removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / readphylip.cpp

diff --git a/readphylip.cpp b/readphylip.cpp
index 130deccaf0adbb1af542034450d1362a20ae8b57..b13dc25c0eded92a950bfc41a782075624e47fdd 100644 (file)
--- a/readphylip.cpp
+++ b/readphylip.cpp
@@ -15,8 +15,17 @@
 ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
         
         successOpen = m->openInputFile(distFile, fileHandle);
+               sim=false;
         
 }
+/***********************************************************************/
+
+ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
+       
+       successOpen = m->openInputFile(distFile, fileHandle);
+       sim=s;
+}
+
 
 /***********************************************************************/
 
@@ -85,7 +94,7 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
                                                                                        
                                                 
                                                         if (distance == -1) { distance = 1000000; }
-                                                                                                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
+                                                                                                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                 
                                                         if(distance < cutoff){
                                                                 PCell value(i, j, distance);
@@ -105,7 +114,7 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
                                                                                                                if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
                                 
                                                         if (distance == -1) { distance = 1000000; }
-                                                                                                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
+                                                                                                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                         
                                                         if(distance < cutoff){
                                                                 PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
@@ -137,7 +146,7 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
                                                                                                                if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
                                                                                                                
                                                         if (distance == -1) { distance = 1000000; }
-                                                                                                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
+                                                                                                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                         
                                                         if(distance < cutoff && j < i){
                                                                 PCell value(i, j, distance);
@@ -157,7 +166,7 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
                                                                                                                if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
                                                                                                                
                                                        if (distance == -1) { distance = 1000000; }
-                                                                                                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.                                                        
+                                                                                                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.                                                        
                                                         
                                                                                                                if(distance < cutoff && j < i){
                                                                 PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);