X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fullmatrix.cpp;h=4451d6645ea8691b941ebbc991f82cc4ce8b4706;hp=5612041528a00e9e0e441422662c6d3738bcb07c;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=9354b70bb84f6dd52ff4a1955754bcbf7edeedbf

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 5612041..4451d66 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -11,21 +11,21 @@
 
 /**************************************************************************/
 //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{
-		globaldata = GlobalData::getInstance();
-		groupmap = globaldata->gGroupmap;
+		m = MothurOut::getInstance();
 		
 		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++) {
 			matrix[i].resize(numSeqs, 0.0);
 		}
 		group = groupmap->getGroup(name);
-		if(group == "not found") {	mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+		if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
 		index.resize(numSeqs);
 		index[0].seqName = name;
 		index[0].groupName = group;
@@ -43,6 +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;
 			}
@@ -53,21 +54,23 @@ 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) {
-		errorOut(e, "FullMatrix", "FullMatrix");
+		m->errorOut(e, "FullMatrix", "FullMatrix");
 		exit(1);
 	}
 }
 /**************************************************************************/
-void FullMatrix::readSquareMatrix(ifstream& filehandle) {
+int FullMatrix::readSquareMatrix(ifstream& filehandle) {
 	try {
 	
 		Progress* reading;
@@ -76,7 +79,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
 		int count = 0;
 		
 		string group, name;
-		
+	
 		for(int i=1;i<numSeqs;i++){
 			filehandle >> name;		
 			
@@ -84,26 +87,35 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
 			index[i].seqName = name;
 			index[i].groupName = group;
 			
-			if(group == "not found") {	mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+			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) {
-		errorOut(e, "FullMatrix", "readSquareMatrix");
+		m->errorOut(e, "FullMatrix", "readSquareMatrix");
 		exit(1);
 	}
 } 
 /**************************************************************************/
-void FullMatrix::readLTMatrix(ifstream& filehandle) {
+int FullMatrix::readLTMatrix(ifstream& filehandle) {
 	try {
+		
 		Progress* reading;
 		reading = new Progress("Reading matrix:     ", numSeqs * (numSeqs - 1) / 2);
 		
@@ -119,21 +131,30 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
 			index[i].seqName = name;
 			index[i].groupName = group;
 	
-			if(group == "not found") {	mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
+			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) {
-		errorOut(e, "FullMatrix", "readLTMatrix");
+		m->errorOut(e, "FullMatrix", "readLTMatrix");
 		exit(1);
 	}
 }
@@ -176,7 +197,7 @@ void FullMatrix::sortGroups(int low, int high){
 	
 	}
 	catch(exception& e) {
-		errorOut(e, "FullMatrix", "sortGroups");
+		m->errorOut(e, "FullMatrix", "sortGroups");
 		exit(1);
 	}
 }
@@ -214,7 +235,7 @@ void FullMatrix::swapRows(int i, int j) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "FullMatrix", "swapRows");
+		m->errorOut(e, "FullMatrix", "swapRows");
 		exit(1);
 	}
 }
@@ -253,7 +274,7 @@ void FullMatrix::printMatrix(ostream& out) {
 		for (int i = 0; i < numSeqs; i++) {  out << i << '\t' <<  index[i].seqName << endl;  }
 	}
 	catch(exception& e) {
-		errorOut(e, "FullMatrix", "printMatrix");
+		m->errorOut(e, "FullMatrix", "printMatrix");
 		exit(1);
 	}
 }