#include "progress.hpp"
/***********************************************************************/
-ClusterClassic::ClusterClassic(float c, string f) : method(f), smallDist(1e6), nseqs(0) {
+ClusterClassic::ClusterClassic(float c, string f, bool s) : method(f), smallDist(1e6), nseqs(0), sim(s) {
try {
mapWanted = false; //set to true by mgcluster to speed up overlap merge
cutoff = c;
aboveCutoff = cutoff + 10000.0;
m = MothurOut::getInstance();
- globaldata = GlobalData::getInstance();
+ if(method == "furthest") { tag = "fn"; }
+ else if (method == "average") { tag = "an"; }
+ else if (method == "weighted") { tag = "wn"; }
+ else if (method == "nearest") { tag = "nn"; }
}
catch(exception& e) {
m->errorOut(e, "ClusterClassic", "ClusterClassic");
ifstream fileHandle;
m->openInputFile(filename, fileHandle);
- fileHandle >> nseqs >> name;
+ string numTest;
+ fileHandle >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
matrixNames.push_back(name);
fileHandle >> distance;
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
//if(distance < cutoff){
dMatrix[i][j] = distance;
if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
//if(distance < cutoff){
if (distance < smallDist) { smallDist = distance; }
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(j < i){
if (distance < smallDist) { smallDist = distance; }
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(j < i){
if (distance < smallDist) { smallDist = distance; }
exit(1);
}
+}
+/***********************************************************************/
+int ClusterClassic::readPhylipFile(string filename, CountTable* countTable) {
+ try {
+ double distance;
+ int square;
+ string name;
+ vector<string> matrixNames;
+
+ ifstream fileHandle;
+ m->openInputFile(filename, fileHandle);
+
+ string numTest;
+ fileHandle >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
+
+ matrixNames.push_back(name);
+
+ if(countTable == NULL){
+ list = new ListVector(nseqs);
+ list->set(0, name);
+ }
+ else{ list = new ListVector(countTable->getListVector()); }
+
+
+ //initialize distance matrix to cutoff
+ dMatrix.resize(nseqs);
+ //rowSmallDists.resize(nseqs, temp);
+ for (int i = 1; i < nseqs; i++) {
+ dMatrix[i].resize(i, aboveCutoff);
+ }
+
+
+ char d;
+ while((d=fileHandle.get()) != EOF){
+
+ if(isalnum(d)){
+ square = 1;
+ fileHandle.putback(d);
+ for(int i=0;i<nseqs;i++){
+ fileHandle >> distance;
+ }
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ Progress* reading;
+
+ if(square == 0){
+
+ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
+
+ int index = 0;
+
+ for(int i=1;i<nseqs;i++){
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+
+ //there's A LOT of repeated code throughout this method...
+ if(countTable == NULL){
+ list->set(i, name);
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ //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; }
+ //}
+ index++;
+ reading->update(index);
+ }
+
+ }
+ else{
+ for(int j=0;j<i;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if (distance < smallDist) { smallDist = distance; }
+
+ int row = countTable->get(matrixNames[i]);
+ int col = countTable->get(matrixNames[j]);
+
+ if (row < col) { dMatrix[col][row] = distance; }
+ else { dMatrix[row][col] = distance; }
+
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+ else{
+
+ reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int index = nseqs;
+
+ for(int i=1;i<nseqs;i++){
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+ if(countTable == NULL){
+ list->set(i, name);
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(j < i){
+ if (distance < smallDist) { smallDist = distance; }
+
+ dMatrix[i][j] = distance;
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ else{
+
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(j < i){
+ if (distance < smallDist) { smallDist = distance; }
+
+ int row = countTable->get(matrixNames[i]);
+ int col = countTable->get(matrixNames[j]);
+
+ if (row < col) { dMatrix[col][row] = distance; }
+ else { dMatrix[row][col] = distance; }
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ delete reading;
+
+ list->setLabel("0");
+ rabund = new RAbundVector();
+ rabund->setLabel(list->getLabel());
+
+ for(int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+ vector<string> binNames;
+ string bin = list->get(i);
+ m->splitAtComma(bin, binNames);
+ int total = 0;
+ for (int j = 0; j < binNames.size(); j++) { total += countTable->getNumSeqs(binNames[j]); }
+ rabund->push_back(total);
+ }
+
+ fileHandle.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterClassic", "readPhylipFile");
+ exit(1);
+ }
+
}
/***********************************************************************/
//sets smallCol and smallRow, returns distance
//parse bin
string names = list->get(i);
- while (names.find_first_of(',') != -1) {
- //get name from bin
- string name = names.substr(0,names.find_first_of(','));
+ vector<string> binnames;
+ m->splitAtComma(names, binnames);
+ for (int j = 0; j < binnames.size(); j++) {
//save name and bin number
- seq2Bin[name] = i;
- names = names.substr(names.find_first_of(',')+1, names.length());
+ seq2Bin[binnames[j]] = i;
}
-
- //get last name
- seq2Bin[names] = i;
}
}
void ClusterClassic::updateMap() {
try {
//update location of seqs in smallRow since they move to smallCol now
- string names = list->get(smallRow);
- while (names.find_first_of(',') != -1) {
- //get name from bin
- string name = names.substr(0,names.find_first_of(','));
- //save name and bin number
- seq2Bin[name] = smallCol;
- names = names.substr(names.find_first_of(',')+1, names.length());
- }
-
- //get last name
- seq2Bin[names] = smallCol;
+ string names = list->get(smallRow);
+ vector<string> binnames;
+ m->splitAtComma(names, binnames);
+ for (int j = 0; j < binnames.size(); j++) {
+ //save name and bin number
+ seq2Bin[binnames[j]] = smallCol;
+ }
}
catch(exception& e) {
try {
//update location of seqs in smallRow since they move to smallCol now
for (int i = 0; i < dMatrix.size(); i++) {
- cout << "row = " << i << '\t';
+ m->mothurOut("row = " + toString(i) + "\t");
for (int j = 0; j < dMatrix[i].size(); j++) {
- cout << dMatrix[i][j] << '\t';
+ m->mothurOut(toString(dMatrix[i][j]) + "\t");
}
- cout << endl;
+ m->mothurOutEndLine();
}
}
catch(exception& e) {
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