+++ /dev/null
-/*
- * fullmatrix.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 3/6/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "fullmatrix.h"
-
-/**************************************************************************/
-//This constructor reads a distance matrix file and stores the data in the matrix.
-FullMatrix::FullMatrix(ifstream& filehandle, GroupMap* g, bool s) : groupmap(g), sim(s) {
- try{
- m = MothurOut::getInstance();
-
- 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, 0.0);
- }
- group = groupmap->getGroup(name);
- 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;
-
- //determine if matrix is square or lower triangle
- //if it is square read the distances for the first sequence
- char d;
- bool square;
- 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];
- if (sim) { matrix[0][i] = 1.0 - 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); }
-
- filehandle.close();
-
- if (!m->control_pressed) { sortGroups(0, numSeqs-1); }
-
- }
- catch(exception& e) {
- m->errorOut(e, "FullMatrix", "FullMatrix");
- exit(1);
- }
-}
-/**************************************************************************/
-int FullMatrix::readSquareMatrix(ifstream& filehandle) {
- try {
-
- Progress* reading;
- reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
-
- int count = 0;
-
- string group, name;
-
- for(int i=1;i<numSeqs;i++){
- filehandle >> name;
-
- group = groupmap->getGroup(name);
- index[i].seqName = name;
- index[i].groupName = group;
-
- 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");
- exit(1);
- }
-}
-/**************************************************************************/
-int 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].seqName = name;
- index[i].groupName = group;
-
- 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");
- exit(1);
- }
-}
-
-/**************************************************************************/
-
-void FullMatrix::sortGroups(int low, int high){
- try{
-
- if (low < high) {
- int i = low+1;
- int j = high;
- int pivot = (low+high) / 2;
-
- swapRows(low, pivot); //puts pivot in final spot
-
- /* compare value */
- //what group does this row belong to
- string key = index[low].groupName;
-
- /* partition */
- while(i <= j) {
- /* find member above ... */
- while((i <= high) && (index[i].groupName <= key)) { i++; }
-
- /* find element below ... */
- while((j >= low) && (index[j].groupName > key)) { j--; }
-
- if(i < j) {
- swapRows(i, j);
- }
- }
-
- swapRows(low, j);
-
- /* recurse */
- sortGroups(low, j-1);
- sortGroups(j+1, high);
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "FullMatrix", "sortGroups");
- exit(1);
- }
-}
-
-/**************************************************************************/
-void FullMatrix::swapRows(int i, int j) {
- try {
-
- float y;
- string z, name;
-
- /* swap rows*/
- for (int h = 0; h < numSeqs; h++) {
- y = matrix[i][h];
- matrix[i][h] = matrix[j][h];
- matrix[j][h] = y;
- }
-
- /* swap columns*/
- for (int b = 0; b < numSeqs; b++) {
- y = matrix[b][i];
- matrix[b][i] = matrix[b][j];
- matrix[b][j] = y;
- }
-
- //swap map elements
- z = index[i].groupName;
- index[i].groupName = index[j].groupName;
- index[j].groupName = z;
-
- name = index[i].seqName;
- index[i].seqName = index[j].seqName;
- index[j].seqName = name;
-
-
- }
- catch(exception& e) {
- m->errorOut(e, "FullMatrix", "swapRows");
- exit(1);
- }
-}
-/**************************************************************************/
-
-float FullMatrix::get(int i, int j){ return matrix[i][j]; }
-
-/**************************************************************************/
-
-vector<string> FullMatrix::getGroups(){ return groups; }
-
-/**************************************************************************/
-
-vector<int> FullMatrix::getSizes(){ return sizes; }
-
-/**************************************************************************/
-
-int FullMatrix::getNumGroups(){ return groups.size(); }
-
-/**************************************************************************/
-
-int FullMatrix::getNumSeqs(){ return numSeqs; }
-
-/**************************************************************************/
-
-void FullMatrix::printMatrix(ostream& out) {
- try{
- for (int i = 0; i < numSeqs; i++) {
- out << "row " << i << " group = " << index[i].groupName << " name = " << index[i].seqName << endl;
- for (int j = 0; j < numSeqs; j++) {
- out << i << '\t' << j << '\t' << matrix[i][j] << endl;
- }
- out << endl;
- }
-
- for (int i = 0; i < numSeqs; i++) { out << i << '\t' << index[i].seqName << endl; }
- }
- catch(exception& e) {
- m->errorOut(e, "FullMatrix", "printMatrix");
- exit(1);
- }
-}
-
-/**************************************************************************/
-
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