X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pairwiseseqscommand.h;h=90c21b25a7c35c47834ea7311f3e7f969163fc98;hp=0e749d5c7e252ceb7c777de1e8878084f61b0a4d;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index 0e749d5..90c21b2 100644
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -40,8 +40,9 @@ public:
 	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"; }
 
@@ -94,7 +95,7 @@ struct pairwiseData {
     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;
@@ -111,6 +112,7 @@ struct pairwiseData {
         alignDB = DB;
 		count = 0;
         output = op;
+        cutoff = cu;
 		threadID = tid;
 	}
 };
@@ -127,7 +129,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
 		outFile.setf(ios::fixed, ios::showpoint);
 		outFile << setprecision(4);
 		
-		pDataArray->count = pDataArray->end;
+		pDataArray->count = 0;
         
         int startTime = time(NULL);
         
@@ -161,6 +163,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
         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
@@ -190,17 +193,19 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
 				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
                 
+                if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
+                
 				outFile << dist << '\t'; 
 			}
 			
 			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;
@@ -223,8 +228,6 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
 		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);
         
@@ -257,7 +260,9 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
         
         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();
@@ -290,6 +295,8 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
 				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
                 
+                if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
+                
 				if(dist <= pDataArray->cutoff){
 					if (pDataArray->output == "column") { outFile << pDataArray->alignDB.get(i).getName() << ' ' << pDataArray->alignDB.get(j).getName() << ' ' << dist << endl; }
 				}
@@ -299,11 +306,11 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
 			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;