X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fullmatrix.cpp;h=4451d6645ea8691b941ebbc991f82cc4ce8b4706;hp=0255d07f00bbcfef3a9c62658149ec39fd6fc5bf;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 0255d07..4451d66 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -11,15 +11,14 @@
 
 /**************************************************************************/
 //This constructor reads a distance matrix file and stores the data in the matrix.
-FullMatrix::FullMatrix(ifstream& filehandle) {
+FullMatrix::FullMatrix(ifstream& filehandle, GroupMap* g, bool s) : groupmap(g), sim(s) {
 	try{
 		m = MothurOut::getInstance();
-		globaldata = GlobalData::getInstance();
-		groupmap = globaldata->gGroupmap;
 		
 		string name, group;
-		filehandle >> numSeqs >> name;
 		
+		filehandle >> numSeqs >> name;
+	
 		//make the matrix filled with zeros
 		matrix.resize(numSeqs); 
 		for(int i = 0; i < numSeqs; i++) {
@@ -44,6 +43,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 				
 				for(int i=0;i<numSeqs;i++){
 					filehandle >> matrix[0][i];
+					if (sim) {  matrix[0][i] = 1.0 - matrix[0][i];  }
 				}
 				break;
 			}
@@ -54,12 +54,14 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 				break;
 			}
 		}
-		
+	
 		//read rest of matrix
-		if (square == true) { readSquareMatrix(filehandle); }
-		else { readLTMatrix(filehandle); }
+		if (square == true) {  readSquareMatrix(filehandle); }
+		else {  readLTMatrix(filehandle); }
 		
-		sortGroups(0, numSeqs-1);	
+		filehandle.close();
+		
+		if (!m->control_pressed) { sortGroups(0, numSeqs-1); }	
 				
 	}
 	catch(exception& e) {
@@ -68,7 +70,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 	}
 }
 /**************************************************************************/
-void FullMatrix::readSquareMatrix(ifstream& filehandle) {
+int FullMatrix::readSquareMatrix(ifstream& filehandle) {
 	try {
 	
 		Progress* reading;
@@ -77,7 +79,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
 		int count = 0;
 		
 		string group, name;
-		
+	
 		for(int i=1;i<numSeqs;i++){
 			filehandle >> name;		
 			
@@ -88,14 +90,22 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
 			if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
 				
 			for(int j=0;j<numSeqs;j++){
+				if (m->control_pressed) { delete reading;  return 0; }
+				
 				filehandle >> matrix[i][j];
+				if (sim) {  matrix[i][j] = 1.0 - matrix[i][j];  }
 				
 				count++;
 				reading->update(count);
 			}
 		}
+		
+		if (m->control_pressed) { delete reading;  return 0; }
+		
 		reading->finish();
 		delete reading;
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "FullMatrix", "readSquareMatrix");
@@ -103,8 +113,9 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
 	}
 } 
 /**************************************************************************/
-void FullMatrix::readLTMatrix(ifstream& filehandle) {
+int FullMatrix::readLTMatrix(ifstream& filehandle) {
 	try {
+		
 		Progress* reading;
 		reading = new Progress("Reading matrix:     ", numSeqs * (numSeqs - 1) / 2);
 		
@@ -123,15 +134,24 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
 			if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
 				
 			for(int j=0;j<i;j++){
+				if (m->control_pressed) { delete reading;  return 0; }
+				
 				filehandle >> distance;
+				if (sim) {  distance = 1.0 - distance;  }
+				
 				matrix[i][j] = distance;  matrix[j][i] = distance;
+				
 				count++;
 				reading->update(count);
 			}
 		}
-
+		
+		if (m->control_pressed) { delete reading;  return 0; }
+		
 		reading->finish();
 		delete reading;
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "FullMatrix", "readLTMatrix");