X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=distancecommand.h;h=2f53232b5943d835e8c27adf7374a5e3a8ce168f;hp=36a1e24b0986bb24a106fb3b72f6cba17f1acfce;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=83b5acbe3d6087a6cd73e80dde4b923387a01d01

diff --git a/distancecommand.h b/distancecommand.h
index 36a1e24..2f53232 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -15,50 +15,218 @@
 #include "validcalculator.h"
 #include "dist.h"
 #include "sequencedb.h"
+#include "ignoregaps.h"
+#include "eachgapdist.h"
+#include "eachgapignore.h"
+#include "onegapdist.h"
+#include "onegapignore.h"
 
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct distanceData {
+	int startLine;
+	int endLine;
+	string dFileName;
+	float cutoff;
+	SequenceDB alignDB;
+	vector<string> Estimators;
+	MothurOut* m;
+	string output;
+	int numNewFasta, count;
+	string countends;
+	
+	distanceData(){}
+	distanceData(int s, int e, string dbname, float c, SequenceDB db, vector<string> Est, MothurOut* mout, string o, int num, string count) {
+		startLine = s;
+		endLine = e;
+		dFileName = dbname;
+		cutoff = c;
+		alignDB = db;
+		Estimators = Est;
+		m = mout;
+		output = o;
+		numNewFasta = num;
+		countends = count;
+		
+	}
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){ 
+	distanceData* pDataArray;
+	pDataArray = (distanceData*)lpParam;
+	
+	try {
+		ValidCalculators validCalculator;
+		Dist* distCalculator;
+		if (pDataArray->m->isTrue(pDataArray->countends) == true) {
+			for (int i=0; i<pDataArray->Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", pDataArray->Estimators[i]) == true) { 
+					if (pDataArray->Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+					else if (pDataArray->Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
+					else if (pDataArray->Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
+				}
+			}
+		}else {
+			for (int i=0; i<pDataArray->Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", pDataArray->Estimators[i]) == true) { 
+					if (pDataArray->Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+					else if (pDataArray->Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+					else if (pDataArray->Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+				}
+			}
+		}
+		
+		int startTime = time(NULL);
+		
+		//column file
+		ofstream outFile(pDataArray->dFileName.c_str(), ios::trunc);
+		outFile.setf(ios::fixed, ios::showpoint);
+		outFile << setprecision(4);
+		pDataArray->count = 0;
+		
+		if (pDataArray->output != "square") { 
+			if((pDataArray->output == "lt") && (pDataArray->startLine == 0)){	outFile << pDataArray->alignDB.getNumSeqs() << endl;	}
+			
+			for(int i=pDataArray->startLine;i<pDataArray->endLine;i++){
+				if(pDataArray->output == "lt")	{	
+					string name = pDataArray->alignDB.get(i).getName();
+					if (name.length() < 10) { //pad with spaces to make compatible
+						while (name.length() < 10) {  name += " ";  }
+					}
+					outFile << name << '\t';	
+				}
+				for(int j=0;j<i;j++){
+					
+					if (pDataArray->m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
+					
+					//if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
+					//the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
+					if ((i >= pDataArray->numNewFasta) && (j >= pDataArray->numNewFasta)) { break; }
+					
+					distCalculator->calcDist(pDataArray->alignDB.get(i), pDataArray->alignDB.get(j));
+					double dist = distCalculator->getDist();
+					
+					if(dist <= pDataArray->cutoff){
+						if (pDataArray->output == "column") { outFile << pDataArray->alignDB.get(i).getName() << ' ' << pDataArray->alignDB.get(j).getName() << ' ' << dist << endl; }
+					}
+					if (pDataArray->output == "lt") {  outFile << dist << '\t'; }
+				}
+				
+				if (pDataArray->output == "lt") { outFile << endl; }
+				
+				if(i % 100 == 0){
+					pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 				}
+				pDataArray->count++;
+			}
+			pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
+		}else{
+			if(pDataArray->startLine == 0){	outFile << pDataArray->alignDB.getNumSeqs() << endl;	}
+			
+			for(int i=pDataArray->startLine;i<pDataArray->endLine;i++){
+				
+				string name = pDataArray->alignDB.get(i).getName();
+				//pad with spaces to make compatible
+				if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
+				
+				outFile << name << '\t';	
+				
+				for(int j=0;j<pDataArray->alignDB.getNumSeqs();j++){
+					
+					if (pDataArray->m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
+					
+					distCalculator->calcDist(pDataArray->alignDB.get(i), pDataArray->alignDB.get(j));
+					double dist = distCalculator->getDist();
+					
+					outFile << dist << '\t'; 
+				}
+				
+				outFile << endl; 
+				
+				if(i % 100 == 0){
+					pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
+				}
+				pDataArray->count++;
+			}
+			pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n"); 
+		}
+		
+		outFile.close();
+		delete distCalculator;
+		
+		return 0; 
+	}
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "DistanceCommand", "MyDistThreadFunction");
+		exit(1);
+	}
+} 
+#endif
 
+/**************************************************************************************************/
 class DistanceCommand : public Command {
 
 public:
 	DistanceCommand(string);
-	~DistanceCommand();
-	int execute();	
-	void help();
+	DistanceCommand();
+	~DistanceCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "dist.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
+	string getDescription()		{ return "calculate the pairwaise distances between aligned sequences"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	struct linePair {
+	struct distlinePair {
 		int start;
 		int end;
+		
 	};
 	
-	Dist* distCalculator;
+	//Dist* distCalculator;
 	SequenceDB alignDB;
 
-	string countends, output, fastafile, calc, outputDir, oldfastafile, column;
+	string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
 	int processors, numNewFasta;
 	float cutoff;
-	map<int, int> processIDS;   //end line, processid
-	vector<linePair*> lines;
+	vector<int> processIDS;   //end line, processid
+	vector<distlinePair> lines;
 	
 	bool abort;
-	vector<string>  Estimators; //holds estimators to be used
+	vector<string>  Estimators, outputNames; //holds estimators to be used
 	
-	//void appendFiles(string, string);
+	//void m->appendFiles(string, string);
 	void createProcesses(string);
 	int driver(/*Dist*, SequenceDB, */int, int, string, float);
+	int driver(int, int, string, string);
 	
 	#ifdef USE_MPI 
 	int driverMPI(int, int, MPI_File&, float);
-	int driverMPI(int, int, string, long&);
+	int driverMPI(int, int, string, unsigned long long&);
+	int driverMPI(int, int, string, unsigned long long&, string);
 	#endif
 	
-	int convertMatrix(string);
+	//int convertMatrix(string);
 	bool sanityCheck();
-	int convertToLowerTriangle(string);
+	//int convertToLowerTriangle(string);
 
 };
 
 #endif
 
+/**************************************************************************************************/
+