X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readcolumn.cpp;h=53a8c4263dddc4687acc5a64cf7c5b1d27aac647;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=f61a40c483b69f7418ca4d2702ca995f4180f3e2;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;p=mothur.git

diff --git a/readcolumn.cpp b/readcolumn.cpp
index f61a40c..53a8c42 100644
--- a/readcolumn.cpp
+++ b/readcolumn.cpp
@@ -14,9 +14,17 @@
 
 ReadColumnMatrix::ReadColumnMatrix(string df) : distFile(df){
 	
-	successOpen = openInputFile(distFile, fileHandle);
+	successOpen = m->openInputFile(distFile, fileHandle);
+	sim = false;
 	
 }
+/***********************************************************************/
+
+ReadColumnMatrix::ReadColumnMatrix(string df, bool s) : distFile(df){
+	
+	successOpen = m->openInputFile(distFile, fileHandle);
+	sim = s;
+}
 
 /***********************************************************************/
 
@@ -47,15 +55,11 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 			map<string,int>::iterator itA = nameMap->find(firstName);
 			map<string,int>::iterator itB = nameMap->find(secondName);
 				
-			if(itA == nameMap->end()){
-				cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);
-			}
-			if(itB == nameMap->end()){
-				cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
-			}
+			if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+			if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 
 			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 && itA != itB){
 				if(itA->second > itB->second){
@@ -90,7 +94,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 				}
 				reading->update(itA->second * nseqs);
 			}
-			gobble(fileHandle);
+			m->gobble(fileHandle);
 		}
 
 		if(lt == 0){  // oops, it was square
@@ -98,7 +102,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 			fileHandle.close();  //let's start over
 			D->clear();  //let's start over
 		   
-			openInputFile(distFile, fileHandle);  //let's start over
+			m->openInputFile(distFile, fileHandle);  //let's start over
 
 			while(fileHandle){
 				fileHandle >> firstName >> secondName >> distance;
@@ -108,15 +112,11 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 				map<string,int>::iterator itA = nameMap->find(firstName);
 				map<string,int>::iterator itB = nameMap->find(secondName);
 				
-				if(itA == nameMap->end()){
-					cerr << "BError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
-				}
-				if(itB == nameMap->end()){
-					cerr << "BError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
-				}
+				if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+				if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 				
 				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 && itA->second > itB->second){
 					PCell value(itA->second, itB->second, distance);
@@ -124,7 +124,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
 					reading->update(itA->second * nseqs);
 				}
 		
-				gobble(fileHandle);
+				m->gobble(fileHandle);
 			}
 		}