Merge pull request #333 from DEploid-dev/style

check style

.ci/checkedList

@@ -16,3 +16,5 @@ tests/unittest/test_vcfReader.cpp
 src/chooseK.hpp
 src/chooseK.cpp
 tests/unittest/test_dEploidIO.cpp
+src/panel.hpp
+src/panel.cpp

.ci/mycppfileList

@@ -1,12 +1,8 @@
 src/dEploidIO.cpp
 src/dEploidIO.hpp
 src/mcmc.cpp
-src/panel.cpp
-src/panel.hpp
 src/updateHap.cpp
 src/updateHap.hpp
-src/utility.cpp
-src/utility.hpp
 src/export/dEploidIOExport.cpp
 src/export/dEploidIOExportPosteriorProb.cpp
 src/export/writeMcmcRelated.cpp
@@ -18,3 +14,5 @@ tests/unittest/test_txtReader.cpp
 tests/unittest/test_updatePairHap.cpp
 tests/unittest/test_updateSingleHap.cpp
 tests/unittest/test_utilities.cpp
+src/utility.hpp
+src/utility.cpp

src/panel.cpp

@@ -64,7 +64,7 @@ Panel::Panel(vector < double > pRec,
 }
 
 
-Panel::Panel(const Panel &copyFrom){
+Panel::Panel(const Panel &copyFrom) {
     nLoci_ = copyFrom.nLoci_;
 
     chrom_ = vector <string> (copyFrom.chrom_.begin(), copyFrom.chrom_.end());
@@ -99,115 +99,128 @@ Panel::Panel(const Panel &copyFrom){
     inbreedingPanelSize_ = copyFrom.inbreedingPanelSize_;
 
     this->fileName_ = copyFrom.fileName_;
-    for (size_t i = 0; i < copyFrom.header_.size(); i++){
+    for (size_t i = 0; i < copyFrom.header_.size(); i++) {
         header_.push_back(copyFrom.header_[i]);
     }
 }
 
 
 
-void Panel::readFromFile( const char inchar[] ) {
-    this->readFromFileBase( inchar );
-    this->setTruePanelSize( this->nInfoLines_ );
-    this->setInbreedingPanelSize( this->truePanelSize() );
+void Panel::readFromFile(const char inchar[]) {
+    this->readFromFileBase(inchar);
+    this->setTruePanelSize(this->nInfoLines_);
+    this->setInbreedingPanelSize(this->truePanelSize());
 }
 
 
-void Panel::checkForExceptions( size_t nLoci, string panelFileName ) {
-    if ( this->content_.size() != nLoci ) {
-        throw LociNumberUnequal( panelFileName );
+void Panel::checkForExceptions(size_t nLoci, string panelFileName) {
+    if (this->content_.size() != nLoci) {
+        throw LociNumberUnequal(panelFileName);
     }
 
-    if ( this->pRec_.size() != nLoci ) {
-        throw LociNumberUnequal( panelFileName );
+    if (this->pRec_.size() != nLoci) {
+        throw LociNumberUnequal(panelFileName);
     }
     return;
 }
 
 
-void Panel::computeRecombProbs( double averageCentimorganDistance, double G, bool useConstRecomb, double constRecombProb, bool forbidCopyFromSame ) {
+void Panel::computeRecombProbs(double averageCentimorganDistance,
+    double G, bool useConstRecomb, double constRecombProb,
+    bool forbidCopyFromSame) {
+
     pRec_.clear();
     pRecEachHap_.clear();
     pNoRec_.clear();
     pRecRec_.clear();
     pRecNoRec_.clear();
     pNoRecNoRec_.clear();
 
-    assert(pRec_.size() == 0 );
-    assert(pRecEachHap_.size() == 0 );
-    assert(pNoRec_.size() == 0 );
-    assert(pRecRec_.size() == 0 );
-    assert(pRecNoRec_.size() == 0 );
-    assert(pNoRecNoRec_.size() == 0 );
+    assert(pRec_.size() == 0);
+    assert(pRecEachHap_.size() == 0);
+    assert(pNoRec_.size() == 0);
+    assert(pRecRec_.size() == 0);
+    assert(pRecNoRec_.size() == 0);
+    assert(pNoRecNoRec_.size() == 0);
 
     double averageMorganDistance = averageCentimorganDistance * 100;
     double geneticDistance;
     double rho;
-    double nPanelDouble = (double)this->truePanelSize();
+    double nPanelDouble = static_cast<double>(this->truePanelSize());
     double nPanlelMinus1 = nPanelDouble - 1.0;
-    for ( size_t i = 0; i < this->position_.size(); i++) {
-        for ( size_t j = 1; j < this->position_[i].size(); j++) {
-            geneticDistance = (double)(this->position_[i][j] - this->position_[i][j-1])/averageMorganDistance ;
-            //rho = geneticDistance * 2 * Ne;
+    for (size_t i = 0; i < this->position_.size(); i++) {
+        for (size_t j = 1; j < this->position_[i].size(); j++) {
+            geneticDistance = static_cast<double>(
+                this->position_[i][j] - this->position_[i][j-1]) /
+                averageMorganDistance;
+            // rho = geneticDistance * 2 * Ne;
             rho = geneticDistance * G;
 
-            double pRecTmp = ( useConstRecomb ) ? constRecombProb : 1.0 - exp(-rho);
-            this->pRec_.push_back( pRecTmp );
+            double pRecTmp = (useConstRecomb) ?
+                constRecombProb : 1.0 - exp(-rho);
+            this->pRec_.push_back(pRecTmp);
 
             double pRecEachHapTmp = pRecTmp / nPanelDouble;
-            this->pRecEachHap_.push_back( pRecTmp / nPanelDouble );
+            this->pRecEachHap_.push_back(pRecTmp / nPanelDouble);
 
             double pNoRecTmp = 1.0 - pRecTmp;
-            this->pNoRec_.push_back( pNoRecTmp );
+            this->pNoRec_.push_back(pNoRecTmp);
 
-            double secondPRecEachHapTmp = ( forbidCopyFromSame ) ? (pRecTmp / nPanlelMinus1) : pRecEachHapTmp; // allowing copy from the same
+            double secondPRecEachHapTmp = (forbidCopyFromSame) ?
+                (pRecTmp / nPanlelMinus1) :
+                pRecEachHapTmp;  // allowing copy from the same
 
-            this->pRecRec_.push_back ( pRecEachHapTmp * secondPRecEachHapTmp );
-            this->pRecNoRec_.push_back ( secondPRecEachHapTmp * pNoRecTmp );
-            this->pNoRecNoRec_.push_back ( pNoRecTmp * pNoRecTmp );
+            this->pRecRec_.push_back(pRecEachHapTmp * secondPRecEachHapTmp);
+            this->pRecNoRec_.push_back(secondPRecEachHapTmp * pNoRecTmp);
+            this->pNoRecNoRec_.push_back(pNoRecTmp * pNoRecTmp);
         }
         this->pRec_.push_back(1.0);
-        this->pRecEachHap_.push_back( 1.0 / nPanelDouble );
+        this->pRecEachHap_.push_back(1.0 / nPanelDouble);
         this->pNoRec_.push_back(0.0);
-        this->pRecRec_.push_back ( ( ( forbidCopyFromSame ) ? (1.0 / nPanelDouble / nPanlelMinus1) : (1.0 / nPanelDouble / nPanelDouble) ) );
-        this->pRecNoRec_.push_back ( 0.0 );
-        this->pNoRecNoRec_.push_back ( 0.0 );
+        this->pRecRec_.push_back(((forbidCopyFromSame) ?
+            (1.0 / nPanelDouble / nPanlelMinus1) :
+            (1.0 / nPanelDouble / nPanelDouble)));
+        this->pRecNoRec_.push_back(0.0);
+        this->pNoRecNoRec_.push_back(0.0);
     }
-    assert(pRec_.size() == this->nLoci_ );
-    assert(pRecEachHap_.size() == this->nLoci_ );
-    assert(pNoRec_.size() == this->nLoci_ );
-    assert(pRecRec_.size() == this->nLoci_ );
-    assert(pRecNoRec_.size() == this->nLoci_ );
-    assert(pNoRecNoRec_.size() == this->nLoci_ );
+    assert(pRec_.size() == this->nLoci_);
+    assert(pRecEachHap_.size() == this->nLoci_);
+    assert(pNoRec_.size() == this->nLoci_);
+    assert(pRecRec_.size() == this->nLoci_);
+    assert(pRecNoRec_.size() == this->nLoci_);
+    assert(pNoRecNoRec_.size() == this->nLoci_);
 }
 
 
 void Panel::buildExamplePanel1() {
     this->chrom_ = vector <string> ({"Pf3D7_01_v3"});
-    this->position_.push_back( vector <int> ({93157, 94422, 94459, 94487, 95518, 95632, 95641 }) );
+    this->position_.push_back(vector <int> (
+        {93157, 94422, 94459, 94487, 95518, 95632, 95641}));
     this->indexOfChromStarts_ = vector <size_t> ({0});
     this->buildExamplePanelContent();
 }
 
 
 void Panel::buildExamplePanel2() {
-    this->chrom_ = vector <string> ({"Pf3D7_01_v3", "Pf3D7_02_v3", "Pf3D7_03_v3"});
-    this->position_.push_back( vector <int> ({93157}) );
-    this->position_.push_back( vector <int> ({94422, 94459, 94487, 95518, 95632}) );
-    this->position_.push_back( vector <int> ({95641 }) );
+    this->chrom_ = vector <string> (
+        {"Pf3D7_01_v3", "Pf3D7_02_v3", "Pf3D7_03_v3"});
+    this->position_.push_back(vector <int> ({93157}));
+    this->position_.push_back(vector <int> (
+        {94422, 94459, 94487, 95518, 95632}));
+    this->position_.push_back(vector <int> ({95641}));
     this->indexOfChromStarts_ = vector <size_t> ({0, 1, 6});
     this->buildExamplePanelContent();
 }
 
 
 void Panel::buildExamplePanelContent() {
-    this->content_.push_back( vector <double> ({0,0,0,1}) );
-    this->content_.push_back( vector <double> ({0,0,0,1}) );
-    this->content_.push_back( vector <double> ({0,0,0,1}) );
-    this->content_.push_back( vector <double> ({0,0,0,1}) );
-    this->content_.push_back( vector <double> ({0,1,1,0}) );
-    this->content_.push_back( vector <double> ({0,0,1,0}) );
-    this->content_.push_back( vector <double> ({0,0,1,0}) );
+    this->content_.push_back(vector <double> ({0, 0, 0, 1}));
+    this->content_.push_back(vector <double> ({0, 0, 0, 1}));
+    this->content_.push_back(vector <double> ({0, 0, 0, 1}));
+    this->content_.push_back(vector <double> ({0, 0, 0, 1}));
+    this->content_.push_back(vector <double> ({0, 1, 1, 0}));
+    this->content_.push_back(vector <double> ({0, 0, 1, 0}));
+    this->content_.push_back(vector <double> ({0, 0, 1, 0}));
     this->nLoci_ = this->content_.size();
     this->nInfoLines_ = this->content_.back().size();
     this->setTruePanelSize(this->nInfoLines_);
@@ -218,41 +231,47 @@ void Panel::buildExamplePanelContent() {
 void Panel::initializeUpdatePanel(size_t inbreedingPanelSizeSetTo) {
     this->setInbreedingPanelSize(inbreedingPanelSizeSetTo);
 
-    // If allows inbreeding, update reference panel by including strain haplotypes
+    // If allows inbreeding,
+    // update reference panel by including strain haplotypes
     dout << "************* Allow inbreeding ************" << endl;
     dout << "** Initialize inbreeding reference panel **" << endl;
 
-    if ( this->truePanelSize() == this->inbreedingPanelSize()) {
+    if (this->truePanelSize() == this->inbreedingPanelSize()) {
         return;
     }
 
     for ( size_t siteI = 0; siteI < this->content_.size(); siteI++ ) {
-        for ( size_t panelStrainJ = this->truePanelSize() ; panelStrainJ < this->inbreedingPanelSize(); panelStrainJ++ ) {
-            this->content_[siteI].push_back( 1 );
+        for (size_t panelStrainJ = this->truePanelSize();
+            panelStrainJ < this->inbreedingPanelSize(); panelStrainJ++) {
+            this->content_[siteI].push_back(1);
         }
         assert(inbreedingPanelSizeSetTo == this->content_[siteI].size());
     }
 }
 
 
-void Panel::updatePanelWithHaps(size_t inbreedingPanelSizeSetTo, size_t excludedStrain, vector < vector<double> > & haps) {
+void Panel::updatePanelWithHaps(size_t inbreedingPanelSizeSetTo,
+    size_t excludedStrain, const vector < vector<double> > & haps) {
     this->setInbreedingPanelSize(inbreedingPanelSizeSetTo);
 
-    // If allows inbreeding, update reference panel by including strain haplotypes
+    // If allows inbreeding,
+    // update reference panel by including strain haplotypes
     dout << "*************** Allow inbreeding **************" << endl;
-    dout << "*** Update reference panel without strain " << excludedStrain << " ***" << endl;
+    dout << "*** Update reference panel without strain " <<
+        excludedStrain << " ***" << endl;
 
-    if ( this->truePanelSize() == this->inbreedingPanelSize()) {
+    if (this->truePanelSize() == this->inbreedingPanelSize()) {
         return;
     }
 
-    for ( size_t siteI = 0; siteI < this->content_.size(); siteI++ ) {
+    for (size_t siteI = 0; siteI < this->content_.size(); siteI++) {
         size_t shiftAfter = this->inbreedingPanelSize();
 
-        for ( size_t panelStrainJ = this->truePanelSize() ; panelStrainJ < this->inbreedingPanelSize(); panelStrainJ++ ) {
+        for (size_t panelStrainJ = this->truePanelSize();
+            panelStrainJ < this->inbreedingPanelSize(); panelStrainJ++) {
             size_t strainIndex = panelStrainJ - this->truePanelSize();
 
-            if ( strainIndex == excludedStrain ) {
+            if (strainIndex == excludedStrain) {
                 shiftAfter = panelStrainJ;
             }
 
@@ -265,14 +284,13 @@ void Panel::updatePanelWithHaps(size_t inbreedingPanelSizeSetTo, size_t excluded
 }
 
 
-void Panel::trimVec(vector <double> &vec, const vector <size_t> &idx) {
+void Panel::trimVec(vector <double> vec, const vector <size_t> &idx) {
     vector <double> ret;
-    for (auto const& value : idx){
+    for (auto const& value : idx) {
         ret.push_back(vec[value]);
     }
-    //return ret;
     vec.clear();
-    for (auto const& value : ret){
+    for (auto const& value : ret) {
         vec.push_back(value);
     }
 }
@@ -309,32 +327,36 @@ void Panel::findAndKeepMarkersGivenIndexHalf(
     this->trimVec(this->pNoRecNoRec_, givenIndex);
 }
 
-void IBDrecombProbs::computeRecombProbs( double averageCentimorganDistance, double G, bool useConstRecomb, double constRecombProb ) {
-    assert(pRec_.size() == 0 );
-    assert(pNoRec_.size() == 0 );
+void IBDrecombProbs::computeRecombProbs(double averageCentimorganDistance,
+    double G, bool useConstRecomb, double constRecombProb) {
+    assert(pRec_.size() == 0);
+    assert(pNoRec_.size() == 0);
     double averageMorganDistance = averageCentimorganDistance * 100;
     double geneticDistance;
     double rho;
-    for ( size_t i = 0; i < this->position_.size(); i++) {
-        for ( size_t j = 1; j < this->position_[i].size(); j++) {
-            geneticDistance = (double)(this->position_[i][j] - this->position_[i][j-1])/averageMorganDistance ;
-            //rho = geneticDistance * 2 * Ne;
+    for (size_t i = 0; i < this->position_.size(); i++) {
+        for (size_t j = 1; j < this->position_[i].size(); j++) {
+            geneticDistance =
+                static_cast<double>(this->position_[i][j] -
+                    this->position_[i][j-1]) / averageMorganDistance;
+            // rho = geneticDistance * 2 * Ne;
             rho = geneticDistance * G;
-            double pRecTmp = ( useConstRecomb ) ? constRecombProb : (1.0 - exp(-rho));
-            this->pRec_.push_back( pRecTmp );
+            double pRecTmp = (useConstRecomb) ?
+                constRecombProb : (1.0 - exp(-rho));
+            this->pRec_.push_back(pRecTmp);
             double pNoRecTmp = 1.0 - pRecTmp;
-            this->pNoRec_.push_back( pNoRecTmp );
+            this->pNoRec_.push_back(pNoRecTmp);
         }
         this->pRec_.push_back(1.0);
         this->pNoRec_.push_back(0.0);
     }
-    assert(pRec_.size() == this->nLoci_ );
-    assert(pNoRec_.size() == this->nLoci_ );
+    assert(pRec_.size() == this->nLoci_);
+    assert(pNoRec_.size() == this->nLoci_);
 }
 
 
-//vector<vector<double>> outtrans(out[0].size(),
-                                    //vector<double>(out.size()));
-    //for (size_t i = 0; i < out.size(); ++i)
-        //for (size_t j = 0; j < out[0].size(); ++j)
-            //outtrans[j][i] = out[i][j];
+// vector<vector<double>> outtrans(out[0].size(),
+                                    // vector<double>(out.size()));
+    // for (size_t i = 0; i < out.size(); ++i)
+        // for (size_t j = 0; j < out[0].size(); ++j)
+            // outtrans[j][i] = out[i][j];