X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readcluster.cpp;h=d8227101b2c339b3904e95144d11f5cccb068dd3;hb=65f2be9d8f9b4cf72b4aafd800fdd11ad26435fd;hp=acbebaeece94faf995cd9d1a26112e40185314b8;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/readcluster.cpp b/readcluster.cpp
index acbebae..d822710 100644
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -11,16 +11,18 @@
 
 /***********************************************************************/
 
-ReadCluster::ReadCluster(string distfile, float c){
-		globaldata = GlobalData::getInstance();
+ReadCluster::ReadCluster(string distfile, float c, string o, bool s){
 		m = MothurOut::getInstance();
         distFile = distfile;
 		cutoff = c;
+		outputDir = o;
+		sortWanted = s;
+		list = NULL;
 }
 
 /***********************************************************************/
 
-int ReadCluster::read(NameAssignment* nameMap){
+int ReadCluster::read(NameAssignment*& nameMap){
 	try {
         
 		if (format == "phylip") { convertPhylip2Column(nameMap); }
@@ -28,7 +30,8 @@ int ReadCluster::read(NameAssignment* nameMap){
 		
 		if (m->control_pressed) { return 0; }
 		
-		OutPutFile = sortFile(distFile);
+		if (sortWanted) {  OutPutFile = m->sortFile(distFile, outputDir);  }
+		else {  OutPutFile = distFile;   } //for use by clusters splitMatrix to convert a phylip matrix to column
 		
 		return 0;
 			
@@ -40,7 +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;
@@ -50,15 +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);
 		
@@ -173,22 +181,21 @@ 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;
@@ -198,14 +205,14 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 			
 			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());
 		distFile = outputFile;
-		
+	
 		if (m->control_pressed) {  remove(outputFile.c_str());  }
 
 		return 0;