X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readphylip.cpp;h=1c529b26f15fdfa172c8a0f7ebcf20187e87b03b;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=edda41593deb0fd3ac908ea4ebd333dee8d03edc;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/readphylip.cpp b/readphylip.cpp
index edda415..1c529b2 100644
--- a/readphylip.cpp
+++ b/readphylip.cpp
@@ -14,9 +14,18 @@
 
 ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
         
-        successOpen = openInputFile(distFile, fileHandle);
+        successOpen = m->openInputFile(distFile, fileHandle);
+		sim=false;
         
 }
+/***********************************************************************/
+
+ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
+	
+	successOpen = m->openInputFile(distFile, fileHandle);
+	sim=s;
+}
+
 
 /***********************************************************************/
 
@@ -27,9 +36,13 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
                         int square, nseqs;
                         string name;
                         vector<string> matrixNames;
-        
-                        fileHandle >> nseqs >> name;
-
+						
+						string numTest;
+						fileHandle >> numTest >> name;
+			
+						if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+						else { convert(numTest, nseqs); }
+			
                         matrixNames.push_back(name);
 
                         if(nameMap == NULL){
@@ -85,6 +98,7 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
 											
                                                 
                                                         if (distance == -1) { distance = 1000000; }
+														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);
@@ -104,6 +118,7 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
 														if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
                                 
                                                         if (distance == -1) { distance = 1000000; }
+														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);
@@ -135,6 +150,7 @@ int ReadPhylipMatrix::read(NameAssignment* nameMap){
 														if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 														
                                                         if (distance == -1) { distance = 1000000; }
+														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);
@@ -153,9 +169,10 @@ 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 (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);
                                                         }