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tab-justify code
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@bqminh
bqminh committed Feb 1, 2016
1 parent 4c2ac94 commit 0b509e5
Showing 1 changed file with 142 additions and 142 deletions.
284 changes: 142 additions & 142 deletions quartet.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1779,161 +1779,161 @@ void PhyloTree::computeQuartetLikelihoods(vector<QuartetInfo> &quartet_info) {
delete quartet_tree;
delete quartet_aln;

// determine likelihood order
int qworder[3]; // local (thread-safe) vector for sorting

if (quartet_info[qid].logl[0] > quartet_info[qid].logl[1]) {
if(quartet_info[qid].logl[2] > quartet_info[qid].logl[0]) {
qworder[0] = 2;
qworder[1] = 0;
qworder[2] = 1;
} else if (quartet_info[qid].logl[2] < quartet_info[qid].logl[1]) {
qworder[0] = 0;
qworder[1] = 1;
qworder[2] = 2;
} else {
qworder[0] = 0;
qworder[1] = 2;
qworder[2] = 1;
}
} else {
if(quartet_info[qid].logl[2] > quartet_info[qid].logl[1]) {
qworder[0] = 2;
qworder[1] = 1;
qworder[2] = 0;
} else if (quartet_info[qid].logl[2] < quartet_info[qid].logl[0]) {
qworder[0] = 1;
qworder[1] = 0;
qworder[2] = 2;
} else {
qworder[0] = 1;
qworder[1] = 2;
qworder[2] = 0;
}
}
// determine likelihood order
int qworder[3]; // local (thread-safe) vector for sorting

if (quartet_info[qid].logl[0] > quartet_info[qid].logl[1]) {
if(quartet_info[qid].logl[2] > quartet_info[qid].logl[0]) {
qworder[0] = 2;
qworder[1] = 0;
qworder[2] = 1;
} else if (quartet_info[qid].logl[2] < quartet_info[qid].logl[1]) {
qworder[0] = 0;
qworder[1] = 1;
qworder[2] = 2;
} else {
qworder[0] = 0;
qworder[1] = 2;
qworder[2] = 1;
}
} else {
if(quartet_info[qid].logl[2] > quartet_info[qid].logl[1]) {
qworder[0] = 2;
qworder[1] = 1;
qworder[2] = 0;
} else if (quartet_info[qid].logl[2] < quartet_info[qid].logl[0]) {
qworder[0] = 1;
qworder[1] = 0;
qworder[2] = 2;
} else {
qworder[0] = 1;
qworder[1] = 2;
qworder[2] = 0;
}
}

// compute Bayesian weights
double temp;
// compute Bayesian weights
double temp;

quartet_info[qid].qweight[0] = quartet_info[qid].logl[0];
quartet_info[qid].qweight[1] = quartet_info[qid].logl[1];
quartet_info[qid].qweight[2] = quartet_info[qid].logl[2];
quartet_info[qid].qweight[0] = quartet_info[qid].logl[0];
quartet_info[qid].qweight[1] = quartet_info[qid].logl[1];
quartet_info[qid].qweight[2] = quartet_info[qid].logl[2];

temp = quartet_info[qid].qweight[qworder[1]]-quartet_info[qid].qweight[qworder[0]];
if(temp < -TP_MAX_EXP_DIFF) /* possible, since 1.0+exp(>36) == 1.0 */
quartet_info[qid].qweight[qworder[1]] = 0.0;
else
quartet_info[qid].qweight[qworder[1]] = exp(temp);
temp = quartet_info[qid].qweight[qworder[1]]-quartet_info[qid].qweight[qworder[0]];
if(temp < -TP_MAX_EXP_DIFF) /* possible, since 1.0+exp(>36) == 1.0 */
quartet_info[qid].qweight[qworder[1]] = 0.0;
else
quartet_info[qid].qweight[qworder[1]] = exp(temp);

temp = quartet_info[qid].qweight[qworder[2]]-quartet_info[qid].qweight[qworder[0]];
if(temp < -TP_MAX_EXP_DIFF) /* possible, since 1.0+exp(>36) == 1.0 */
quartet_info[qid].qweight[qworder[2]] = 0.0;
else
quartet_info[qid].qweight[qworder[2]] = exp(temp);
temp = quartet_info[qid].qweight[qworder[2]]-quartet_info[qid].qweight[qworder[0]];
if(temp < -TP_MAX_EXP_DIFF) /* possible, since 1.0+exp(>36) == 1.0 */
quartet_info[qid].qweight[qworder[2]] = 0.0;
else
quartet_info[qid].qweight[qworder[2]] = exp(temp);

quartet_info[qid].qweight[qworder[0]] = 1.0;
quartet_info[qid].qweight[qworder[0]] = 1.0;

temp = quartet_info[qid].qweight[0] + quartet_info[qid].qweight[1] + quartet_info[qid].qweight[2];
quartet_info[qid].qweight[0] = quartet_info[qid].qweight[0]/temp;
quartet_info[qid].qweight[1] = quartet_info[qid].qweight[1]/temp;
quartet_info[qid].qweight[2] = quartet_info[qid].qweight[2]/temp;
temp = quartet_info[qid].qweight[0] + quartet_info[qid].qweight[1] + quartet_info[qid].qweight[2];
quartet_info[qid].qweight[0] = quartet_info[qid].qweight[0]/temp;
quartet_info[qid].qweight[1] = quartet_info[qid].qweight[1]/temp;
quartet_info[qid].qweight[2] = quartet_info[qid].qweight[2]/temp;

// determine which of the three corners (only meaningful if seqIDs NOT sorted)
if (treebits[qworder[0]] == 1) {
quartet_info[qid].corner=0;
} else {
if (treebits[qworder[0]] == 2) {
quartet_info[qid].corner=1;
} else {
quartet_info[qid].corner=2;
}
}

// determine which of the 7 regions (only meaningful if seqIDs NOT sorted)
double temp1, temp2, temp3;
unsigned char discreteweight[3];
double sqdiff[3];

/* 100 distribution */
temp1 = 1.0 - quartet_info[qid].qweight[qworder[0]];
sqdiff[0] = temp1*temp1 +
quartet_info[qid].qweight[qworder[1]]*quartet_info[qid].qweight[qworder[1]] +
quartet_info[qid].qweight[qworder[2]]*quartet_info[qid].qweight[qworder[2]];
discreteweight[0] = treebits[qworder[0]];

/* 110 distribution */
temp1 = 0.5 - quartet_info[qid].qweight[qworder[0]];
temp2 = 0.5 - quartet_info[qid].qweight[qworder[1]];
sqdiff[1] = temp1*temp1 + temp2*temp2 +
quartet_info[qid].qweight[qworder[2]]*quartet_info[qid].qweight[qworder[2]];
discreteweight[1] = treebits[qworder[0]] + treebits[qworder[1]];

/* 111 distribution */
temp1 = onethird - quartet_info[qid].qweight[qworder[0]];
temp2 = onethird - quartet_info[qid].qweight[qworder[1]];
temp3 = onethird - quartet_info[qid].qweight[qworder[2]];
sqdiff[2] = temp1 * temp1 + temp2 * temp2 + temp3 * temp3;
discreteweight[2] = (unsigned char) 7;
// determine which of the three corners (only meaningful if seqIDs NOT sorted)
if (treebits[qworder[0]] == 1) {
quartet_info[qid].corner=0;
} else {
if (treebits[qworder[0]] == 2) {
quartet_info[qid].corner=1;
} else {
quartet_info[qid].corner=2;
}
}

/* sort in descending order */
int sqorder[3]; // local (thread-safe) vector for sorting
if (sqdiff[0] > sqdiff[1]) {
if(sqdiff[2] > sqdiff[0]) {
sqorder[0] = 2;
sqorder[1] = 0;
sqorder[2] = 1;
} else if (sqdiff[2] < sqdiff[1]) {
sqorder[0] = 0;
sqorder[1] = 1;
sqorder[2] = 2;
} else {
sqorder[0] = 0;
sqorder[1] = 2;
sqorder[2] = 1;
}
} else {
if(sqdiff[2] > sqdiff[1]) {
sqorder[0] = 2;
sqorder[1] = 1;
sqorder[2] = 0;
} else if (sqdiff[2] < sqdiff[0]) {
sqorder[0] = 1;
sqorder[1] = 0;
sqorder[2] = 2;
} else {
sqorder[0] = 1;
sqorder[1] = 2;
sqorder[2] = 0;
}
}
// determine which of the 7 regions (only meaningful if seqIDs NOT sorted)
double temp1, temp2, temp3;
unsigned char discreteweight[3];
double sqdiff[3];

/* 100 distribution */
temp1 = 1.0 - quartet_info[qid].qweight[qworder[0]];
sqdiff[0] = temp1*temp1 +
quartet_info[qid].qweight[qworder[1]]*quartet_info[qid].qweight[qworder[1]] +
quartet_info[qid].qweight[qworder[2]]*quartet_info[qid].qweight[qworder[2]];
discreteweight[0] = treebits[qworder[0]];

/* 110 distribution */
temp1 = 0.5 - quartet_info[qid].qweight[qworder[0]];
temp2 = 0.5 - quartet_info[qid].qweight[qworder[1]];
sqdiff[1] = temp1*temp1 + temp2*temp2 +
quartet_info[qid].qweight[qworder[2]]*quartet_info[qid].qweight[qworder[2]];
discreteweight[1] = treebits[qworder[0]] + treebits[qworder[1]];

/* 111 distribution */
temp1 = onethird - quartet_info[qid].qweight[qworder[0]];
temp2 = onethird - quartet_info[qid].qweight[qworder[1]];
temp3 = onethird - quartet_info[qid].qweight[qworder[2]];
sqdiff[2] = temp1 * temp1 + temp2 * temp2 + temp3 * temp3;
discreteweight[2] = (unsigned char) 7;

/* sort in descending order */
int sqorder[3]; // local (thread-safe) vector for sorting
if (sqdiff[0] > sqdiff[1]) {
if(sqdiff[2] > sqdiff[0]) {
sqorder[0] = 2;
sqorder[1] = 0;
sqorder[2] = 1;
} else if (sqdiff[2] < sqdiff[1]) {
sqorder[0] = 0;
sqorder[1] = 1;
sqorder[2] = 2;
} else {
sqorder[0] = 0;
sqorder[1] = 2;
sqorder[2] = 1;
}
} else {
if(sqdiff[2] > sqdiff[1]) {
sqorder[0] = 2;
sqorder[1] = 1;
sqorder[2] = 0;
} else if (sqdiff[2] < sqdiff[0]) {
sqorder[0] = 1;
sqorder[1] = 0;
sqorder[2] = 2;
} else {
sqorder[0] = 1;
sqorder[1] = 2;
sqorder[2] = 0;
}
}


// determine which of the 7 regions (only meaningful if seqIDs NOT sorted)
unsigned char qpbranching = (unsigned char) discreteweight[sqorder[2]];
// determine which of the 7 regions (only meaningful if seqIDs NOT sorted)
unsigned char qpbranching = (unsigned char) discreteweight[sqorder[2]];

if (qpbranching == 1) {
quartet_info[qid].area=0; // LM_REG1 - top
}
if (qpbranching == 2) {
quartet_info[qid].area=1; // LM_REG2 - right
}
if (qpbranching == 4) {
quartet_info[qid].area=2; // LM_REG3 - left
}
if (qpbranching == 1) {
quartet_info[qid].area=0; // LM_REG1 - top
}
if (qpbranching == 2) {
quartet_info[qid].area=1; // LM_REG2 - right
}
if (qpbranching == 4) {
quartet_info[qid].area=2; // LM_REG3 - left
}

if (qpbranching == 3) {
quartet_info[qid].area=3; // LM_REG4
}
if (qpbranching == 6) {
quartet_info[qid].area=4; // LM_REG5
}
if (qpbranching == 5) {
quartet_info[qid].area=5; // LM_REG6
}
if (qpbranching == 3) {
quartet_info[qid].area=3; // LM_REG4
}
if (qpbranching == 6) {
quartet_info[qid].area=4; // LM_REG5
}
if (qpbranching == 5) {
quartet_info[qid].area=5; // LM_REG6
}

if (qpbranching == 7) {
quartet_info[qid].area=6; // LM_REG7 - center
}
if (qpbranching == 7) {
quartet_info[qid].area=6; // LM_REG7 - center
}



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