//save so you can modify as it changes in average neighbor
cutoff = c;
+ aboveCutoff = cutoff + 10000.0;
m = MothurOut::getInstance();
globaldata = GlobalData::getInstance();
}
//initialize distance matrix to cutoff
dMatrix.resize(nseqs);
- colDist temp(0, 0, cutoff);
- rowSmallDists.resize(nseqs, temp);
+ //colDist temp(0, 0, aboveCutoff);
+ //rowSmallDists.resize(nseqs, temp);
for (int i = 1; i < nseqs; i++) {
- dMatrix[i].resize(i, cutoff);
+ dMatrix[i].resize(i, aboveCutoff);
}
if (distance == -1) { distance = 1000000; }
else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
- if(distance < cutoff){
+ //if(distance < cutoff){
dMatrix[i][j] = distance;
if (distance < smallDist) { smallDist = distance; }
- if (rowSmallDists[i].dist > distance) { rowSmallDists[i].dist = distance; rowSmallDists[i].col = j; rowSmallDists[i].row = i; }
- if (rowSmallDists[j].dist > distance) { rowSmallDists[j].dist = distance; rowSmallDists[j].col = i; rowSmallDists[j].row = j; }
- }
+ //if (rowSmallDists[i].dist > distance) { rowSmallDists[i].dist = distance; rowSmallDists[i].col = j; rowSmallDists[i].row = i; }
+ //if (rowSmallDists[j].dist > distance) { rowSmallDists[j].dist = distance; rowSmallDists[j].col = i; rowSmallDists[j].row = j; }
+ //}
index++;
reading->update(index);
}
if (distance == -1) { distance = 1000000; }
else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
- if(distance < cutoff){
+ //if(distance < cutoff){
if (distance < smallDist) { smallDist = distance; }
int row = nameMap->get(matrixNames[i]);
if (row < col) { dMatrix[col][row] = distance; }
else { dMatrix[row][col] = distance; }
- if (rowSmallDists[row].dist > distance) { rowSmallDists[row].dist = distance; rowSmallDists[row].col = col; rowSmallDists[row].row = row; }
- if (rowSmallDists[col].dist > distance) { rowSmallDists[col].dist = distance; rowSmallDists[col].col = row; rowSmallDists[col].row = col; }
- }
+ //if (rowSmallDists[row].dist > distance) { rowSmallDists[row].dist = distance; rowSmallDists[row].col = col; rowSmallDists[row].row = row; }
+ //if (rowSmallDists[col].dist > distance) { rowSmallDists[col].dist = distance; rowSmallDists[col].col = row; rowSmallDists[col].row = col; }
+ //}
index++;
reading->update(index);
}
if (distance == -1) { distance = 1000000; }
else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
- if(distance < cutoff && j < i){
+ if(j < i){
if (distance < smallDist) { smallDist = distance; }
dMatrix[i][j] = distance;
- if (rowSmallDists[i].dist > distance) { rowSmallDists[i].dist = distance; rowSmallDists[i].col = j; rowSmallDists[i].row = i; }
- if (rowSmallDists[j].dist > distance) { rowSmallDists[j].dist = distance; rowSmallDists[j].col = i; rowSmallDists[j].row = j; }
+ //if (rowSmallDists[i].dist > distance) { rowSmallDists[i].dist = distance; rowSmallDists[i].col = j; rowSmallDists[i].row = i; }
+ //if (rowSmallDists[j].dist > distance) { rowSmallDists[j].dist = distance; rowSmallDists[j].col = i; rowSmallDists[j].row = j; }
}
index++;
reading->update(index);
if (distance == -1) { distance = 1000000; }
else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
- if(distance < cutoff && j < i){
+ if(j < i){
if (distance < smallDist) { smallDist = distance; }
int row = nameMap->get(matrixNames[i]);
if (row < col) { dMatrix[col][row] = distance; }
else { dMatrix[row][col] = distance; }
- if (rowSmallDists[row].dist > distance) { rowSmallDists[row].dist = distance; rowSmallDists[row].col = col; rowSmallDists[row].row = row; }
- if (rowSmallDists[col].dist > distance) { rowSmallDists[col].dist = distance; rowSmallDists[col].col = row; rowSmallDists[col].row = col; }
+ //if (rowSmallDists[row].dist > distance) { rowSmallDists[row].dist = distance; rowSmallDists[row].col = col; rowSmallDists[row].row = row; }
+ //if (rowSmallDists[col].dist > distance) { rowSmallDists[col].dist = distance; rowSmallDists[col].col = row; rowSmallDists[col].row = col; }
}
index++;
reading->update(index);
//sets smallCol and smallRow, returns distance
double ClusterClassic::getSmallCell() {
try {
-
- smallDist = cutoff;
+
+ smallDist = aboveCutoff;
smallRow = 1;
smallCol = 0;
vector<colDist> mins;
- for(int i=0;i<nseqs;i++){
+ for(int i=1;i<nseqs;i++){
+ for(int j=0;j<i;j++){
+ if (dMatrix[i][j] < smallDist) {
+ mins.clear();
+ colDist temp(i, j, dMatrix[i][j]);
+ mins.push_back(temp);
+ smallDist = dMatrix[i][j];
+ }else if (dMatrix[i][j] == smallDist) {
+ colDist temp(i, j, dMatrix[i][j]);
+ mins.push_back(temp);
- if (rowSmallDists[i].dist < smallDist) {
- mins.clear();
- mins.push_back(rowSmallDists[i]);
- smallDist = rowSmallDists[i].dist;
- }else if (rowSmallDists[i].dist == smallDist) {
- mins.push_back(rowSmallDists[i]);
+ }
}
}
}
//cout << smallRow << '\t' << smallCol << '\t' << smallDist << endl;
-
- if (smallRow < smallCol) { dMatrix[smallCol][smallRow] = cutoff; }
- else { dMatrix[smallRow][smallCol] = cutoff; }
+ //eliminate smallCell
+ if (smallRow < smallCol) { dMatrix[smallCol][smallRow] = aboveCutoff; }
+ else { dMatrix[smallRow][smallCol] = aboveCutoff; }
return smallDist;
try {
// cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol);
- rabund->set(smallCol, rabund->get(smallRow)+rabund->get(smallCol));
- rabund->set(smallRow, 0);
+ rabund->set(smallRow, rabund->get(smallRow)+rabund->get(smallCol));
+ rabund->set(smallCol, 0);
+ /*for (int i = smallCol+1; i < rabund->size(); i++) {
+ rabund->set((i-1), rabund->get(i));
+ }
+ rabund->resize((rabund->size()-1));*/
rabund->setLabel(toString(smallDist));
// cout << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol) << endl;
// cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << list->get(smallRow) << '\t' << list->get(smallCol);
if (mapWanted) { updateMap(); }
- list->set(smallCol, list->get(smallRow)+','+list->get(smallCol));
- list->set(smallRow, "");
+ list->set(smallRow, list->get(smallRow)+','+list->get(smallCol));
+ list->set(smallCol, "");
+ /*for (int i = smallCol+1; i < list->size(); i++) {
+ list->set((i-1), list->get(i));
+ }
+ list->resize((list->size()-1));*/
list->setLabel(toString(smallDist));
// cout << '\t' << list->get(smallRow) << '\t' << list->get(smallCol) << endl;
/***********************************************************************/
void ClusterClassic::update(double& cutOFF){
try {
-//cout << "before update " << endl;
//print();
getSmallCell();
int r, c;
- //because we only store lt, we need to make sure we grab the right location
- if (smallRow < smallCol) { c = smallRow; r = smallCol; } //smallRow is really our column value
- else { r = smallRow; c = smallCol; } //smallRow is the row value
-
- //reset rows smallest distance
- rowSmallDists[r].dist = cutoff; rowSmallDists[r].row = 0; rowSmallDists[r].col = 0;
- rowSmallDists[c].dist = cutoff; rowSmallDists[c].row = 0; rowSmallDists[c].col = 0;
-
- //if your rows smallest distance is from smallRow or smallCol, reset
- for(int i=0;i<nseqs;i++){
- if ((rowSmallDists[i].row == r) || (rowSmallDists[i].row == c) || (rowSmallDists[i].col == r) || (rowSmallDists[i].col == c)) {
- rowSmallDists[i].dist = cutoff; rowSmallDists[i].row = 0; rowSmallDists[i].col = 0;
- }
- }
-
+ r = smallRow; c = smallCol;
+
for(int i=0;i<nseqs;i++){
if(i != r && i != c){
double distRow, distCol, newDist;
if (i > r) { distRow = dMatrix[i][r]; }
else { distRow = dMatrix[r][i]; }
+
+ if (i > c) { distCol = dMatrix[i][c]; dMatrix[i][c] = aboveCutoff; } //like removeCell
+ else { distCol = dMatrix[c][i]; dMatrix[c][i] = aboveCutoff; }
- if (i > c) { distCol = dMatrix[i][c]; dMatrix[i][c] = cutoff; } //like removeCell
- else { distCol = dMatrix[c][i]; dMatrix[c][i] = cutoff; }
-
if(method == "furthest"){
newDist = max(distRow, distCol);
}
else if (method == "average"){
- if ((distRow == cutoff) && (distCol == cutoff)) { //you are merging with a value above cutoff
- newDist = cutoff; //eliminate value
- }else if ((distRow == cutoff) && (distCol != cutoff)) { //you are merging with a value above cutoff
- newDist = cutoff; //eliminate value
- if (cutOFF > distCol) { cutOFF = distCol; }
- }else if ((distRow != cutoff) && (distCol == cutoff)) { //you are merging with a value above cutoff
- newDist = cutoff; //eliminate value
- if (cutOFF > distRow) { cutOFF = distRow; }
- }else {
- int rowBin = rabund->get(r);
- int colBin = rabund->get(c);
- newDist = (colBin * distCol + rowBin * distRow) / (rowBin + colBin);
- }
+ int rowBin = rabund->get(r);
+ int colBin = rabund->get(c);
+ newDist = (colBin * distCol + rowBin * distRow) / (rowBin + colBin);
}
else if (method == "weighted"){
- if ((distRow == cutoff) && (distCol == cutoff)) { //you are merging with a value above cutoff
- newDist = cutoff; //eliminate value
- }else if ((distRow == cutoff) && (distCol != cutoff)) { //you are merging with a value above cutoff
- newDist = cutoff; //eliminate value
- if (cutOFF > distCol) { cutOFF = distCol; }
- }else if ((distRow != cutoff) && (distCol == cutoff)) { //you are merging with a value above cutoff
- newDist = cutoff; //eliminate value
- if (cutOFF > distRow) { cutOFF = distRow; }
- }else {
- newDist = (distCol + distRow) / 2.0;
- }
+ newDist = (distCol + distRow) / 2.0;
}
else if (method == "nearest"){
newDist = min(distRow, distCol);
}
-
+ //cout << "newDist = " << newDist << endl;
if (i > r) { dMatrix[i][r] = newDist; }
else { dMatrix[r][i] = newDist; }
- if (newDist < rowSmallDists[i].dist) { rowSmallDists[i].dist = newDist; rowSmallDists[i].col = r; rowSmallDists[i].row = i; }
}
- //cout << "rowsmall = " << i << '\t' << rowSmallDists[i].dist << endl;
}
clusterBins();
clusterNames();
-
- //find new small for 2 rows we just merged
- colDist temp(0,0,100.0);
- rowSmallDists[r] = temp;
-
- for (int i = 0; i < dMatrix[r].size(); i++) {
- if (dMatrix[r][i] < rowSmallDists[r].dist) { rowSmallDists[r].dist = dMatrix[r][i]; rowSmallDists[r].col = r; rowSmallDists[r].row = i; }
- }
- for (int i = dMatrix[r].size()+1; i < dMatrix.size(); i++) {
- if (dMatrix[i][dMatrix[r].size()] < rowSmallDists[r].dist) { rowSmallDists[r].dist = dMatrix[i][dMatrix[r].size()]; rowSmallDists[r].col = r; rowSmallDists[r].row = i; }
- }
- rowSmallDists[c] = temp;
- for (int i = 0; i < dMatrix[c].size(); i++) {
- if (dMatrix[c][i] < rowSmallDists[c].dist) { rowSmallDists[c].dist = dMatrix[c][i]; rowSmallDists[c].col = c; rowSmallDists[c].row = i; }
- }
- for (int i = dMatrix[c].size()+1; i < dMatrix.size(); i++) {
- if (dMatrix[i][dMatrix[c].size()] < rowSmallDists[c].dist) { rowSmallDists[c].dist = dMatrix[i][dMatrix[c].size()]; rowSmallDists[c].col = c; rowSmallDists[c].row = i; }
- }
+ //resize each row
+ /*for(int i=0;i<nseqs;i++){
+ for(int j=c+1;j<dMatrix[i].size();j++){
+ dMatrix[i][j-1]=dMatrix[i][j];
+ }
+ }
- //cout << "after update " << endl;
- //print();
+ //resize each col
+ for(int i=c+1;i<nseqs;i++){
+ for(int j=0;j < dMatrix[i-1].size();j++){
+ dMatrix[i-1][j]=dMatrix[i][j];
+ }
+ }
+
+ nseqs--;
+ dMatrix.pop_back();*/
+
}
catch(exception& e) {
m->errorOut(e, "ClusterClassic", "update");