log(dP);
}
}
/*contribution from right parent*/
if(nY > 0){
dP = 0.0;
for(i = nYA; i <= nY; i++){
dP += gsl_ran_binomial_pdf(i, pA, nY);
}
dRet += -log(dP);
}
/*contribution from left*/
if(nX > 0){
dP = 0.0;
for(i = nXB; i <= nX; i++){
dP += gsl_ran_binomial_pdf(i, pB, nX);
}
dRet += -log(dP);
}
}
(*pnSplit) = nSplit;
(*pnParentD) = nParentD;
/*free up memory*/
destroyData(&tAlign);
return dRet;
}
DrawProfiler::~DrawProfiler() {
destroyData();
}
int driver(const char* szFileStub, int nKStart, int nLMin, unsigned long lSeed, int nMaxIter, double dEpsilon, int bCOut)
{
t_Params tParams;
t_Data tData;
gsl_rng *ptGSLRNG = NULL;
const gsl_rng_type *ptGSLRNGType = NULL;
int i = 0, k = 0, nD = 0, nN = 0;
char szOFile[MAX_FILE_NAME_LENGTH];
FILE *ofp = NULL;
t_VBParams tVBParams;
t_Cluster *ptBestCluster = NULL;
gsl_matrix *ptTemp = NULL;
gsl_matrix *ptTVar = NULL;
/*initialise GSL RNG*/
gsl_rng_env_setup();
gsl_set_error_handler_off();
ptGSLRNGType = gsl_rng_default;
ptGSLRNG = gsl_rng_alloc(ptGSLRNGType);
/*get command line params*/
tParams.nKStart = nKStart;
tParams.nLMin = nLMin;
tParams.nMaxIter = nMaxIter;
tParams.dEpsilon = dEpsilon;
tParams.lSeed = lSeed;
setParams(&tParams,szFileStub);
/*read in input data*/
readInputData(tParams.szInputFile, &tData);
readPInputData(tParams.szPInputFile, &tData);
nD = tData.nD;
nN = tData.nN;
ptTemp = gsl_matrix_alloc(tData.nT,nD);
ptTVar = gsl_matrix_alloc(tData.nT,tData.nT);
setVBParams(&tVBParams, &tData);
ptBestCluster = (t_Cluster *) malloc(sizeof(t_Cluster));
ptBestCluster->nN = nN;
ptBestCluster->nK = tParams.nKStart;
ptBestCluster->nD = nD;
ptBestCluster->ptData = &tData;
ptBestCluster->ptVBParams = &tVBParams;
ptBestCluster->lSeed = tParams.lSeed;
ptBestCluster->nMaxIter = tParams.nMaxIter;
ptBestCluster->dEpsilon = tParams.dEpsilon;
if(bCOut > 0){
ptBestCluster->szCOutFile = szFileStub;
}
else{
ptBestCluster->szCOutFile = NULL;
}
runRThreads((void *) &ptBestCluster);
compressCluster(ptBestCluster);
calcCovarMatrices(ptBestCluster,&tData);
sprintf(szOFile,"%sclustering_gt%d.csv",tParams.szOutFileStub,tParams.nLMin);
writeClusters(szOFile,ptBestCluster,&tData);
sprintf(szOFile,"%spca_means_gt%d.csv",tParams.szOutFileStub,tParams.nLMin);
writeMeans(szOFile,ptBestCluster);
sprintf(szOFile,"%smeans_gt%d.csv",tParams.szOutFileStub,tParams.nLMin);
writeTMeans(szOFile,ptBestCluster,&tData);
for(k = 0; k < ptBestCluster->nK; k++){
sprintf(szOFile,"%spca_variances_gt%d_dim%d.csv",tParams.szOutFileStub,tParams.nLMin,k);
writeSquareMatrix(szOFile, ptBestCluster->aptSigma[k], nD);
/*not entirely sure this is correct?*/
gsl_blas_dgemm (CblasNoTrans,CblasNoTrans,1.0,tData.ptTMatrix,ptBestCluster->aptSigma[k],0.0,ptTemp);
gsl_blas_dgemm (CblasNoTrans,CblasTrans,1.0,ptTemp,tData.ptTMatrix,0.0,ptTVar);
sprintf(szOFile,"%svariances_gt%d_dim%d.csv",tParams.szOutFileStub,tParams.nLMin,k);
writeSquareMatrix(szOFile, ptTVar, nD);
}
sprintf(szOFile,"%sresponsibilities.csv",tParams.szOutFileStub);
ofp = fopen(szOFile,"w");
if(ofp){
for(i = 0; i < nN; i++){
for(k = 0; k < ptBestCluster->nK - 1; k++){
fprintf(ofp,"%f,",ptBestCluster->aadZ[i][k]);
}
fprintf(ofp,"%f\n",ptBestCluster->aadZ[i][ptBestCluster->nK - 1]);
}
fclose(ofp);
}
else{
fprintf(stderr,"Failed openining %s in main\n", szOFile);
fflush(stderr);
}
sprintf(szOFile,"%svbl.csv",tParams.szOutFileStub);
ofp = fopen(szOFile,"w");
if(ofp){
fprintf(ofp,"%d,%f,%d\n",ptBestCluster->nK,ptBestCluster->dVBL,ptBestCluster->nThread);
fclose(ofp);
}
else{
fprintf(stderr,"Failed openining %s in main\n", szOFile);
fflush(stderr);
}
/*free up memory in data object*/
destroyData(&tData);
/*free up best BIC clusters*/
destroyCluster(ptBestCluster);
free(ptBestCluster);
destroyParams(&tParams);
gsl_rng_free(ptGSLRNG);
gsl_matrix_free(tVBParams.ptInvW0);
gsl_matrix_free(ptTemp);
gsl_matrix_free(ptTVar);
return EXIT_SUCCESS;
}