X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=8019def31cad9acc54c1308171bf796e949890a1;hb=957d67f7d8bbadfd2930de061e89fd9b149270fd;hp=678912c2076a10af0580f9b778238e3134542c44;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 678912c..8019def 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(){	
@@ -53,6 +54,28 @@ string ClusterCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ClusterCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "list") {  outputFileName =  "list"; }
+            else if (type == "rabund") {  outputFileName =  "rabund"; }
+            else if (type == "sabund") {  outputFileName =  "sabund"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ClusterCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ClusterCommand::ClusterCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -182,7 +205,7 @@ 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);
@@ -192,7 +215,7 @@ 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);
@@ -207,7 +230,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			timing = validParameter.validFile(parameters, "timing", false);
 			if (timing == "not found") { timing = "F"; }
 			
-			}
+		}
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ClusterCommand", "ClusterCommand");
@@ -223,6 +246,34 @@ 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); }
@@ -258,13 +309,17 @@ int ClusterCommand::execute(){
 		if (outputDir == "") { outputDir += m->hasPath(distfile); }
 		fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
 		
-		m->openOutputFile(fileroot+ tag + ".sabund",	sabundFile);
-		m->openOutputFile(fileroot+ tag + ".rabund",	rabundFile);
-		m->openOutputFile(fileroot+ tag + ".list",		listFile);
+        string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
+        string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
+        string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+        
+		m->openOutputFile(sabundFileName,	sabundFile);
+		m->openOutputFile(rabundFileName,	rabundFile);
+		m->openOutputFile(listFileName,	listFile);
 		
-		outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
-		outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
-		outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
+		outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+		outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+		outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
 		
 		
 		time_t estart = time(NULL);