descriptions

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index 0893a146a84c9e71eb95475eabe66c2b80314c93..d8227101b2c339b3904e95144d11f5cccb068dd3 100644 (file)
--- 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);
                
@@ -177,22 +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;
@@ -202,14 +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;