X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.cpp;h=c61109c78ce2cdcca001455a0408be34692c47d1;hb=9651e8e7172d86707b34af15e95ec60ad4c3c3f9;hp=3f1344c6c930bfebadcc0cb10a3939379db27886;hpb=a85da7303079652b569291eacb9c2964060e072b;p=mothur.git

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 3f1344c..c61109c 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -9,18 +9,60 @@
 
 #include "fullmatrix.h"
 
-
 /**************************************************************************/
 //This constructor reads a distance matrix file and stores the data in the matrix.
-FullMatrix::FullMatrix(ifstream& f) {
+FullMatrix::FullMatrix(ifstream& filehandle) {
 	try{
-		string name;
-		f >> numSeqs >> name;
+		globaldata = GlobalData::getInstance();
+		groupmap = globaldata->gGroupmap;
 		
-		matrix.resize(numSeqs);  
+		string name, group;
+		filehandle >> numSeqs >> name;
 		
+		//make the matrix filled with zeros
+		matrix.resize(numSeqs); 
+		for(int i = 0; i < numSeqs; i++) {
+			matrix[i].resize(numSeqs, 0);
+		}
+		
+		group = groupmap->getGroup(name);
+		if(group == "not found") {	cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
+		index[0] = group; 
+		
+		//determine if matrix is square or lower triangle
+		//if it is square read the distances for the first sequence
+		char d;
+		while((d=filehandle.get()) != EOF){
+			
+			//is d a number meaning its square
+			if(isalnum(d)){ 
+				square = true;
+				filehandle.putback(d);
+				for(int i=0;i<numSeqs;i++){
+					filehandle >> matrix[0][i];
+				}
+				break;
+			}
+			
+			//is d a line return meaning its lower triangle
+			if(d == '\n'){
+				square = false;
+				break;
+			}
+		}
+		
+		//read rest of matrix
+		if (square == true) { readSquareMatrix(filehandle); }
+		else { readLTMatrix(filehandle); }
+		
+		
+		
+	printMatrix(cout);
+		//sort sequences so they are gathered in groups for processing
+		sortGroups();
+		cout << "after sort" << endl;
+	printMatrix(cout);
 		
-	
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -31,6 +73,188 @@ FullMatrix::FullMatrix(ifstream& f) {
 		exit(1);
 	}
 }
+/**************************************************************************/
+void FullMatrix::readSquareMatrix(ifstream& filehandle) {
+	try {
+	
+		Progress* reading;
+		reading = new Progress("Reading matrix:    ", numSeqs * numSeqs);
+		
+		int count = 0;
+		float distance;
+		string group, name;
+		
+		for(int i=1;i<numSeqs;i++){
+			filehandle >> name;		
+			
+			group = groupmap->getGroup(name);
+			index[i] = group;
+			
+			if(group == "not found") {	cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
+				
+			for(int j=0;j<numSeqs;j++){
+				filehandle >> distance;
+					
+				matrix[i][j] = distance;
+				count++;
+				reading->update(count);
+			}
+		}
+		reading->finish();
+		delete reading;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FullMatrix class function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+} 
+/**************************************************************************/
+void FullMatrix::readLTMatrix(ifstream& filehandle) {
+	try {
+		Progress* reading;
+		reading = new Progress("Reading matrix:    ", numSeqs * (numSeqs - 1) / 2);
+		
+		int count = 0;
+		float distance;
+		string group, name;
+		
+		for(int i=1;i<numSeqs;i++){
+			filehandle >> name;		
+						
+			group = groupmap->getGroup(name);
+			index[i] = group;
+	
+			if(group == "not found") {	cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl;  exit(1); }
+				
+			for(int j=0;j<i;j++){
+				filehandle >> distance;
+					
+				matrix[i][j] = distance;  matrix[j][i] = distance;
+				count++;
+				reading->update(count);
+			}
+		}
+		reading->finish();
+		delete reading;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FullMatrix class function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+}
+
+/**************************************************************************/
+void FullMatrix::sortGroups(){
+	try{
+		//sort each row by group and when you do, swap rows too.
+		for (int i = 0; i < numSeqs; i++) {
+			quicksort(0, numSeqs-1, i);
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+}
+/**************************************************************************/
+//this is a version of quicksort taken from http://www.c.happycodings.com/Sorting_Searching/code13.html
+/* sort everything inbetween `low' <-> `high' */
+void FullMatrix::quicksort(int low, int high, int row) {
+	try {
+		int i = low;
+		int j = high;
+		int y = 0;
+		
+		/* compare value */
+		//what group does this row belong to
+		string z = index[(low + high) / 2];
+
+		/* partition */
+		do {
+			/* find member above ... */
+			while(index[i] < z) i++;
+
+			/* find element below ... */
+			while(index[j] > z) j--;
+			
+			if(i <= j) {
+				/* swap two elements in row*/
+				y = matrix[row][i];
+				matrix[row][i] = matrix[row][j]; 
+				matrix[row][j] = y;
+				
+				/* swap two elements in column*/
+				y = matrix[i][row];
+				matrix[i][row] = matrix[j][row]; 
+				matrix[j][row] = y;
+				
+				//swap map elements
+				z = index[i];
+				index[i] = index[j];
+				index[j] = z;
+				
+				i++; 
+				j--;
+//cout << "swapping elements " << i << " " << j << endl;
+//printMatrix(cout); cout << endl;
+			}
+		} while(i <= j);
+
+		/* recurse */
+		if(low < j) 
+		quicksort(low, j, row);
+
+		if(i < high) 
+		quicksort(i, high, row); 
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FullMatrix class function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
 /**************************************************************************/	
 int FullMatrix::getNumSeqs(){ return numSeqs; }
-/**************************************************************************/
\ No newline at end of file
+/**************************************************************************/
+//print out matrix
+void FullMatrix::printMatrix(ostream& out) {
+	try{
+		for (int i = 0; i < numSeqs; i++) {
+			out << "row " << i << " group = " << index[i] << endl;
+			for (int j = 0; j < numSeqs; j++) {
+				out << matrix[i][j] << " ";
+			}
+			out << endl;
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+}
+/**************************************************************************/
+