From: westcott <westcott>
Date: Thu, 9 Sep 2010 15:10:01 +0000 (+0000)
Subject: done testing 1.13.0
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=43921e55e68146936cf72f65fbc92553bc05977b

done testing 1.13.0
---

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 5903946..1a7ab1f 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -174,7 +174,7 @@ int ClearcutCommand::execute() {
 	try {
 		
 		if (abort == true) { return 0; }
-				
+		
 		//prepare filename
 		string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
 		
@@ -201,25 +201,14 @@ int ClearcutCommand::execute() {
 		if (shuffle)			{  char* temp = new char[9];  strcpy(temp, "--shuffle");  cPara.push_back(temp);	}
 		if (neighbor)			{  char* temp = new char[10];  strcpy(temp, "--neighbor");  cPara.push_back(temp);	}
 		
-		string tempIn = "";
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			tempIn += "--in=" + inputFile; 
-		#else
-			tempIn += "--in=\"" + inputFile + "\"";  
-		#endif
-		
+		string tempIn = "--in=" + inputFile;  
 		char* tempI = new char[tempIn.length()];
 		strcpy(tempI, tempIn.c_str());
 		cPara.push_back(tempI);
 		
 		if (stdoutWanted)		{  char* temp = new char[8];  strcpy(temp, "--stdout");  cPara.push_back(temp);	}
 		else{  
-			string tempOut = "";
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				tempOut += "--out=" + outputName;  
-			#else
-				tempOut += "--out=\"" + outputName + "\""; 
-			#endif
+			string tempOut = "--out=" + outputName;  
 			
 			char* temp = new char[tempOut.length()];
 			strcpy(temp, tempOut.c_str());
diff --git a/distancecommand.cpp b/distancecommand.cpp
index b3f0a2d..8bdd7cd 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -422,6 +422,13 @@ int DistanceCommand::execute(){
 				remove(outputFile.c_str());
 				outputFile = column;
 			}
+			
+			if (outputDir != "") { 
+				string newOutputName = outputDir + m->getSimpleName(outputFile);
+				rename(outputFile.c_str(), newOutputName.c_str());
+				remove(outputFile.c_str());
+				outputFile = newOutputName;
+			}
 		}
 
 		
diff --git a/distclearcut.cpp b/distclearcut.cpp
index a4ac777..cf69649 100644
--- a/distclearcut.cpp
+++ b/distclearcut.cpp
@@ -78,7 +78,7 @@ NJ_build_distance_matrix(NJ_ARGS *nj_args) {
   /* Read an alignment in FASTA format */
   alignment = 
     NJ_read_fasta(nj_args);
-  
+ 
   if(!alignment) {
     return(NULL);
   }
@@ -91,6 +91,7 @@ NJ_build_distance_matrix(NJ_ARGS *nj_args) {
    * From proteins, we may want to allow users to specify
    * a substitution matrix (feature)
    */
+
   dmat = 
     NJ_compute_dmat(nj_args,
 		    alignment);
@@ -100,7 +101,7 @@ NJ_build_distance_matrix(NJ_ARGS *nj_args) {
   if(!dmat) {
     fprintf(stderr, "Clearcut: Error computing distance matrix\n");
   }
-  
+ 
   /* now free the memory associated with the alignment */
   NJ_free_alignment(alignment);
 
@@ -156,6 +157,7 @@ NJ_compute_dmat(NJ_ARGS *nj_args,
 
   /* allocate val matrix in dmat */
   dmat->val = (float *)calloc(dmat->ntaxa*dmat->ntaxa, sizeof(float));
+
   if(!dmat->val) {
     fprintf(stderr, "Clearcut: Memory allocation error in NJ_compute_dmat()\n");
     return(NULL);
@@ -209,7 +211,7 @@ NJ_compute_dmat(NJ_ARGS *nj_args,
     fprintf(stderr, "Clearcut: Invalid distance correction model.\n");
     return(NULL);
   }
-  
+ 
   return(dmat);
 }
 
diff --git a/dmat.cpp b/dmat.cpp
index 1d00cff..64fd67e 100644
--- a/dmat.cpp
+++ b/dmat.cpp
@@ -465,7 +465,7 @@ NJ_parse_distance_matrix(NJ_ARGS *nj_args) {
     fp = stdin;
   } else {
     fp = fopen(nj_args->infilename, "r");
-    if(!fp) {
+    if(fp==NULL) {
       fprintf(stderr, "Clearcut: Could not open distance matrix: %s\n", nj_args->infilename);
       perror("Clearcut");
       goto XIT_BAD;
diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index a3f88cf..d85d5be 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -208,7 +208,7 @@ int ListSeqsCommand::readFasta(){
 		ifstream in;
 		m->openInputFile(fastafile, in);
 		string name;
-		
+	
 		while(!in.eof()){
 			
 			if (m->control_pressed) { in.close(); return 0; }
diff --git a/makefile b/makefile
index ffee66e..278a3ad 100644
--- a/makefile
+++ b/makefile
@@ -13,9 +13,9 @@
 
 CXXFLAGS += -O3
 
-MOTHUR_FILES = "\"../Release\""
+MOTHUR_FILES = "\"Enter_your_default_path_here\""
 
-RELEASE_DATE = "\"8/30/2010\""
+RELEASE_DATE = "\"9/9/2010\""
 VERSION = "\"1.13.0\""
 
 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}