+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MySumThreadFunction(LPVOID lpParam){
+ sumData* pDataArray;
+ pDataArray = (sumData*)lpParam;
+
+ try {
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ in.seekg(0);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ pDataArray->count++;
+
+ if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+
+ Sequence current(in); pDataArray->m->gobble(in);
+
+ if (current.getName() != "") {
+
+ int num = 1;
+ if ((pDataArray->namefile != "") || (pDataArray->countfile !="")){
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
+
+ if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ int numns = current.getNumNs();
+ for (int i = 0; i < num; i++) {
+ pDataArray->startPosition.push_back(current.getStartPos());
+ pDataArray->endPosition.push_back(current.getEndPos());
+ pDataArray->seqLength.push_back(current.getNumBases());
+ pDataArray->ambigBases.push_back(current.getAmbigBases());
+ pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
+ pDataArray->numNs.push_back(numns);
+ }
+ }
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumThreadFunction");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+static DWORD WINAPI MyContigsSumThreadFunction(LPVOID lpParam){
+ contigsSumData* pDataArray;
+ pDataArray = (contigsSumData*)lpParam;
+
+ try {
+ string name;
+ //Name Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns
+ int length, OLength, thisOStart, thisOEnd, numMisMatches, numns;
+
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ in.seekg(0); pDataArray->m->getline(in); pDataArray->m->gobble(in);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ pDataArray->count++;
+
+ if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+
+ //seqname start end nbases ambigs polymer numSeqs
+ in >> name >> length >> OLength >> thisOStart >> thisOEnd >> numMisMatches >> numns; pDataArray->m->gobble(in);
+
+ int num = 1;
+ if ((pDataArray->namefile != "") || (pDataArray->countfile !="")){
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = pDataArray->nameMap.find(name);
+
+ if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ pDataArray->ostartPosition.push_back(thisOStart);
+ pDataArray->oendPosition.push_back(thisOEnd);
+ pDataArray->oLength.push_back(OLength);
+ pDataArray->omismatches.push_back(numMisMatches);
+ pDataArray->numNs.push_back(numns);
+ }
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MyContigsThreadFunction");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+static DWORD WINAPI MyAlignsThreadFunction(LPVOID lpParam){
+ alignsData* pDataArray;
+ pDataArray = (alignsData*)lpParam;
+
+ try {
+
+ string name, TemplateName, SearchMethod, AlignmentMethod;
+ //QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template
+ //checking for minScore, maxInsert, minSim
+ int length, TemplateLength, QueryStart, QueryEnd, TemplateStart, TemplateEnd, PairwiseAlignmentLength, GapsInQuery, GapsInTemplate, LongestInsert;
+ float SearchScore, SimBtwnQueryTemplate;
+
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ in.seekg(0); pDataArray->m->getline(in); pDataArray->m->gobble(in);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ pDataArray->count++;
+
+ if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+
+ in >> name >> length >> TemplateName >> TemplateLength >> SearchMethod >> SearchScore >> AlignmentMethod >> QueryStart >> QueryEnd >> TemplateStart >> TemplateEnd >> PairwiseAlignmentLength >> GapsInQuery >> GapsInTemplate >> LongestInsert >> SimBtwnQueryTemplate; pDataArray->m->gobble(in);
+ cout << i << '\t' << name << endl;
+ int num = 1;
+ if ((pDataArray->namefile != "") || (pDataArray->countfile !="")){
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = pDataArray->nameMap.find(name);
+
+ if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ pDataArray->sims.push_back(SimBtwnQueryTemplate);
+ pDataArray->scores.push_back(SearchScore);
+ pDataArray->inserts.push_back(LongestInsert);
+ }
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MyAlignsThreadFunction");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+static DWORD WINAPI MySumScreenThreadFunction(LPVOID lpParam){
+ sumScreenData* pDataArray;
+ pDataArray = (sumScreenData*)lpParam;
+
+ try {
+
+ ofstream goodFile;
+ pDataArray->m->openOutputFile(pDataArray->goodFName, goodFile);
+
+ ofstream badAccnosFile;
+ pDataArray->m->openOutputFile(pDataArray->badAccnosFName, badAccnosFile);
+
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ in.seekg(0);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ pDataArray->count++;
+
+ if (pDataArray->m->control_pressed) { in.close(); badAccnosFile.close(); goodFile.close(); pDataArray->count = 1; return 1; }
+
+ Sequence currSeq(in); pDataArray->m->gobble(in);
+
+ if (currSeq.getName() != "") {
+ bool goodSeq = 1; // innocent until proven guilty
+ string trashCode = "";
+ //have the report files found you bad
+ map<string, string>::iterator it = pDataArray->badSeqNames.find(currSeq.getName());
+ if (it != pDataArray->badSeqNames.end()) { goodSeq = 0; trashCode = it->second; } //found it
+
+ if (pDataArray->summaryfile == "") {
+ if(pDataArray->startPos != -1 && pDataArray->startPos < currSeq.getStartPos()) { goodSeq = 0; trashCode += "start|"; }
+ if(pDataArray->endPos != -1 && pDataArray->endPos > currSeq.getEndPos()) { goodSeq = 0; trashCode += "end|"; }
+ if(pDataArray->maxAmbig != -1 && pDataArray->maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; trashCode += "ambig|"; }
+ if(pDataArray->maxHomoP != -1 && pDataArray->maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; trashCode += "homop|"; }
+ if(pDataArray->minLength != -1 && pDataArray->minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "<length|"; }
+ if(pDataArray->maxLength != -1 && pDataArray->maxLength < currSeq.getNumBases()) { goodSeq = 0; trashCode += ">length|"; }
+ }
+ if (pDataArray->contigsreport == "") { //contigs report includes this so no need to check again
+ if(pDataArray->maxN != -1 && pDataArray->maxN < currSeq.getNumNs()) { goodSeq = 0; trashCode += "n|"; }
+ }
+
+
+ if(goodSeq == 1){
+ currSeq.printSequence(goodFile);
+ }
+ else{
+ badAccnosFile << currSeq.getName() << '\t' << trashCode.substr(0, trashCode.length()-1) << endl;
+ pDataArray->badSeqNames[currSeq.getName()] = trashCode;
+ }
+
+ }
+ //report progress
+ if((i+1) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(i+1)); pDataArray->m->mothurOutEndLine(); }
+ }
+ //report progress
+ if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
+
+
+
+ in.close();
+ goodFile.close();
+ badAccnosFile.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ScreenSeqsCommand", "MySumScreenThreadFunction");
+ exit(1);
+ }
+}
+
+#endif
+
+/**************************************************************************************************/
+
+
+