added a few evenness calculators and fixed a couple of bugs in filter.seqs and pre...

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index acbebaeece94faf995cd9d1a26112e40185314b8..af71cbc96f1cca200bb8e5f66258703917f6ac53 100644 (file)
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -11,11 +11,14 @@
 
 /***********************************************************************/
 
-ReadCluster::ReadCluster(string distfile, float c){
+ReadCluster::ReadCluster(string distfile, float c, string o, bool s){
                globaldata = GlobalData::getInstance();
                m = MothurOut::getInstance();
         distFile = distfile;
                cutoff = c;
+               outputDir = o;
+               sortWanted = s;
+               list = NULL;
 }
 
 /***********************************************************************/
@@ -28,7 +31,8 @@ int ReadCluster::read(NameAssignment* nameMap){
                
                if (m->control_pressed) { return 0; }
                
-               OutPutFile = sortFile(distFile);
+               if (sortWanted) {  OutPutFile = sortFile(distFile, outputDir);  }
+               else {  OutPutFile = distFile;   } //for use by clusters splitMatrix to convert a phylip matrix to column
                
                return 0;
                        
@@ -50,7 +54,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                ofstream out;
                string tempFile = distFile + ".column.temp";
                
-               openInputFile(distFile, in);
+               openInputFile(distFile, in);  gobble(in);
                openOutputFile(tempFile, out);
                
                float distance;
@@ -173,7 +177,7 @@ 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++){
@@ -205,7 +209,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                
                remove(tempFile.c_str());
                distFile = outputFile;
-               
+       
                if (m->control_pressed) {  remove(outputFile.c_str());  }
 
                return 0;