Playlist(int count, const char *const aSongs[]) : mStream(0), mSource(0)
{
for (int i = 0; i < count; ++i) {
mSongs.push_back(aSongs[i]);
}
mCurrentSong = mSongs.begin();
Init();
}
Playlist(const stringList& aSongs) :
mStream(0),
mSource(0),
mThreadAlive(false)
{
mSongs.assign(aSongs.begin(), aSongs.end());
mCurrentSong = mSongs.begin();
Init();
}
//Get all Name in order
bool PWM::_getOrderedPositionNames(stringList& pos, stringList& names){
for(size_t i=0;i<pos.size();i++){
size_t nameHeader=pos[i].find("NAME:");
if (nameHeader == std::string::npos){
continue;
}
size_t nameLineEnding=pos[i].find_first_of("\n",nameHeader);
std::string name = pos[i].substr(nameHeader+5,nameLineEnding-(nameHeader+5));
clear_whitespace(name, " \t\n");
if (names.contains(name)){
std::cerr << "Position with name of: " << name << " is defined twice in the model\n";
return false;
}
else{
names.push_back(name);
}
}
return true;
}
void EvaMemoReplyPacket::setMemo( const stringList &infos )
{
m_Memo.name = infos.at(0);
m_Memo.mobile = infos.at(1);
m_Memo.telephone = infos.at(2);
m_Memo.address = infos.at(3);
m_Memo.email = infos.at(4);
m_Memo.zipcode = infos.at(5);
m_Memo.note = infos.at(6);
}
// correct MD sepearte list
// also collect deletion base list
string correctMDstring(numList MDnum, stringList MDLetter, stringList &deletions)
{
string MDList;
int i = 0;
//make deletion list
for (int i = 0; i < MDnum.size(); i ++)
{
if (MDLetter[i][0] == '^')
{
deletions.push_back(MDLetter[i]);
}
}
MDList = creatMDstring(MDnum,MDLetter);
return MDList;
}
//Split states into individual state strings
bool PWM::_splitPositions(std::string& txt ,stringList& sts){
size_t start=0;
size_t end=0;
while(start!=std::string::npos){
end=txt.find("NAME:",start+1);
std::string st = txt.substr(start,end-start);
clear_whitespace(st, "#><");
sts.push_back(st);
start=txt.find("NAME:",end);
}
return true;
}
// extract from each line different columns
// and give them to further processing
int processLine(stringList columns, int qualThreshold, int covThreshold, int &seqCount)
{
string transcriptID, pos, refbase, reads, baseQuals;
int cov;
if (columns.size() == 6)
{
cov = atoi(columns[3].c_str());
refbase = columns[2];
if (cov > covThreshold)
{
transcriptID = columns[0];
pos = columns[1];
reads = columns[4];
baseQuals = columns[5];
assert (baseQuals.length() == cov) ;
extractMismatches(reads,baseQuals,cov, transcriptID,pos,refbase, qualThreshold, seqCount);
}
}
return 0;
}
// extract from each line different columns
// and give them to further processing
void processLine( stringList columns, int qualThreshold, int coverageThreshold)
{
if (columns[2] != "N" && columns[2] != "." && columns[2] != "_" )
{
string transcriptID, pos, ref, reads, baseQuals;
int cov;
if (columns.size() == 6)
{
cov = atoi(columns[3].c_str());
if (cov > coverageThreshold)
{
transcriptID = columns[0];
pos = columns[1];
ref = columns[2];
reads = columns[4];
baseQuals = columns[5];
assert ( baseQuals.length() == cov ) ;
extractMismatches(reads, baseQuals, cov, transcriptID,
pos, ref, qualThreshold, coverageThreshold);
}
}
}
}
//define extra field
int findField(stringList columns,string &XGfield,
string &NMfield, string &MDfield)
{
int i;
string field;
for (i = 10 ; i < columns.size(); i++)
{
field = columns[i];
if (field.substr(0,2) == "XG")
{
XGfield = field;
}
else if (field.substr(0,2) == "NM")
{
NMfield = field;
}
else if (field.substr(0,2) == "MD")
{
MDfield = field;
}
}
return 0;
}
//!Parse the stringList from model import
bool transitionFuncParam::parse(stringList& lst, tracks& trcks, weights* wts, StateFuncs* funcs) {
size_t idx;
//FUNCTION NAME (REQUIRED)
if (lst.contains("FUNCTION")) {
idx=lst.indexOf("FUNCTION");
idx++;
transFuncName = lst[idx];
if (funcs!=NULL) {
transFunc = funcs->getTransitionFunction(transFuncName);
}
}
else {
std::cerr << "Tag was parsed but contains no FUNCTION: . Please check the formatting of the tags\n" << std::endl;
return false;
//errorInfo(sCantParseLine, "Tag was parsed but contains no FUNCTION: . Please check the formatting of the tags\n");
}
//Implement Which track to pass to function
if (lst.contains("TRACK")) {
idx=lst.indexOf("TRACK");
idx++;
trackName=lst[idx];
transFuncTrack = trcks.getTrack(trackName);
}
else {
std::cerr << "Tag was parsed but contains no TRACK: . Please check the formatting of the tags\n" << std::endl;
return false;
//errorInfo(sCantParseLine, "Tag was parsed but contains no TRACK: . Please check the formatting of the tags\n");
}
if (lst.contains("SCALE")) {
idx=lst.indexOf("SCALE");
idx++;
if (isNumeric(lst[idx])) {
transFuncScaling = new(std::nothrow) weight;
if (transFuncScaling==NULL) {
std::cerr << "OUT OF MEMORY\nFile" << __FILE__ << "Line:\t"<< __LINE__ << std::endl;
exit(1);
}
double tempValue;
if (!stringToDouble(lst[idx], tempValue)) {
std::cerr << "Ambiguous Value couldn't be parsed: "<< lst[idx] << std::endl;
return false;
}
transFuncScaling->setAbsolute(tempValue);
}
else {
std::string weightName=lst[idx];
if (wts->count(weightName)) {
transFuncScaling = (*wts)[weightName];
}
}
}
//Process Traceback Commands
//Parse the TO Traceback Labels in the function tag
const std::string tbLabels[]= {"TO_LABEL","TB->LABEL","TO_GFF","TB->GFF","TO_STATE","TB->STATE","TO_START","TB->START","DIFF_STATE"};
const tracebackIdentifier typs[]= {STATE_LABEL,STATE_LABEL,STATE_GFF,STATE_GFF,STATE_NAME,STATE_NAME,START_INIT,START_INIT,DIFF_STATE};
for(int i=0; i<9; i++) {
if (lst.contains(tbLabels[i])) {
transFuncTraceback=true;
idx=lst.indexOf(tbLabels[i]);
transFuncTracebackIdentifier=typs[i];
if (typs[i]!=START_INIT || typs[i]!=DIFF_STATE) {
transFuncTracebackString=lst[idx+1];
}
}
}
// Parse the Combine tags
if (transFuncTraceback) {
//Process Traceback Combining Commands
std::string combineLabels[] = {"COMBINE_LABEL","COMBINE_GFF","COMBINE_STATE", "NO_COMBINE"};
const combineIdentifier comtyps[] = {STATELABEL,STATEGFF,STATENAME,FULL};
bool combineTypeProvided=false;
for(int i=0; i<4; i++) {
if (lst.contains(combineLabels[i])) {
idx=lst.indexOf(combineLabels[i]);
transFuncCombineIdentifier=comtyps[i];
transFuncCombineString=lst[idx+1];
combineTypeProvided=true;
}
}
if (!combineTypeProvided) {
std::cerr << "Transition Function tag with a traceback was called, but no CombineType was provided. If no traceback is needed then please remove traceback command. \n" << std::endl;
return false;
//errorInfo(sTagIncorrect, "Transition Function tag with a traceback was called, but no CombineType was provided. If no traceback is needed then please remove traceback command. \n");
}
}
return true;
}
//!Parse the stringList from model import
bool emissionFuncParam::parse(stringList& lst, tracks& trcks, weights* wts, StateFuncs* funcs) {
size_t idx;
//FUNCTION NAME (REQUIRED)
if (lst.contains("FUNCTION")) {
idx=lst.indexOf("FUNCTION");
idx++;
emissionFuncName = lst[idx];
if (funcs!=NULL) {
emissionFunction = funcs->getEmissionFunction(emissionFuncName);
}
}
else {
std::cerr << "Tag was parsed but contains no FUNCTION: . Please check the formatting of the tags\n" << std::endl;
return false;
//errorInfo(sCantParseLine, "Tag was parsed but contains no FUNCTION: . Please check the formatting of the tags\n");
}
//Implement Which track to pass to function
if (lst.contains("TRACK")) {
idx=lst.indexOf("TRACK");
idx++;
trackName=lst[idx];
emissionFuncTrack = trcks.getTrack(trackName);
trackNumber = emissionFuncTrack->getIndex();
}
else {
std::cerr << "Tag was parsed but contains no TRACK: . Please check the formatting of the tags\n" << std::endl;
return false;
//errorInfo(sCantParseLine, "Tag was parsed but contains no TRACK: . Please check the formatting of the tags\n");
}
if (lst.contains("SCALE")) {
idx=lst.indexOf("SCALE");
idx++;
if (isNumeric(lst[idx])) {
emissionFuncScaling = new(std::nothrow) weight;
if (emissionFuncScaling==NULL) {
std::cerr << "OUT OF MEMORY\nFile" << __FILE__ << "Line:\t"<< __LINE__ << std::endl;
exit(1);
}
double tempValue;
if (!stringToDouble(lst[idx], tempValue)) {
std::cerr << "SCALE value could not be converted to numerical value: "<< lst[idx] << std::endl;
return false;
}
emissionFuncScaling->setAbsolute(tempValue);
}
else {
std::string weightName=lst[idx];
if (wts->count(weightName)) {
emissionFuncScaling = (*wts)[weightName];
}
}
}
return true;
}
// Fix sequence, MDline, cigarLine
// i. collect clipped bases
// ii. collect insertion bases
// iii. remove insertion bases on
// 1. query sequence and
// 2. cigar line
// iv. count mismatch pattern (e.g. AtoG, GtoT)
stringList insertionAndMismatch(string cigarLine, string MDline, string sequence, stringList &insertion,
string &softclippedHead, string &softclippedTail, string id, int numOfMis)
{
stringList mismatchList(numOfMis);
string fixedCigarLine, fixedSeq, mismatch, ref, read;
int mis, i = 0, size = cigarLine.length();
while( i < size)
{
if (cigarLine.at(i) == 'S')
{
if (i == 0)
{
while ( cigarLine.at(i) == 'S')
{
i ++ ;
}
softclippedHead = sequence.substr(0,i);
}
else
{
softclippedTail = sequence.substr(i,size-i);
i += size;
}
}
else if (cigarLine.at(i) == 'I')
{
insertion.push_back(string(1,sequence[i]));
i ++;
}
else
{
fixedCigarLine.push_back(cigarLine[i]);
fixedSeq.push_back(sequence[i]);
i ++;
}
}
/*
//debugging
cerr << fixedCigarLine << endl;
cerr << MDline << endl;
cerr << fixedSeq <<endl;
cerr << sequence << endl ;
cerr << cigarLine << endl;
cerr << softclippedHead << '\t' << softclippedTail << endl;
*/
//assertion
assert(fixedCigarLine.length() == MDline.length());
assert(fixedSeq.length() == MDline.length());
//extract misincorporations
mis = 0;
for (int i = 0; i < fixedCigarLine.length(); i++)
{
if (fixedCigarLine.at(i) == 'M' && MDline.at(i) != '=')
{
ref = MDline.substr(i,1) ;
read = fixedSeq.substr(i,1);
assert (ref != read);
mismatch = ref +"to"+ read;
mismatchList[mis] = mismatch;
mis ++;
}
}
return mismatchList;
}
//指定文字列が文字列リストに存在するかどうかどうかのチェック
bool SNetList::quaryExist(stringList& strlist,string& str)
{
if(strlist.end() != find(strlist.begin(),strlist.end(),str)) return true;
else return false;
}
