C++ Progress::finish方法代码示例

//.........这里部分代码省略.........
            {
                idx=0; // start a new read

                //skips NN
                while (*pt_begin =='N' && pt_begin < (rseq+ readlen))
                {
                    pt_begin ++;
                }
                // goes to next N or end of seq
                while ( (pt_begin[idx] !='N') &&  ((pt_begin +idx) < (rseq+ readlen))  )
                {
                    idx++;
                }
                
                //we have a seq beginning at  pt_begin of size idx  ,without any N, will be treated as a read:
                binread->write_read(pt_begin,idx);
		revcomp_sequence(pt_begin,idx); // reverse complement the string 
		binread->write_read(pt_begin,idx); // write reverse complement string 
		revcomp_sequence(pt_begin,idx); // restore the string 

		pt_begin += idx;
            }
            
            // binread->write_read(rseq,readlen);
            
            
            NbRead++;
            if ((NbRead%10000)==0)
            {
                progress_conversion.inc(10000);
            }
        }
	//printf("Number of reads converted to binary %d \n",NbRead);
        progress_conversion.finish();
        binread->close();

    }
    ///fin conversion
    if (clear_cache)
    {
#ifdef OSX
        system("purge");
#else
        system("echo 3 > /proc/sys/vm/drop_caches");
#endif
    }
    
    
    
#if SINGLE_BAR
    Progress progress;
    char message[1000];
    sprintf(message,"Counting kmers");
    progress.timer_mode=1;
    if (verbose == 0 )
        progress.init(total_IO,message);
#endif
    
    //use_compressed_reads=false; // for testing compute_kmer_from_one_seq 
    // how many times we will traverse the whole reads file (has an influence on temp disk space)

   uint64_t iter_partition=0;
    for (uint32_t current_pass = 0; current_pass < nb_passes; current_pass ++)
    {
	// stop computing if all partitions are done Added by Raunaq
        if (iter_partition==temp_partition)

//.........这里部分代码省略.........
		string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
		
		//use the unix sort 
		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
			string command = "sort -n " + squareFile + " -o " + outfile;
			system(command.c_str());
		#else //sort using windows sort
			string command = "sort " + squareFile + " /O " + outfile;
			system(command.c_str());
		#endif
		
		if (m->control_pressed) { m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }

		//output to new file distance for each row and save positions in file where new row begins
		ifstream in;
		m->openInputFile(outfile, in);
		
		distFile = outfile + ".rowFormatted";
		m->openOutputFile(distFile, out);
		
		rowPos.resize(nseqs, -1);
		int currentRow;
		int first, second;
		float dist;
		map<int, float> rowMap;
		map<int, float>::iterator itRow;
		
		//get first currentRow
		in >> first;
		currentRow = first;
		
		string firstString = toString(first);
		for(int k = 0; k < firstString.length(); k++)  {   in.putback(firstString[k]);  }
		
		while(!in.eof()) {
			
			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
			
			in >> first >> second >> dist; m->gobble(in);
			
			if (first != currentRow) {
				//save position in file of each new row
				rowPos[currentRow] = out.tellp();
				
				out << currentRow << '\t' << rowMap.size() << '\t';
				
				for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
					out << itRow->first << '\t' << itRow->second << '\t';
				}
				out << endl;
				
				currentRow = first;
				rowMap.clear();
				
				//save row you just read
				if (dist < cutoff) {
					rowMap[second] = dist;
				}
			}else{
				if (dist < cutoff) {
					rowMap[second] = dist;
				}
			}
		}
		
		//print last Row
		//save position in file of each new row
		rowPos[currentRow] = out.tellp();
		
		out << currentRow << '\t' << rowMap.size() << '\t';
		
		for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
			out << itRow->first << '\t' << itRow->second << '\t';
		}
		out << endl;
		
		
		in.close();
		out.close();
		
		if (m->control_pressed) {  m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile);  delete reading; return 0; }
		
		m->mothurRemove(tempOutFile);
		m->mothurRemove(outfile);
		
		reading->finish();
		
		delete reading;
		list->setLabel("0");
		
		if (m->control_pressed) {  m->mothurRemove(distFile);  return 0; }

		return 1;

	}
	catch(exception& e) {
		m->errorOut(e, "FormatColumnMatrix", "read");
		exit(1);
	}
}

//.........这里部分代码省略.........
				randT = new Tree(ct);
				//create random relationships between nodes

				randT->assembleRandomTree();
				
				if (m->control_pressed) { 
					delete reading; delete output; delete randT; delete ct; 
					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
				}


				//get pscore of random tree
				randomData = pars.getValues(randT, processors, outputDir);
				
				if (m->control_pressed) { 
					delete reading; delete output; delete randT; delete ct; 
					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
				}
			
				for(int r = 0; r < numComp; r++) {
					//add trees pscore to map of scores
					map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
					if (it != rscoreFreq[r].end()) {//already have that score
						rscoreFreq[r][randomData[r]]++;
					}else{//first time we have seen this score
						rscoreFreq[r][randomData[r]] = 1;
					}
			
					//add randoms score to validscores
					validScores[randomData[r]] = randomData[r];
				}
				
				//update progress bar
				reading->update(j);
				
				delete randT;
			}
		}

		for(int a = 0; a < numComp; a++) {
			float rcumul = 0.0000;
			float ucumul = 0.0000;
			//this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
			for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) { 
				if (randomtree == "") {
					map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
					//user data has that score 
					if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second;  }
					else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
					//make uCumul map
					uCumul[a][it->first] = ucumul;
				}
			
				//make rscoreFreq map and rCumul
				map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
				//get percentage of random trees with that info
				if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul+= it2->second;  }
				else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
				rCumul[a][it->first] = rcumul;
			}
			
			//find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
			for (int h = 0; h < userTreeScores[a].size(); h++) {
				UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
			}
		}
		
		if (m->control_pressed) { 
				delete reading; delete output;
				delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
				if (randomtree == "") {  outSum.close();  }
				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
				return 0;
		}
		
		//finish progress bar
		reading->finish();
		delete reading;
		
		printParsimonyFile();
		if (randomtree == "") { printUSummaryFile(); }
				
        delete output; delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
		
		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
		
		m->mothurOutEndLine();
		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
		m->mothurOutEndLine();

		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "ParsimonyCommand", "execute");
		exit(1);
	}
}