QVariant UserSearchModel::data(UserSearchResult* item, int role) {
switch (role) {
case Qt::DisplayRole: return QVariant(nameLine(item));
case DetailTextRole: return QVariant(detailLine(item));
default: return QVariant();
}
}
void BlastParser::parseFile(string blastResultFileLocation) {
string blastResultFile(blastResultFileLocation);
blastResultFile += rootName;
blastResultFile += "/query.blaPDB";
FILE* fptr = fopen((char*) blastResultFile.c_str(), "r");
if (fptr == NULL) {
cout << "input file: " << blastResultFile << " can't open" << endl;
} else {
int lineLength = 5000;
char line[lineLength];
BlastRecord blastRecord;
char prevState = 'N';
char currentState = 'N';
while (fgets(line, lineLength, fptr) != NULL) {
//cout << line << endl;
if (strstr(line, ">") != NULL) {
currentState = 'A';
} else if (strstr(line, "Score =") != NULL) {
currentState = 'B';
} else if (strstr(line, "Query: ") != NULL && prevState == 'B') {
currentState = 'C';
} else if ((strstr(line, "Query: ") != NULL && prevState == 'C')
|| (strstr(line, "Query: ") != NULL && prevState == 'D')) {
currentState = 'D';
} else {
continue;
}
/*cout << "prev: " << prevState << " current: " << currentState
<< endl;*/
if ((prevState == 'D' && currentState == 'B')
|| (prevState == 'C' && currentState == 'B')
|| (prevState == 'D' && currentState == 'A')
|| (prevState == 'C' && currentState == 'A')) {
blastRecords.push_back(blastRecord);
//blastRecord.displayRecordInfo();
string emptyString("");
blastRecord.setQueryPart(emptyString);
blastRecord.setSubjectPart(emptyString);
}
if (currentState == 'A') {
string nameLine(line);
string hitName = nameLine.substr(1, 6);
//cout << "hitName is " << hitName << endl;
blastRecord.setHitName(hitName);
} else if (currentState == 'B') {
char* pch = strstr(line, "=");
double score;
sscanf(pch + 1, "%lf", &score);
char* pch2 = strstr(pch + 1, "=");
double expect;
sscanf(pch2 + 1, "%lf", &expect);
blastRecord.setScore(score);
blastRecord.setExpect(expect);
/*cout << "score: " << score << endl;
cout << "expect: " << expect << endl;*/
} else if (currentState == 'C') {
char info0[6], queryPart[200];
int queryStart, queryEnd;
sscanf(line, "%s %d %s %d", info0, &queryStart, queryPart,
&queryEnd);
string _queryPart(queryPart);
fgets(line, lineLength, fptr); //skip a line
fgets(line, lineLength, fptr); //fetch subject line info
char info1[6], subjectPart[200];
int subjectStart, subjectEnd;
sscanf(line, "%s %d %s %d", info1, &subjectStart, subjectPart,
&subjectEnd);
string _subjectPart(subjectPart);
blastRecord.setQueryStart(queryStart);
blastRecord.setQueryPart(_queryPart);
blastRecord.setQueryEnd(queryEnd);
blastRecord.setSubjectStart(subjectStart);
blastRecord.setSubjectPart(_subjectPart);
blastRecord.setSubjectEnd(subjectEnd);
/*cout << "query info: " << queryStart << queryPart << queryEnd
<< endl;
cout << "subject info: " << subjectStart << subjectPart
<< subjectEnd << endl;*/
} else if (currentState == 'D') {
char info0[6], queryPart[200];
int queryStart, queryEnd;
sscanf(line, "%s %d %s %d", info0, &queryStart, queryPart,
&queryEnd);
string _queryPart(queryPart);
fgets(line, lineLength, fptr); //skip a line
fgets(line, lineLength, fptr); //fetch subject line info
char info1[6], subjectPart[200];
int subjectStart, subjectEnd;
sscanf(line, "%s %d %s %d", info1, &subjectStart, subjectPart,
&subjectEnd);
string _subjectPart(subjectPart);
string oldQueryPart = blastRecord.getQueryPart();
oldQueryPart += _queryPart;
blastRecord.setQueryPart(oldQueryPart);
blastRecord.setQueryEnd(queryEnd);
string oldSubjectPart = blastRecord.getSubjectPart();
oldSubjectPart += _subjectPart;
blastRecord.setSubjectPart(oldSubjectPart);
blastRecord.setSubjectEnd(subjectEnd);
/*cout << "query info: " << blastRecord.getQueryStart()
<< blastRecord.getQueryPart()
<< blastRecord.getQueryEnd() << endl;
cout << "subject info: " << blastRecord.getSubjectStart()
<< blastRecord.getSubjectPart()
<< blastRecord.getSubjectEnd() << endl;
*/
}
prevState = currentState;
}
blastRecords.push_back(blastRecord); //don't forget the last hit
//blastRecord.displayRecordInfo();
}
}
