//---Preorder
void Skeleton::printJoint(Joint& joint, int depth) {
string logOutput = "";
for (int i = 0; i < depth; i++) {
logOutput += "\t";
}
logOutput += joint.getName();
logOutput += "\n";
for (int i = 0; i < depth; i++) {
logOutput += "\t";
}
logDEBUG("%s(%d,%d,%d)",logOutput.c_str());
vector<string> childrenJointsNames = joint.getChildrenJointsNames();
for (unsigned int i = 0; i < childrenJointsNames.size(); i++) {
printJoint(getJoint(childrenJointsNames.at(i)), depth + 1);
}
}
void Skeleton::print() {
printJoint(getRootJoint());
}
static PyObject *msaomes(PyObject *self, PyObject *args, PyObject *kwargs) {
PyArrayObject *msa, *omes;
int ambiguity = 1, turbo = 1, debug = 0;
static char *kwlist[] = {"msa", "omes",
"ambiguity", "turbo", "debug", NULL};
if (!PyArg_ParseTupleAndKeywords(args, kwargs, "OO|iii", kwlist,
&msa, &omes,
&ambiguity, &turbo, &debug))
return NULL;
/* make sure to have a contiguous and well-behaved array */
msa = PyArray_GETCONTIGUOUS(msa);
/* check dimensions */
long number = PyArray_DIMS(msa)[0], length = PyArray_DIMS(msa)[1];
/* get pointers to data */
char *seq = (char *) PyArray_DATA(msa); /*size: number x length */
double *data = (double *) PyArray_DATA(omes);
long i, j;
/* allocate memory */
unsigned char *iseq = malloc(number * sizeof(unsigned char));
if (!iseq)
return PyErr_NoMemory();
/* hold transpose of the sorted character array */
unsigned char **trans = malloc(length * sizeof(unsigned char *));
if (!trans) {
turbo = 0;
}
if (turbo) {
/* allocate rows that will store columns of MSA */
trans[0] = iseq;
for (i = 1; i < length; i++) {
trans[i] = malloc(number * sizeof(unsigned char));
if (!trans[i]) {
for (j = 1; j < i; j++)
free(trans[j]);
free(trans);
turbo = 0;
}
}
}
unsigned char *jseq = iseq; /* so that we don't get uninitialized warning*/
/* length*27, a row for each column in the MSA */
double **probs = malloc(length * sizeof(double *)), *prow;
if (!probs) {
if (turbo)
for (j = 1; j < length; j++)
free(trans[j]);
free(trans);
free(iseq);
return PyErr_NoMemory();
}
/* 27x27, alphabet characters and a gap*/
double **joint = malloc(NUMCHARS * sizeof(double *)), *jrow;
if (!joint) {
if (turbo)
for (j = 1; j < length; j++)
free(trans[j]);
free(trans);
free(iseq);
free(probs);
return PyErr_NoMemory();
}
for (i = 0; i < length; i++) {
prow = malloc(NUMCHARS * sizeof(double));
if (!prow) {
for (j = 0; j < i; j++)
free(probs[j]);
free(probs);
free(joint);
if (turbo)
for (j = 1; j < length; j++)
free(trans[j]);
free(trans);
free(iseq);
return PyErr_NoMemory();
}
probs[i] = prow;
for (j = 0; j < NUMCHARS; j++)
prow[j] = 0;
}
for (i = 0; i < NUMCHARS; i++) {
joint[i] = malloc(NUMCHARS * sizeof(double));
if (!joint[i]) {
for (j = 0; j < i; j++)
free(joint[j]);
free(joint);
for (j = 0; j < length; j++)
free(probs[j]);
free(probs);
if (turbo)
for (j = 1; j < length; j++)
free(trans[j]);
free(trans);
free(iseq);
return PyErr_NoMemory();
}
}
if (debug)
printProbs(probs, length);
unsigned char a, b;
long k, l, diff, offset;
double p_incr = 1. / number;
double prb = 0;
prow = probs[0];
/* START OMES calculation */
/* calculate first row of OMES matrix and all column probabilities */
i = 0;
data[0] = 0;
for (j = 1; j < length; j++) {
data[j * length + j] = 0; /* using empty, so needed for diagonal */
jrow = probs[j];
zeroJoint(joint);
diff = j - 1;
if (turbo) /* in turbo mode, there is a row for refined sequences */
jseq = trans[j];
for (k = 0; k < number; k++) {
offset = k * length;
if (diff) {
a = iseq[k];
} else {
a = (unsigned char) seq[offset + i];
if (a > 90)
a -= 96;
else
a -= 64;
if (a < 1 || a > 26)
a = 0; /* gap character */
iseq[k] = a;
prow[a] += p_incr;
}
b = (unsigned char) seq[offset + j];
if (b > 90)
b -= 96;
else
b -= 64;
if (b < 1 || b > 26)
b = 0; /* gap character */
if (turbo) /* we keep the refined chars for all sequences*/
jseq[k] = b;
joint[a][b] += p_incr;
jrow[b] += p_incr;
}
if (ambiguity) {
if (debug)
printProbs(probs, length);
if (diff)
k = j;
else
k = 0;
for (; k <= j; k++) {
prow = probs[k];
prb = prow[2];
if (prb > 0) { /* B -> D, N */
prb = prb / 2.;
prow[4] += prb;
prow[14] += prb;
prow[2] = 0;
}
prb = prow[10];
if (prb > 0) { /* J -> I, L */
prb = prb / 2.;
prow[9] += prb;
prow[12] += prb;
prow[10] = 0;
}
prb = prow[26];
if (prb > 0) { /* Z -> E, Q */
prb = prb / 2.;
prow[5] += prb;
prow[17] += prb;
prow[26] = 0;
}
if (prow[24] > 0) { /* X -> 20 AA */
prb = prow[24] / 20.;
for (l = 0; l < 20; l++)
prow[twenty[l]] += prb;
prow[24] = 0;
}
}
if (debug)
printProbs(probs, length);
if (debug)
printJoint(joint, i, j);
sortJoint(joint);
if (debug)
printJoint(joint, i, j);
}
data[j] = data[length * j] = calcOMES(joint, probs, i, j, number);
}
if (debug)
printProbs(probs, length);
if (turbo)
free(iseq);
/* calculate rest of OMES matrix */
long ioffset;
for (i = 1; i < length; i++) {
ioffset = i * length;
if (turbo)
iseq = trans[i];
for (j = i + 1; j < length; j++) {
zeroJoint(joint);
if (turbo) {
jseq = trans[j];
for (k = 0; k < number; k++)
joint[iseq[k]][jseq[k]] += p_incr;
} else {
diff = j - i - 1;
for (k = 0; k < number; k++) {
offset = k * length;
if (diff) {
a = iseq[k];
} else {
a = (unsigned char) seq[offset + i];
if (a > 90)
a -= 96;
else
a -= 64;
if (a < 1 || a > 26)
a = 0; /* gap character */
iseq[k] = a;
}
b = (unsigned char) seq[offset + j];
if (b > 90)
b -= 96;
else
b -= 64;
if (b < 1 || b > 26)
b = 0; /* gap character */
joint[a][b] += p_incr;
}
}
if (ambiguity)
sortJoint(joint);
data[ioffset + j] = data[i + length * j] =
calcOMES(joint, probs, i, j, number);
}
}
/* free memory */
for (i = 0; i < length; i++){
free(probs[i]);
}
free(probs);
for (i = 0; i < NUMCHARS; i++){
free(joint[i]);
}
free(joint);
if (turbo)
for (j = 1; j < length; j++)
free(trans[j]);
free(trans);
return Py_BuildValue("O", omes);
}