X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readphylip.cpp;h=130deccaf0adbb1af542034450d1362a20ae8b57;hb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;hp=edda41593deb0fd3ac908ea4ebd333dee8d03edc;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/readphylip.cpp b/readphylip.cpp
index edda415..130decc 100644
--- a/readphylip.cpp
+++ b/readphylip.cpp
@@ -14,7 +14,7 @@
 
 ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
         
-        successOpen = openInputFile(distFile, fileHandle);
+        successOpen = m->openInputFile(distFile, fileHandle);
         
 }
 
@@ -85,6 +85,7 @@ 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.
                                                 
                                                         if(distance < cutoff){
                                                                 PCell value(i, j, distance);
@@ -104,6 +105,7 @@ 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.
                                                         
                                                         if(distance < cutoff){
                                                                 PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
@@ -135,6 +137,7 @@ 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.
                                                         
                                                         if(distance < cutoff && j < i){
                                                                 PCell value(i, j, distance);
@@ -153,9 +156,10 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
 														
 														if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 														
-                                                        if (distance == -1) { distance = 1000000; }
+                                                       if (distance == -1) { distance = 1000000; }
+														else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.                                                        
                                                         
-                                                        if(distance < cutoff && j < i){
+														if(distance < cutoff && j < i){
                                                                 PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
                                                                 D->addCell(value);
                                                         }