X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clearcutcommand.cpp;h=d6c284d68159b66255d3cdb29d57217e9dd73af6;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=fc028a2f91fae5f2c50e3ba33fef889806f46a6c;hpb=b1bcc272003b50a8c06dc9120754da1f5b744598;p=mothur.git

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index fc028a2..d6c284d 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -8,7 +8,6 @@
  */
 
 #include "clearcutcommand.h"
-#include "globaldata.hpp"
 
 /**************************************************************************************/
 ClearcutCommand::ClearcutCommand(string option)  {	
@@ -21,7 +20,7 @@ ClearcutCommand::ClearcutCommand(string option)  {
 		else {
 			//valid paramters for this command
 			string Array[] =  {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",
-								"expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","stdin","outputdir","inputdir"};
+								"expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -43,7 +42,7 @@ ClearcutCommand::ClearcutCommand(string option)  {
 				it = parameters.find("fasta");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["fasta"] = inputDir + it->second;		}
 				}
@@ -51,7 +50,7 @@ ClearcutCommand::ClearcutCommand(string option)  {
 				it = parameters.find("phylip");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["phylip"] = inputDir + it->second;		}
 				}
@@ -73,56 +72,53 @@ ClearcutCommand::ClearcutCommand(string option)  {
 
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
-			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";	}
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(inputFile);	}
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "version", false);		if (temp == "not found"){	temp = "F";			}
-			version = isTrue(temp);
+			version = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "verbose", false);		if (temp == "not found"){	temp = "F";			}
-			verbose = isTrue(temp); 
+			verbose = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "quiet", false);		if (temp == "not found"){	temp = "F";			}
-			quiet = isTrue(temp); 
+			quiet = m->isTrue(temp); 
 			
 			seed = validParameter.validFile(parameters, "seed", false);			if (seed == "not found"){	seed = "*";			}
 			
 			temp = validParameter.validFile(parameters, "norandom", false);		if (temp == "not found"){	temp = "F";			}
-			norandom = isTrue(temp); 
+			norandom = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "shuffle", false);		if (temp == "not found"){	temp = "F";			}
-			shuffle = isTrue(temp); 
+			shuffle = m->isTrue(temp); 
 			
-			temp = validParameter.validFile(parameters, "neighbor", false);		if (temp == "not found"){	temp = "F";			}
-			neighbor = isTrue(temp); 
-			
-			temp = validParameter.validFile(parameters, "stdin", false);		if (temp == "not found"){	temp = "F";			}
-			stdin = isTrue(temp); 
+			temp = validParameter.validFile(parameters, "neighbor", false);		if (temp == "not found"){	temp = "T";			}
+			neighbor = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "DNA", false);			if (temp == "not found"){	temp = "F";			}
-			DNA = isTrue(temp);
+			DNA = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "protein", false);		if (temp == "not found"){	temp = "F";			}
-			protein = isTrue(temp);
+			protein = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "jukes", false);		if (temp == "not found"){	temp = "F";			}
-			jukes = isTrue(temp);
+			jukes = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "kimura", false);		if (temp == "not found"){	temp = "F";			}
-			kimura = isTrue(temp);
+			kimura = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "stdout", false);		if (temp == "not found"){	temp = "F";			}
-			stdout = isTrue(temp); 
+			stdoutWanted = m->isTrue(temp); 
 			
 			matrixout = validParameter.validFile(parameters, "matrixout", false);	if (matrixout == "not found"){	matrixout = "";		}
 			
 			ntrees = validParameter.validFile(parameters, "ntrees", false);		if (ntrees == "not found"){	ntrees = "1";		}
 			
 			temp = validParameter.validFile(parameters, "expblen", false);		if (temp == "not found"){	temp = "F";			}
-			expblen = isTrue(temp);
+			expblen = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "expdist", false);		if (temp == "not found"){	temp = "F";			}
-			expdist = isTrue(temp);
+			expdist = m->isTrue(temp);
 			
 			if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }
 		}
@@ -139,7 +135,8 @@ void ClearcutCommand::help(){
 	try {
 		m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");
 		m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");
-		m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA, stdin. \n");
+		m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
+		m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n");
 		m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");
 		m->mothurOut("The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n");
 		
@@ -149,9 +146,8 @@ void ClearcutCommand::help(){
 		m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");
 		m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");
 		m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");
-		m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");
+		m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=T. \n");
 		
-		m->mothurOut("The stdin parameter reads input from STDIN, default=F. \n");
 		m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");
 		m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");
 		
@@ -164,6 +160,7 @@ void ClearcutCommand::help(){
 		m->mothurOut("The clearcut command should be in the following format: \n");
 		m->mothurOut("clearcut(phylip=yourDistanceFile) \n");
 		m->mothurOut("Example: clearcut(phylip=abrecovery.phylip.dist) \n");	
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ClearcutCommand", "help");
@@ -178,15 +175,15 @@ int ClearcutCommand::execute() {
 		if (abort == true) { return 0; }
 				
 		//prepare filename
-		string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";
+		string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
 		
 		//get location of clearcut
 		GlobalData* globaldata = GlobalData::getInstance();
 		string path = globaldata->argv;
 		path = path.substr(0, (path.find_last_of('m')));
-
-		string clearcutCommand = path + "clearcut/clearcut ";
 		
+		string clearcutCommand = path + "clearcut ";
+				
 		//you gave us a distance matrix
 		if (phylipfile != "") { clearcutCommand += "--distance "; 	}
 		
@@ -201,27 +198,37 @@ int ClearcutCommand::execute() {
 		if (shuffle)			{  clearcutCommand += "--shuffle ";		}
 		if (neighbor)			{  clearcutCommand += "--neighbor ";	}
 		
-		if (stdin)				{  clearcutCommand += "--stdin ";		}
-		else					{  clearcutCommand += "--in=" + inputFile + " "; }
-		if (stdout)				{  clearcutCommand += "--stdout ";		}
-		else					{  clearcutCommand += "--out=" + outputName + " "; }
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			clearcutCommand += "--in=" + inputFile + " "; 
+		#else
+			clearcutCommand += "--in=\"" + inputFile + "\" "; 
+		#endif
+		
+		if (stdoutWanted)		{  clearcutCommand += "--stdout ";		}
+		else{  
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				clearcutCommand += "--out=" + outputName + " "; }
+			#else
+				clearcutCommand += "--out=\"" + outputName + "\" "; }
+			#endif
 		
 		if (DNA)				{  clearcutCommand += "--DNA ";			}
 		if (protein)			{  clearcutCommand += "--protein ";		}
 		if (jukes)				{  clearcutCommand += "--jukes ";		}
 		if (kimura)				{  clearcutCommand += "--kimura ";		}
-		if (matrixout != "")	{  clearcutCommand += "--matrixout=" + matrixout + " "; }
+		if (matrixout != "")	{  clearcutCommand += "--matrixout=" + matrixout + " ";  }
 		if (ntrees != "1")		{  clearcutCommand += "--ntrees=" + ntrees + " "; }
 		if (expblen)			{  clearcutCommand += "--expblen ";		}
 		if (expdist)			{  clearcutCommand += "--expdist ";		}
-		
+	
 		//run clearcut
 		system(clearcutCommand.c_str());
 		
-		if (!stdout) {	
+		if (!stdoutWanted) {	
 			m->mothurOutEndLine();
 			m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-			m->mothurOut(outputName); m->mothurOutEndLine();	
+			m->mothurOut(outputName); m->mothurOutEndLine();
+			if (matrixout != "")	{  m->mothurOut(matrixout); m->mothurOutEndLine();  }
 			m->mothurOutEndLine();
 		}
 
@@ -233,3 +240,7 @@ int ClearcutCommand::execute() {
 	}
 }
 /**************************************************************************************/
+
+
+
+