X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=528f71c11c24f7a47133bef2d60a6906249abe92;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=16348c8d324a962ca336c82a2ad303f156cde9e3;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 16348c8..528f71c 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -11,6 +11,7 @@
 #include "readphylip.h"
 #include "readcolumn.h"
 #include "readmatrix.hpp"
+#include "clusterdoturcommand.h"
 
 //**********************************************************************************************************************
 vector<string> ClusterCommand::setParameters(){	
@@ -135,16 +136,17 @@ ClusterCommand::ClusterCommand(string option)  {
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }	
-			else {  distfile = phylipfile;  format = "phylip"; 	}
+			else {  distfile = phylipfile;  format = "phylip"; 	m->setPhylipFile(phylipfile); }
 			
 			columnfile = validParameter.validFile(parameters, "column", true);
 			if (columnfile == "not open") { columnfile = ""; abort = true; }	
 			else if (columnfile == "not found") { columnfile = ""; }
-			else {  distfile = columnfile; format = "column";	}
+			else {  distfile = columnfile; format = "column"; m->setColumnFile(columnfile);	}
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			if ((phylipfile == "") && (columnfile == "")) { 
 				//is there are current file available for either of these?
@@ -181,7 +183,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
@@ -191,7 +193,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));  
 			
 			method = validParameter.validFile(parameters, "method", false);
@@ -206,7 +208,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			timing = validParameter.validFile(parameters, "timing", false);
 			if (timing == "not found") { timing = "F"; }
 			
-			}
+		}
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ClusterCommand", "ClusterCommand");
@@ -222,6 +224,34 @@ int ClusterCommand::execute(){
 	
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
+		//phylip file given and cutoff not given - use cluster.classic because it uses less memory and is faster
+		if ((format == "phylip") && (cutoff > 10.0)) {
+			m->mothurOutEndLine(); m->mothurOut("You are using a phylip file and no cutoff.  I will run cluster.classic to save memory and time."); m->mothurOutEndLine();
+			
+			//run unique.seqs for deconvolute results
+			string inputString = "phylip=" + distfile;
+			if (namefile != "") { inputString += ", name=" + namefile; }
+			inputString += ", precision=" + toString(precision);
+			inputString += ", method=" + method;
+			if (hard)	{ inputString += ", hard=T";	}
+			else		{ inputString += ", hard=F";	}
+			if (sim)	{ inputString += ", sim=T";		}
+			else		{ inputString += ", sim=F";		}
+
+			
+			m->mothurOutEndLine(); 
+			m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine(); 
+			m->mothurOut("Running command: cluster.classic(" + inputString + ")"); m->mothurOutEndLine(); 
+			
+			Command* clusterClassicCommand = new ClusterDoturCommand(inputString);
+			clusterClassicCommand->execute();
+			delete clusterClassicCommand;
+			
+			m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine();  
+
+			return 0;
+		}
+		
 		ReadMatrix* read;
 		if (format == "column") { read = new ReadColumnMatrix(columnfile, sim); }	//sim indicates whether its a similarity matrix
 		else if (format == "phylip") { read = new ReadPhylipMatrix(phylipfile, sim); }
@@ -243,7 +273,7 @@ int ClusterCommand::execute(){
 		if (m->control_pressed) { //clean up
 			delete list; delete matrix; delete rabund;
 			sabundFile.close();rabundFile.close();listFile.close();
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear();
 			return 0;
 		}
 		
@@ -282,7 +312,7 @@ int ClusterCommand::execute(){
 			if (m->control_pressed) { //clean up
 				delete list; delete matrix; delete rabund; delete cluster;
 				sabundFile.close();rabundFile.close();listFile.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear();
 				return 0;
 			}
 		
@@ -325,7 +355,7 @@ int ClusterCommand::execute(){
 			cout.flush();
 	 		print_start = false;
 		}
-	
+		
 		if(previousDist <= 0.0000){
 			printData("unique");
 		}