X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readcolumn.cpp;h=53a8c4263dddc4687acc5a64cf7c5b1d27aac647;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=c03c37f1feeb888c341ca4daa01c644069c155a5;hpb=163b300cfd7d4ca4e70c454be20f07b1d8346650;p=mothur.git

diff --git a/readcolumn.cpp b/readcolumn.cpp
index c03c37f..53a8c42 100644
--- a/readcolumn.cpp
+++ b/readcolumn.cpp
@@ -14,13 +14,21 @@
 
 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;
+}
 
 /***********************************************************************/
 
-void ReadColumnMatrix::read(NameAssignment* nameMap){
+int ReadColumnMatrix::read(NameAssignment* nameMap){
 	try {		
 
 		string firstName, secondName;
@@ -38,20 +46,20 @@ void ReadColumnMatrix::read(NameAssignment* nameMap){
 		//need to see if this is a square or a triangular matrix...
 	
 		while(fileHandle && lt == 1){  //let's assume it's a triangular matrix...
+
 		
 			fileHandle >> firstName >> secondName >> distance;	// get the row and column names and distance
+			
+			if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 	
 			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";
-			}
-			if(itB == nameMap->end()){
-				cerr << "ABError: 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 (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){
@@ -86,29 +94,29 @@ void ReadColumnMatrix::read(NameAssignment* nameMap){
 				}
 				reading->update(itA->second * nseqs);
 			}
-			gobble(fileHandle);
+			m->gobble(fileHandle);
 		}
 
 		if(lt == 0){  // oops, it was square
+	
 			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;
+				
+				if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 		
 				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 (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);
@@ -116,25 +124,24 @@ void ReadColumnMatrix::read(NameAssignment* nameMap){
 					reading->update(itA->second * nseqs);
 				}
 		
-				gobble(fileHandle);
+				m->gobble(fileHandle);
 			}
 		}
-
+		
+		if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+		
 		reading->finish();
 		fileHandle.close();
 
 		list->setLabel("0");
+		
+		return 1;
 
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReadColumnMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ReadColumnMatrix", "read");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReadColumnMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
 
 /***********************************************************************/