X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=528f71c11c24f7a47133bef2d60a6906249abe92;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=cdcc6ca9745d8bdf3509c3505ef5c15dc61fd991;hpb=e51cb7e261265800fa2d2831b6516e33ebc7d78b;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index cdcc6ca..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(){	
@@ -75,6 +76,7 @@ ClusterCommand::ClusterCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -134,25 +136,26 @@ 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?
 				//give priority to column, then phylip
 				columnfile = m->getColumnFile(); 
-				if (columnfile != "") {  m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+				if (columnfile != "") {  distfile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
 				else { 
 					phylipfile = m->getPhylipFile(); 
-					if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+					if (phylipfile != "") { distfile = phylipfile;  format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 					else { 
 						m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the cluster command."); m->mothurOutEndLine(); 
 						abort = true;
@@ -180,7 +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);
@@ -190,7 +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);
@@ -205,7 +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");
@@ -221,6 +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); }
@@ -242,7 +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;
 		}
 		
@@ -281,7 +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;
 			}
 		
@@ -324,7 +355,7 @@ int ClusterCommand::execute(){
 			cout.flush();
 	 		print_start = false;
 		}
-	
+		
 		if(previousDist <= 0.0000){
 			printData("unique");
 		}