void docItem::openItem(){
if (list.size() == 0){
ui.lineEdit_title->clear();
} else if (list.size() > 0){
QSqlQuery query(QString("select book_item.book, books.title, book_item.identifier "
"from book_item,doc_item, books "
"where doc_item.book_item = book_item.id and books.id = book_item.book "
"and doc_item.id = \'%1\' ").arg(list.at(curr)));
query.next();
ui.spinBox_id_book->setValue(query.value(0).toInt());
ui.lineEdit_title->setText(query.value(1).toString());
//ui.spinBox_coun->setValue(query.value(2).toInt());
ui.lineEdit_identifier->setText(query.value(2).toString());
}
viewItems();
//test for deleting
if (vid == 1){
QSqlQuery testRead(QString("select Count(card_read.id) "
"from card_read, book_item "
"where card_read.book_item = book_item.id and book_item.identifier = \'%1\'")
.arg(ui.lineEdit_identifier->text()));
testRead.next();
QSqlQuery testDoc(QString("select Count(doc_item.id) "
"from doc_item, docs, book_item "
"where doc_item.book_item = book_item.id and doc_item.doc = docs.id and docs.vid = 2 "
"and book_item.identifier = \'%1\'")
.arg(ui.lineEdit_identifier->text()));
testDoc.next();
if (testRead.value(0).toInt() == 0 and testDoc.value(0).toInt() == 0){
ui.pushButton_del->setEnabled(true);
} else if (testRead.value(0).toInt() > 0 or testDoc.value(0).toInt() > 0){
ui.pushButton_del->setEnabled(false);
}
} else if (vid == 2){
ui.pushButton_del->setEnabled(true);
}
//
if (list.size() == 0){
ui.pushButton_toFirst->setEnabled(false);
ui.pushButton_toLast->setEnabled(false);
ui.pushButton_toNext->setEnabled(false);
ui.pushButton_toPrev->setEnabled(false);
} else if (list.size() > 0) {
if (curr == 0){
ui.pushButton_toFirst->setEnabled(false);
ui.pushButton_toPrev->setEnabled(false);
} else {
ui.pushButton_toFirst->setEnabled(true);
ui.pushButton_toPrev->setEnabled(true);
}
if (curr == list.size() - 1){
ui.pushButton_toLast->setEnabled(false);
ui.pushButton_toNext->setEnabled(false);
} else {
ui.pushButton_toLast->setEnabled(true);
ui.pushButton_toNext->setEnabled(true);
}
}
}
int main(int argc, char** argv)
{
printf("start\n");
ObjStoreContext* pContext = (ObjStoreContext*)malloc(sizeof(ObjStoreContext));
InitObjStore(pContext, "/tmp/objstore/");
if (argc == 1)
{
//for debug
testWrite(pContext, 10, 0x5f, 9097);
testRead(pContext, 10, 0x5f, 9097);
testCheck(pContext, 10, 9097);
testWriteRange(pContext, 10, 0x6f, 4096, 4096);
testReadRange(pContext, 10, 0x6f, 4096, 4096);
}
else
{
if (argc == 5)
{
int maxobjid = atoi(argv[2]);
int mask = atoi(argv[3]);
int datasize = atoi(argv[4]);
if(strcmp(argv[1],"-w") == 0)
{
printf("start write...\n");
testWrite(pContext, maxobjid, mask, datasize);
}
else if (strcmp(argv[1], "-r") == 0)
{
printf("start read...\n");
testRead(pContext, maxobjid, mask, datasize);
}
else
{
usage();
return 1;
}
}
else if (argc == 4)
{
int maxobjid = atoi(argv[2]);
int datasize = atoi(argv[3]);
if (strcmp(argv[1], "-c") == 0)
{
printf("start check...\n");
testCheck(pContext, maxobjid, datasize);
}
else
{
usage();
return 1;
}
}
else if (argc == 6)
{
int maxobjid = atoi(argv[2]);
int mask = atoi(argv[3]);
int startpos = atoi(argv[4]);
int datasize = atoi(argv[5]);
if (strcmp(argv[1], "-wp") == 0)
{
printf("start write range ...\n");
testWriteRange(pContext, maxobjid, mask, startpos, datasize);
}
else if (strcmp(argv[1], "-rp") == 0)
{
printf("start read range ... \n");
testReadRange(pContext, maxobjid, mask, startpos, datasize);
}
else if (strcmp(argv[1], "-cp") == 0)
{
printf("start check range ... \n");
testCheckRange(pContext, maxobjid, mask,startpos, datasize);
}
}
else
{
usage();
return 1;
}
}
system("pause");
return 0;
}
/**********************************************************************************************************************
This function reads the sdataset from FASTA/FASTQ files
**********************************************************************************************************************/
bool Dataset::readDataset(string fileName, UINT64 minOverlap, UINT64 datasetNumber)
{
CLOCKSTART;
cout << "Reading dataset: " << datasetNumber << " from file: " << fileName << endl;
ifstream myFile;
myFile.open (fileName.c_str());
if(myFile == NULL)
MYEXIT("Unable to open file: "+fileName)
UINT64 goodReads = 0, badReads = 0;
vector<string> line;
string line1, text, line1ReverseComplement,line2ReverseComplement;
enum FileType { FASTA, FASTQ, UNDEFINED};
FileType fileType = UNDEFINED;
while(!myFile.eof())
{
if( (goodReads + badReads ) != 0 && (goodReads + badReads)%1000000 == 0)
cout<< setw(10) << goodReads + badReads << " reads processed in dataset " << setw(2) << datasetNumber <<". " << setw(10) << goodReads << " good reads." << setw(10) << badReads << " bad reads." << endl;
if(fileType == UNDEFINED)
{
getline (myFile,text);
if(text[0] == '>')
fileType = FASTA;
else if(text[0] == '@')
fileType = FASTQ;
else
MYEXIT("Unknown input file format.");
myFile.seekg(0, ios::beg);
}
line.clear();
if(fileType == FASTA) // Fasta file
{
getline (myFile,text);
line.push_back(text);
getline (myFile,text,'>');
line.push_back(text);
line.at(1).erase(std::remove(line.at(1).begin(), line.at(1).end(), '\n'), line.at(1).end());
line1 = line.at(1); // The first string is in the 2nd line.
}
else if(fileType == FASTQ) // Fastq file.
{
for(UINT64 i = 0; i < 4; i++) // Read the remaining 3 lines. Total of 4 lines represent one sequence in a fastq file.
{
getline (myFile,text);
line.push_back(text);
}
line1 = line.at(1); // The first string is in the 2nd line.
}
for (std::string::iterator p = line1.begin(); line1.end() != p; ++p) // Change the case
*p = toupper(*p);
if(line1.length() > minOverlap && testRead(line1) ) // Test the read is of good quality.
{
Read *r1=new Read;
line1ReverseComplement = reverseComplement(line1);
if(line1.compare(line1ReverseComplement) < 0) // Store lexicographically smaller between the read and its reverse complement.
r1->setRead(line1);
else
r1->setRead(line1ReverseComplement);
UINT64 len = r1->getReadLength();
if(len > longestReadLength)
longestReadLength = len;
if(len < shortestReadLength)
shortestReadLength = len;
reads->push_back(r1); // Store the first string in the dataset.
numberOfReads++; // Counter of the total number of reads.
goodReads++;
}
else
badReads++;
}
myFile.close();
cout << endl << "Dataset: " << setw(2) << datasetNumber << endl;
cout << "File name: " << fileName << endl;
cout << setw(10) << goodReads << " good reads in current dataset." << endl;
cout << setw(10) << badReads << " bad reads in current dataset." << endl;
cout << setw(10) << goodReads + badReads << " total reads in current dataset." << endl;
cout << setw(10) << numberOfReads << " good reads in all datasets." << endl << endl;;
CLOCKSTOP;
return true;
}
/**********************************************************************************************************************
This function reads the file again and store matepair infromation.
**********************************************************************************************************************/
bool Dataset::storeMatePairInformation(string fileName, UINT64 minOverlap, UINT64 datasetNumber)
{
CLOCKSTART;
cout << "Store paired-end information of dataset: " << datasetNumber << " from file: " << fileName << endl;
UINT64 goodMatePairs = 0, badMatePairs = 0;
ifstream myFile;
myFile.open (fileName.c_str());
if(myFile == NULL)
MYEXIT("Unable to open file: "+fileName)
vector<string> line;
string line1, line2, text, line1ReverseComplement,line2ReverseComplement;
Read r1, r2;
enum FileType { FASTA, FASTQ, UNDEFINED};
FileType fileType = UNDEFINED;
while(!myFile.eof())
{
if(goodMatePairs+badMatePairs != 0 && (goodMatePairs+badMatePairs)%1000000 == 0)
{
cout << setw(10) << goodMatePairs + badMatePairs << " reads processed in store mate-pair information." << setw(10) << goodMatePairs << " reads in good mate-pairs." << setw(10) << badMatePairs << " reads in bad mate-pairs." << endl;
}
if(fileType == UNDEFINED)
{
getline (myFile,text);
if(text[0] == '>')
fileType = FASTA;
else if(text[0] == '@')
fileType = FASTQ;
else
MYEXIT("Unknown input file format.");
myFile.seekg(0, ios::beg);
}
line.clear();
if(fileType == FASTA) // Fasta file
{
getline (myFile,text);
line.push_back(text);
getline (myFile,text,'>');
line.push_back(text);
getline (myFile,text);
line.push_back(text);
getline (myFile,text,'>');
line.push_back(text);
line.at(1).erase(std::remove(line.at(1).begin(), line.at(1).end(), '\n'), line.at(1).end());
line1 = line.at(1); // The first string is in the 2nd line.
line.at(3).erase(std::remove(line.at(3).begin(), line.at(3).end(), '\n'), line.at(3).end());
line2 = line.at(3); // The second string is in the 4th line.
}
else if(fileType == FASTQ) // Fastq file.
{
for(UINT64 i = 0; i < 8; i++) // Read the remaining 7 lines. Total of 8 lines represent two sequence in a fastq file.
{
getline (myFile,text);
line.push_back(text);
}
line1 = line.at(1); // The first string is in the 2nd line.
line2 = line.at(5); // The second string is in the 6th lien.
}
for (std::string::iterator p = line1.begin(); line1.end() != p; ++p) // Change the case
*p = toupper(*p);
for (std::string::iterator p = line2.begin(); line2.end() != p; ++p) // Change the case
*p = toupper(*p);
if(line1.length() > minOverlap && line2.length() > minOverlap && testRead(line1) && testRead(line2)) // Test if both reads are of good quality.
{
Read * r1 = getReadFromString(line1),* r2 = getReadFromString(line2);
if (r1->superReadID != 0) // This read is contained by the superRead
r1 = getReadFromID(r1->superReadID);
if (r2->superReadID != 0) // This read is contained by the superRead.
r2 = getReadFromID(r2->superReadID);
goodMatePairs += 2;
UINT16 orient1, orient2;
string read1Froward = r1->getStringForward();
string read2Froward = r2->getStringForward();
orient1 = read1Froward.find(line1) != string::npos ? 1 : 0;
orient2 = read2Froward.find(line2) != string::npos ? 1 : 0;
r1->addMatePair(r2, orient1 * 2 + orient2, datasetNumber); // Two bits are used to represent the orientation of the reads in a matepair.
r2->addMatePair(r1, orient1 + orient2 * 2, datasetNumber); // 0 = 00 means the reverse of r1 and the reverse of r2 are matepairs.
// 1 = 01 means the reverse of r1 and the forward of r2 are matepairs.
// 2 = 10 means the forward of r1 and the reverse of r2 are matepairs.
// 3 = 11 means the forward of r1 and the forward of r2 are matepairs.
}
else
badMatePairs +=2;
}
cout << endl << "Dataset: " << setw(2) << datasetNumber << endl;
cout << "File name: " << fileName << endl;
cout << setw(10) << goodMatePairs << " reads in " << setw(10) << goodMatePairs/2 << " mate-pairs are good." << endl;
cout << setw(10) << badMatePairs << " reads in " << setw(10) << badMatePairs/2 << " mate-pairs are discarded." << endl << endl;
myFile.close();
CLOCKSTOP;
return true;
}
int main()
{
testWrite();
testRead();
return 0;
}
