X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readcluster.cpp;h=b6cb71de5fdbb888f4a7c1614987f74cd0bf8b1a;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=0893a146a84c9e71eb95475eabe66c2b80314c93;hpb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7;p=mothur.git

diff --git a/readcluster.cpp b/readcluster.cpp
index 0893a14..b6cb71d 100644
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -12,7 +12,6 @@
 /***********************************************************************/
 
 ReadCluster::ReadCluster(string distfile, float c, string o, bool s){
-		globaldata = GlobalData::getInstance();
 		m = MothurOut::getInstance();
         distFile = distfile;
 		cutoff = c;
@@ -23,7 +22,7 @@ ReadCluster::ReadCluster(string distfile, float c, string o, bool s){
 
 /***********************************************************************/
 
-int ReadCluster::read(NameAssignment* nameMap){
+int ReadCluster::read(NameAssignment*& nameMap){
 	try {
         
 		if (format == "phylip") { convertPhylip2Column(nameMap); }
@@ -31,7 +30,7 @@ int ReadCluster::read(NameAssignment* nameMap){
 		
 		if (m->control_pressed) { return 0; }
 		
-		if (sortWanted) {  OutPutFile = sortFile(distFile, outputDir);  }
+		if (sortWanted) {  OutPutFile = m->sortFile(distFile, outputDir);  }
 		else {  OutPutFile = distFile;   } //for use by clusters splitMatrix to convert a phylip matrix to column
 		
 		return 0;
@@ -44,7 +43,7 @@ int ReadCluster::read(NameAssignment* nameMap){
 }
 /***********************************************************************/
 
-int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
+int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
 	try {	
 		//convert phylip file to column file
 		map<int, string> rowToName;
@@ -54,15 +53,20 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 		ofstream out;
 		string tempFile = distFile + ".column.temp";
 		
-		openInputFile(distFile, in);
-		openOutputFile(tempFile, out);
+		m->openInputFile(distFile, in);  m->gobble(in);
+		m->openOutputFile(tempFile, out);
 		
 		float distance;
 		int square, nseqs;
 		string name;
 		vector<string> matrixNames;
-        
-		in >> nseqs >> name;
+		
+		string numTest;
+		in >> numTest >> name;
+		
+		if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+		else { convert(numTest, nseqs); }
+		
 		rowToName[0] = name;
 		matrixNames.push_back(name);
 		
@@ -105,7 +109,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 					
 					for(int j=0;j<i;j++){
 					
-						if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+						if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
 						
 						in >> distance;
 						
@@ -122,7 +126,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 					
 					for(int j=0;j<i;j++){
 						
-						if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+						if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
 						
 						in >> distance;
 						
@@ -144,7 +148,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 				if(nameMap == NULL){
 					list->set(i, name);
 					for(int j=0;j<nseqs;j++){
-						if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+						if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
 						
 						in >> distance;
 					
@@ -159,7 +163,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 					if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
 					
 					for(int j=0;j<nseqs;j++){
-						if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+						if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
 						
 						in >> distance;
                         
@@ -177,40 +181,39 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 		list->setLabel("0");
 		in.close();
 		out.close();
-		
+	
 		if(nameMap == NULL){
 			nameMap = new NameAssignment();
 			for(int i=0;i<matrixNames.size();i++){
 				nameMap->push_back(matrixNames[i]);
 			}
-			globaldata->nameMap = nameMap;
 		}
 		
 	
 		ifstream in2;
 		ofstream out2;
 		
-		string outputFile = getRootName(distFile) + "column.dist";
-		openInputFile(tempFile, in2);
-		openOutputFile(outputFile, out2);
+		string outputFile = m->getRootName(distFile) + "column.dist";
+		m->openInputFile(tempFile, in2);
+		m->openOutputFile(outputFile, out2);
 		
 		int first, second;
 		float dist;
 		
 		while (in2) {
-			if (m->control_pressed) { in2.close(); out2.close(); remove(tempFile.c_str()); remove(outputFile.c_str()); return 0; }
+			if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(tempFile); m->mothurRemove(outputFile); return 0; }
 			
 			in2 >> first >> second >> dist;
 			out2 << rowToName[first] << '\t' << rowToName[second] << '\t' << dist << endl;
-			gobble(in2);
+			m->gobble(in2);
 		}
 		in2.close();
 		out2.close();
 		
-		remove(tempFile.c_str());
+		m->mothurRemove(tempFile);
 		distFile = outputFile;
-		
-		if (m->control_pressed) {  remove(outputFile.c_str());  }
+	
+		if (m->control_pressed) {  m->mothurRemove(outputFile);  }
 
 		return 0;
 	}