void UtilityInterface::findProteinSeqLength() {
string inFilename(proteinLocation);
inFilename += "/";
inFilename += rootName;
inFilename += ".fasta";
//cout<<inFilename<<endl;
FILE* fptr = fopen((char*) inFilename.c_str(), "r");
if (fptr == NULL) {
cout << "input file: " << inFilename << " can't open" << endl;
}
char line[500];
fgets(line, 500, fptr);
fgets(line, 500, fptr);
char *pos;
if ((pos=strchr(line, '\n')) != NULL){
*pos = '\0';
}
proteinSeqLength = strlen(line);
originalProteinSeq.resize(proteinSeqLength);
for (int j = 0; j < proteinSeqLength; j++) {
originalProteinSeq[j] = line[j];
}
//cout<<"proteinSeqLength"<<proteinSeqLength<<endl;
fclose(fptr);
}
// Main function (driver).
int main(int argc, char **argv) {
if (argc !=3) {
std::cerr << "# Usage: <execution filename> <input filename> ";
std::cerr << "<output filename> \n";
std::cerr << " Example: $ a.out in.csv out.csv\n";
std::exit(1);
};
// Filenames for input and output csv files.
// (input: puzzle, output: solution)
string inFilename(argv[1]), outFilename(argv[2]);
const short size = 9; // The given size of the board of Sudoku.
try {
// Create a (size x size) sodoku puzzle (default: 9x9).
Sudoku3 puzzle;
cout << "* Created " << size << 'x' << size \
<< " Sodoku puzzle." << endl;
// Reading the file.
cout << "* Reading the input file, " << inFilename << endl;
puzzle.read(inFilename);
cout << "* Solving..." << endl;
if (puzzle.solve()) {
cout << "* Solved, and writing to the output file, " \
<< outFilename << endl;
puzzle.write(outFilename);
}
else
cout << "* Unsolvable puzzle. Nothing is written." << endl;
}
catch(BadSize e) {
std::cerr << "* Bad size of the board (grid) is given.\n";
std::exit(1);
}
catch(BadInput e) {
std::cerr << "* Bad input is given.\n";
std::exit(1);
}
catch(BadValue e) {
std::cerr << "* Bad value is given in the input.\n";
std::exit(1);
}
catch(NoInputFile e) {
std::cerr << "* File, " << inFilename << ", does not exist.\n";
std::exit(1);
}
catch(InvalidPuzzle e) {
std::cerr << "* Given puzzle is invalid.\n";
std::cerr << " Causes: (1) Any given value is not following" \
<< " the rule, or (2) any given value is not in the" \
<< " range.\n";
std::exit(1);
};
return 0;
};
void BLANR2Json::convert() {
char line[500];
int counter = 0;
string inFilename(inputFileLocation);
inFilename += inputFilename;
FILE* fptr = fopen((char*) inFilename.c_str(), "r");
if (fptr == NULL) {
cout << "input file: " << inFilename << " can't open" << endl;
}
BLANRResult result;
while (fgets(line, 500, fptr) != NULL) {
if ((strstr(line, ">") != NULL) && !result.isFirstStateReached()) {
//set first block information
char proteinName[7];
char* pos1 = strstr(line, ">");
sscanf(pos1 + 1, "%s", proteinName);
string proteinNameStr(proteinName);
result.setProteinName(proteinNameStr);
while (strstr(line, "Length =") == NULL) {
fgets(line, 500, fptr); //skip long name
}
char temp[10];
int seqLen;
sscanf(line, "%s = %d", temp, &seqLen);
result.setLength(seqLen);
//set first state reached
result.setFirstStateReached(true);
}
if ((strstr(line, "Score =") != NULL)
&& !result.isSecondStateReached()) {
//set second block information
float score;
char* pos1 = strstr(line, "=");
sscanf(pos1 + 1, "%f", &score);
result.setScore(score);
char* pos2 = strstr(pos1 + 1, "=");
float eValue;
sscanf(pos2 + 1, "%f", &eValue);
result.setExpect(eValue);
fgets(line, 500, fptr);
pos1 = strstr(line, "(");
int identities;
sscanf(pos1 + 1, "%d", &identities);
result.setIdentities(identities);
pos2 = strstr(pos1 + 1, "(");
int positives;
sscanf(pos2 + 1, "%d", &positives);
result.setPositives(positives);
char* pos3 = strstr(pos2 + 1, "(");
if (pos3 == NULL) {
//there is no gaps
result.setGaps(0);
} else {
int gaps;
sscanf(pos3 + 1, "%d", &gaps);
result.setGaps(gaps);
}
//set second state reached
result.setSecondStateReached(true);
}
if ((strstr(line, "Query:") != NULL) && !result.isThirdStateReached()) {
//set third block information
int nInt1, nInt2;
char var1[20], var2[20];
char tmpQuery[200];
sscanf(line, "%s %d %s %d", var1, &nInt1, tmpQuery, &nInt2);
result.setQueryStart(nInt1);
string tmpQueryStr(tmpQuery);
result.setQuery(tmpQueryStr);
result.setQueryEnd(nInt2);
fgets(line, 500, fptr);
string tmpLineStr(line);
result.setAlignment(tmpLineStr);
fgets(line, 500, fptr);
char tmpSubject[200];
sscanf(line, "%s %d %s %d", var1, &nInt1, tmpSubject, &nInt2);
result.setSubjectStart(nInt1);
string tmpSubjectStr(tmpSubject);
result.setSubject(tmpSubjectStr);
result.setSubjectEnd(nInt2);
//set third state reached
result.setThirdStateReached(true);
}
if ((strstr(line, "Query:") != NULL) && result.isThirdStateReached()) {
//update third block information, so in this case
//query, alignment and subject should be long string
//the queryEnd and subjectEnd should also be updated
int nInt1, nInt2;
char var1[20], var2[20];
char tmpQuery[200];
sscanf(line, "%s %d %s %d", var1, &nInt1, tmpQuery, &nInt2);
string newQuery = result.getQuery();
newQuery += tmpQuery;
result.setQuery(newQuery);
result.setQueryEnd(nInt2);
fgets(line, 500, fptr);
string newAlignment = result.getAlignment();
newAlignment += line;
result.setAlignment(newAlignment);
fgets(line, 500, fptr);
char tmpSubject[200];
sscanf(line, "%s %d %s %d", var1, &nInt1, tmpSubject, &nInt2);
string newSubject = result.getSubject();
newSubject += tmpSubject;
result.setSubject(newSubject);
result.setSubjectEnd(nInt2);
}
if ((strstr(line, "Score =") != NULL)
&& result.isSecondStateReached()) {
//first write the protein information to json
BLANRResultVector.push_back(result);
counter++;
//then update the information and set the second state flag
float score;
char* pos1 = strstr(line, "=");
sscanf(pos1 + 1, "%f", &score);
result.setScore(score);
char* pos2 = strstr(pos1 + 1, "=");
float eValue;
sscanf(pos2 + 1, "%f", &eValue);
result.setExpect(eValue);
fgets(line, 500, fptr);
pos1 = strstr(line, "(");
int identities;
sscanf(pos1 + 1, "%d", &identities);
result.setIdentities(identities);
pos2 = strstr(pos1 + 1, "(");
int positives;
sscanf(pos2 + 1, "%d", &positives);
result.setPositives(positives);
char* pos3 = strstr(pos2 + 1, "(");
if (pos3 == NULL) {
//there is no gaps
result.setGaps(0);
} else {
int gaps;
sscanf(pos3 + 1, "%d", &gaps);
result.setGaps(gaps);
}
result.setSecondStateReached(true);
//unset the third block flag
result.setThirdStateReached(false);
}
if ((strstr(line, ">") != NULL) && result.isFirstStateReached()) {
BLANRResultVector.push_back(result);
counter++;
//then update the information set the first state flag
char proteinName[7];
char* pos1 = strstr(line, ">");
sscanf(pos1 + 1, "%s", proteinName);
string proteinNameStr(proteinName);
result.setProteinName(proteinNameStr);
while (strstr(line, "Length =") == NULL) {
fgets(line, 500, fptr); //skip long name
}
char temp[10];
int seqLen;
sscanf(line, "%s = %d", temp, &seqLen);
result.setLength(seqLen);
//unset second block flag and third block flag
result.setSecondStateReached(false);
result.setThirdStateReached(false);
}
}
BLANRResultVector.push_back(result);
fclose(fptr);
}
void HHRNR2Json::convert() {
char line[500];
int counter = 0;
string inFilename(inputFileLocation);
inFilename += inputFilename;
FILE* inputFile = fopen((char*) inFilename.c_str(), "r");
if (inputFile == NULL) {
cout << "input file: " << inFilename << " can't open" << endl;
}
HHRNRResult result;
while (fgets(line, 200, inputFile) != NULL) {
if (strstr(line, ">") != NULL) {
counter++;
char proteinName[7];
char* pos1 = strstr(line, ">");
sscanf(pos1 + 1, "%s", proteinName);
string proteinNameStr(proteinName);
result.setProteinName(proteinNameStr);
while (strstr(line, "Probab=") == NULL) {
fgets(line, 500, inputFile); //skip long name
}
//get probab, E-value, Score, Aligned_cols, Identities, Similarity, Sum_probs
pos1 = strstr(line, "=");
float probab;
sscanf(pos1 + 1, "%f", &probab);
result.setProbab(probab);
char* pos2 = strstr(pos1 + 1, "=");
float eValue;
sscanf(pos2 + 1, "%f", &eValue);
result.setExpect(eValue);
char* pos3 = strstr(pos2 + 1, "=");
float score;
sscanf(pos3 + 1, "%f", &score);
result.setScore(score);
char* pos4 = strstr(pos3 + 1, "=");
int alignedCols;
sscanf(pos4 + 1, "%d", &alignedCols);
result.setAlignedCols(alignedCols);
char* pos5 = strstr(pos4 + 1, "=");
float identities;
sscanf(pos5 + 1, "%f", &identities);
result.setIdentities(identities);
char* pos6 = strstr(pos5 + 1, "=");
float similarity;
sscanf(pos6 + 1, "%f", &similarity);
result.setSimilarities(similarity);
char* pos7 = strstr(pos6 + 1, "=");
float sumProbs;
sscanf(pos7 + 1, "%f", &sumProbs);
result.setSumProbs(sumProbs);
fgets(line, 200, inputFile); //blank
//get the query
fgets(line, 200, inputFile);
char query_ss_pred[100];
sscanf(line + 17, "%s", query_ss_pred);
string strQuery_ss_pred(query_ss_pred);
result.setQuerySsPred(strQuery_ss_pred);
fgets(line, 200, inputFile);
int queryStart;
char query[100];
int queryEnd;
sscanf(line + 17, "%d %s %d", &queryStart, query, &queryEnd);
result.setQueryStart(queryStart);
string strQuery(query);
result.setQuery(strQuery);
result.setQueryEnd(queryEnd);
//get the Q Consensus
fgets(line, 200, inputFile);
int QConsensusStart;
char QConsensus[100];
int QConsensusEnd;
sscanf(line + 17, "%d %s %d", &QConsensusStart, QConsensus,
&QConsensusEnd);
string strQConsensus(QConsensus);
result.setQueryConsensus(strQConsensus);
//get alignment
fgets(line, 200, inputFile);
char alignment[100];
sscanf(line + 17, "%s", alignment);
string strAlignment(alignment);
result.setAlignment(strAlignment);
//get the T Consensus
fgets(line, 200, inputFile);
int targetStart;
char targetConsensus[100];
int targetEnd;
sscanf(line + 17, "%d %s %d", &targetStart, targetConsensus,
&targetEnd);
result.setTargetStart(targetStart);
string strTargetConsensus(targetConsensus);
result.setTargetConsensus(strTargetConsensus);
result.setTargetEnd(targetEnd);
//get the Target
fgets(line, 200, inputFile);
char target[100];
sscanf(line + 17, "%d %s %d", &targetStart, target, &targetEnd);
string strTarget(target);
result.setTarget(strTarget);
//get the TDssp
fgets(line, 200, inputFile);
char tDssp[100];
sscanf(line + 17, "%s", tDssp);
string strTDssp(tDssp);
result.setTargetSsDssp(strTDssp);
//get the TPred
fgets(line, 200, inputFile);
char tPred[100];
sscanf(line + 17, "%s", tPred);
string strTPred(tPred);
result.setTargetSsPred(strTPred);
counter++;
HHRNRResultVector.push_back(result);
}
}
fclose(inputFile);
}
void HHRImpl::populateResultVector() {
char line[500];
int counter = 0;
string inFilename(inputFileLocation);
inFilename += "/";
inFilename += rootName;
inFilename += "/";
inFilename += "/query.hhr";
//cout << inFilename << endl;
FILE* inputFile = fopen((char*) inFilename.c_str(), "r");
if (inputFile == NULL) {
cout << "input file: " << inFilename << " can't open" << endl;
}
HHRResult result;
while (fgets(line, 500, inputFile) != NULL) {
if (strstr(line, ">") != NULL && !result.isFirstStateReached()) {
//set first block information
char proteinName[7];
char* pos1 = strstr(line, ">");
sscanf(pos1 + 1, "%s", proteinName);
string proteinNameStr(proteinName);
result.setProteinName(proteinNameStr);
while (strstr(line, "Probab=") == NULL) {
fgets(line, 500, inputFile); //skip long name
}
//get probab, E-value, Score, Aligned_cols, Identities, Similarity, Sum_probs
pos1 = strstr(line, "=");
float probab;
sscanf(pos1 + 1, "%f", &probab);
result.setProbab(probab);
char* pos2 = strstr(pos1 + 1, "=");
float eValue;
sscanf(pos2 + 1, "%f", &eValue);
result.setExpect(eValue);
char* pos3 = strstr(pos2 + 1, "=");
float score;
sscanf(pos3 + 1, "%f", &score);
result.setScore(score);
char* pos4 = strstr(pos3 + 1, "=");
int alignedCols;
sscanf(pos4 + 1, "%d", &alignedCols);
result.setAlignedCols(alignedCols);
char* pos5 = strstr(pos4 + 1, "=");
float identities;
sscanf(pos5 + 1, "%f", &identities);
result.setIdentities(identities);
result.setFirstStateReached(true);
}
if ((strstr(line, "Q ref|") != NULL)
&& !result.isSecondStateReached()) {
//set second block information
//get the query
int queryStart;
char query[100];
int queryEnd;
sscanf(line + 17, "%d %s %d", &queryStart, query, &queryEnd);
result.setQueryStart(queryStart);
string strQuery(query);
result.setQuery(strQuery);
result.setQueryEnd(queryEnd);
//get the Q Consensus
fgets(line, 200, inputFile);
int QConsensusStart;
char QConsensus[100];
int QConsensusEnd;
sscanf(line + 17, "%d %s %d", &QConsensusStart, QConsensus,
&QConsensusEnd);
string strQConsensus(QConsensus);
result.setQueryConsensus(strQConsensus);
//get alignment
fgets(line, 200, inputFile);
char alignment[100];
sscanf(line + 17, "%s", alignment);
string strAlignment(alignment);
result.setAlignment(strAlignment);
//get the T Consensus
fgets(line, 200, inputFile);
int targetStart;
char targetConsensus[100];
int targetEnd;
sscanf(line + 17, "%d %s %d", &targetStart, targetConsensus,
&targetEnd);
result.setTargetStart(targetStart);
string strTargetConsensus(targetConsensus);
result.setTargetConsensus(strTargetConsensus);
result.setTargetEnd(targetEnd);
//get the Target
fgets(line, 200, inputFile);
char target[100];
sscanf(line + 17, "%d %s %d", &targetStart, target, &targetEnd);
string strTarget(target);
result.setTarget(strTarget);
//get the TPred
fgets(line, 200, inputFile);
char tPred[100];
sscanf(line + 17, "%s", tPred);
string strTPred(tPred);
result.setTargetSsPred(strTPred);
//get the TConf
fgets(line, 200, inputFile);
char tConf[100];
sscanf(line + 17, "%s", tConf);
string strTConf(tConf);
result.setConfidence(strTConf);
result.setSecondStateReached(true);
}
if ((strstr(line, "Q ref|") != NULL) && result.isSecondStateReached()) {
//update second block information, so in this case
//quert, alignment and target should be long string
//the queryEnd and targetEnd should also be updated
//get the query
int queryStart;
char query[100];
int queryEnd;
sscanf(line + 17, "%d %s %d", &queryStart, query, &queryEnd);
string additionalQuery(query);
string newQuery = result.getQuery();
newQuery += additionalQuery;
result.setQuery(newQuery);
result.setQueryEnd(queryEnd);
//get the Q Consensus
fgets(line, 200, inputFile);
int QConsensusStart;
char QConsensus[100];
int QConsensusEnd;
sscanf(line + 17, "%d %s %d", &QConsensusStart, QConsensus,
&QConsensusEnd);
string additionalQConsensus(QConsensus);
string newQConsesus = result.getQueryConsensus();
newQConsesus += additionalQConsensus;
result.setQueryConsensus(newQConsesus);
//get alignment
fgets(line, 200, inputFile);
char alignment[100];
sscanf(line + 17, "%s", alignment);
string additionalAlignment(alignment);
string newAlignment = result.getAlignment();
newAlignment += additionalAlignment;
result.setAlignment(newAlignment);
//get the T Consensus
fgets(line, 200, inputFile);
int targetStart;
char targetConsensus[100];
int targetEnd;
sscanf(line + 17, "%d %s %d", &targetStart, targetConsensus,
&targetEnd);
string additionalTargetConsensus(targetConsensus);
string newTargetConsensus = result.getTargetConsensus();
newTargetConsensus += additionalTargetConsensus;
result.setTargetConsensus(newTargetConsensus);
result.setTargetEnd(targetEnd);
//get the Target
fgets(line, 200, inputFile);
char target[100];
sscanf(line + 17, "%d %s %d", &targetStart, target, &targetEnd);
string additionalTarget(target);
string newTarget = result.getTarget();
newTarget += additionalTarget;
result.setTarget(newTarget);
//get the TPred
fgets(line, 200, inputFile);
char tPred[100];
sscanf(line + 17, "%s", tPred);
string additionalTPred(tPred);
string newTPred = result.getTargetSsPred();
newTPred += additionalTPred;
result.setTargetSsPred(newTPred);
//get the TConf
fgets(line, 200, inputFile);
char tConf[100];
sscanf(line + 17, "%s", tConf);
string additionalTConf(tConf);
string newTConf = result.getConfidence();
newTConf += additionalTConf;
result.setConfidence(newTConf);
}
if ((strstr(line, ">") != NULL) && result.isFirstStateReached()) {
//first push the result to the vector
hhrResultVector.push_back(result);
//then update the information set the first state flag
//set first block information
char proteinName[7];
char* pos1 = strstr(line, ">");
sscanf(pos1 + 1, "%s", proteinName);
string proteinNameStr(proteinName);
result.setProteinName(proteinNameStr);
while (strstr(line, "Probab=") == NULL) {
fgets(line, 500, inputFile); //skip long name
}
//get probab, E-value, Score, Aligned_cols, Identities, Similarity, Sum_probs
pos1 = strstr(line, "=");
float probab;
sscanf(pos1 + 1, "%f", &probab);
result.setProbab(probab);
char* pos2 = strstr(pos1 + 1, "=");
float eValue;
sscanf(pos2 + 1, "%f", &eValue);
result.setExpect(eValue);
char* pos3 = strstr(pos2 + 1, "=");
float score;
sscanf(pos3 + 1, "%f", &score);
result.setScore(score);
char* pos4 = strstr(pos3 + 1, "=");
int alignedCols;
sscanf(pos4 + 1, "%d", &alignedCols);
result.setAlignedCols(alignedCols);
char* pos5 = strstr(pos4 + 1, "=");
float identities;
sscanf(pos5 + 1, "%f", &identities);
result.setIdentities(identities);
result.setFirstStateReached(true);
result.setSecondStateReached(false);
}
}
hhrResultVector.push_back(result);
fclose(inputFile);
}
