vector<string> setParameters();
string getCommandName() { return "pairwise.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
string getDescription() { return "calculates pairwise distances from an unaligned fasta file"; }
SequenceDB alignDB;
pairwiseData(){}
- pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, int tid) {
+ pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, float cu, int tid) {
outputFileName = ofn;
m = mout;
start = st;
alignDB = DB;
count = 0;
output = op;
+ cutoff = cu;
threadID = tid;
}
};
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
- pDataArray->count = pDataArray->end;
+ pDataArray->count = 0;
int startTime = time(NULL);
if(pDataArray->start == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
for(int i=pDataArray->start;i<pDataArray->end;i++){
+ pDataArray->count++;
string name = pDataArray->alignDB.get(i).getName();
//pad with spaces to make compatible
outFile << endl;
if(i % 100 == 0){
- pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
}
- pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
outFile.close();
delete alignment;
ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
-
- pDataArray->count = pDataArray->end;
int startTime = time(NULL);
if((pDataArray->output == "lt") && pDataArray->start == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
+ pDataArray->count = 0;
for(int i=pDataArray->start;i<pDataArray->end;i++){
+ pDataArray->count++;
if(pDataArray->output == "lt") {
string name = pDataArray->alignDB.get(i).getName();
if (pDataArray->output == "lt") { outFile << endl; }
if(i % 100 == 0){
- pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
}
- pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)+"\n");
outFile.close();
delete alignment;