X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.cpp;fp=fullmatrix.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=4451d6645ea8691b941ebbc991f82cc4ce8b4706;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/fullmatrix.cpp b/fullmatrix.cpp deleted file mode 100644 index 4451d66..0000000 --- a/fullmatrix.cpp +++ /dev/null @@ -1,283 +0,0 @@ -/* - * 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> 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> 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;jcontrol_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> 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;jcontrol_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 FullMatrix::getGroups(){ return groups; } - -/**************************************************************************/ - -vector 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); - } -} - -/**************************************************************************/ -