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/*
* cluster.cpp
*
*
* Created by Pat Schloss on 8/14/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#include "cluster.hpp"
#include "rabundvector.hpp"
#include "listvector.hpp"
/***********************************************************************/
Cluster::Cluster(RAbundVector* rav, ListVector* lv, SparseDistanceMatrix* dm, float c, string f, float cs) :
rabund(rav), list(lv), dMatrix(dm), method(f), adjust(cs)
{
try {
mapWanted = false; //set to true by mgcluster to speed up overlap merge
//save so you can modify as it changes in average neighbor
cutoff = c;
m = MothurOut::getInstance();
}
catch(exception& e) {
m->errorOut(e, "Cluster", "Cluster");
exit(1);
}
}
/***********************************************************************/
void Cluster::clusterBins(){
try {
rabund->set(smallCol, rabund->get(smallRow)+rabund->get(smallCol));
rabund->set(smallRow, 0);
rabund->setLabel(toString(smallDist));
}
catch(exception& e) {
m->errorOut(e, "Cluster", "clusterBins");
exit(1);
}
}
/***********************************************************************/
void Cluster::clusterNames(){
try {
if (mapWanted) { updateMap(); }
list->set(smallCol, list->get(smallRow)+','+list->get(smallCol));
list->set(smallRow, "");
list->setLabel(toString(smallDist));
}
catch(exception& e) {
m->errorOut(e, "Cluster", "clusterNames");
exit(1);
}
}
/***********************************************************************/
bool Cluster::update(double& cutOFF){
try {
smallCol = dMatrix->getSmallestCell(smallRow);
nColCells = dMatrix->seqVec[smallCol].size();
nRowCells = dMatrix->seqVec[smallRow].size();
vector<int> foundCol(nColCells, 0);
int search;
bool changed = false;
for (int i=nRowCells-1;i>=0;i--) { //matrix indexes sorted from largest to smallest, so start at smallest index
if (m->getControl_pressed()) { break; }
//if you are not the smallCell
if (dMatrix->seqVec[smallRow][i].index != smallCol) {
search = dMatrix->seqVec[smallRow][i].index;
bool merged = false;
for (int j=0;j<nColCells;j++) { //go through each distance the smallCol has looking for matching distance to find
if (dMatrix->seqVec[smallCol][j].index != smallRow) { //if you are not the smallest distance
if (dMatrix->seqVec[smallCol][j].index == search) { //we found a distance for the merge
foundCol[j] = 1;
merged = true;
changed = updateDistance(dMatrix->seqVec[smallCol][j], dMatrix->seqVec[smallRow][i]);
dMatrix->updateCellCompliment(smallCol, j);
break;
}else if (dMatrix->seqVec[smallCol][j].index < search) { //we don't have a distance for this cell
if (!util.isEqual(adjust, -1)) { //adjust
merged = true;
PDistCell value(search, adjust); //create a distance for the missing value
int location = dMatrix->addCellSorted(smallCol, value);
changed = updateDistance(dMatrix->seqVec[smallCol][location], dMatrix->seqVec[smallRow][i]);
dMatrix->updateCellCompliment(smallCol, location);
nColCells++;
foundCol.push_back(0); //add a new found column
//adjust value
for (int k = foundCol.size()-1; k > location; k--) { foundCol[k] = foundCol[k-1]; }
foundCol[location] = 1;
}
j+=nColCells; //jump out of loop and remove cell below
}
}
}
//if not merged it you need it for warning
if ((!merged) && (method == "average" || method == "weighted")) { if (cutOFF > dMatrix->seqVec[smallRow][i].dist) { cutOFF = dMatrix->seqVec[smallRow][i].dist; } }
if ((method == "nearest") && (!merged)) { //you are a row dist without a column dist, add you as a column dist
PDistCell value(search, dMatrix->seqVec[smallRow][i].dist); //create a distance for the missing value
int location = dMatrix->addCellSorted(smallCol, value); nColCells++;
foundCol.push_back(0); //add a new found column
//adjust value
for (int k = foundCol.size()-1; k > location; k--) { foundCol[k] = foundCol[k-1]; }
foundCol[location] = 1;
}
dMatrix->rmCell(smallRow, i);
}
}
clusterBins();
clusterNames();
if (method == "nearest") {
for (int i=nColCells-1;i>=0;i--) { //remove any unfound dists from merged column, need special case for nn, since unfound dists mean above the cutoff -> keep smaller dist in col
if (foundCol[i] == 0) { //not found
if (dMatrix->seqVec[smallCol][i].index == smallRow) { //you are smallest distance
dMatrix->rmCell(smallCol, i);
break;
}
}
}
}else {
for (int i=nColCells-1;i>=0;i--) { //remove any unfound dists from merged column, need special case for nn, since unfound dists mean above the cutoff -> keep smaller dist in col
if (foundCol[i] == 0) { //not found
if (!util.isEqual(adjust, -1)) { //adjust
PDistCell value(smallCol, adjust); //create a distance for the missing value
changed = updateDistance(dMatrix->seqVec[smallCol][i], value);
dMatrix->updateCellCompliment(smallCol, i);
}else {
if (method == "average" || method == "weighted") {
if (dMatrix->seqVec[smallCol][i].index != smallRow) { //if you are not hte smallest distance
if (cutOFF > dMatrix->seqVec[smallCol][i].dist) { cutOFF = dMatrix->seqVec[smallCol][i].dist; }
}
}
}
dMatrix->rmCell(smallCol, i);
}
}
}
//dMatrix->print();
return changed;
}
catch(exception& e) {
m->errorOut(e, "Cluster", "update");
exit(1);
}
}
/***********************************************************************/
void Cluster::setMapWanted(bool f) {
try {
mapWanted = f;
//initialize map
for (int k = 0; k < list->getNumBins(); k++) {
string names = list->get(k);
//parse bin
string individual = "";
int binNameslength = names.size();
for(int j=0;j<binNameslength;j++){
if(names[j] == ','){
seq2Bin[individual] = k;
individual = "";
}
else{ individual += names[j]; }
}
//get last name
seq2Bin[individual] = k;
}
}
catch(exception& e) {
m->errorOut(e, "Cluster", "setMapWanted");
exit(1);
}
}
/***********************************************************************/
void Cluster::updateMap() {
try {
//update location of seqs in smallRow since they move to smallCol now
string names = list->get(smallRow);
string individual = "";
int binNameslength = names.size();
for(int j=0;j<binNameslength;j++){
if(names[j] == ','){
seq2Bin[individual] = smallCol;
individual = "";
}
else{ individual += names[j]; }
}
//get last name
seq2Bin[individual] = smallCol;
}
catch(exception& e) {
m->errorOut(e, "Cluster", "updateMap");
exit(1);
}
}
/***********************************************************************/
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