X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterclassic.cpp;fp=clusterclassic.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=1ce81c4f2affda469164709f862bb36ff023c163;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/clusterclassic.cpp b/clusterclassic.cpp
deleted file mode 100644
index 1ce81c4..0000000
--- a/clusterclassic.cpp
+++ /dev/null
@@ -1,450 +0,0 @@
-/*
- *  clusterclassic.cpp
- *  Mothur
- *
- *  Created by westcott on 10/29/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "clusterclassic.h"
-#include "progress.hpp"
-
-/***********************************************************************/
-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
-	
-		//save so you can modify as it changes in average neighbor
-		cutoff = c;
-		aboveCutoff = cutoff + 10000.0;
-		m = MothurOut::getInstance();
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ClusterClassic", "ClusterClassic");
-		exit(1);
-	}
-}
-/***********************************************************************/
-int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
-	try {
-		double distance;
-		int square;
-		string name;
-		vector<string> matrixNames;
-		
-		ifstream fileHandle;
-		m->openInputFile(filename, fileHandle);
-		
-		fileHandle >> nseqs >> name;
-
-		matrixNames.push_back(name);
-
-		if(nameMap == NULL){
-				list = new ListVector(nseqs);
-				list->set(0, name);
-		}
-		else{
-				list = new ListVector(nameMap->getListVector());
-				if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
-		}
-		
-		//initialize distance matrix to cutoff
-		dMatrix.resize(nseqs);
-		//colDist temp(0, 0, aboveCutoff);
-		//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(nameMap == 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{
-								if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
-				
-								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 < cutoff){
-											if (distance < smallDist) { smallDist = distance; }
-											
-											int row = nameMap->get(matrixNames[i]);
-											int col = nameMap->get(matrixNames[j]);
-											
-											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; }
-										//}
-										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(nameMap == 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;
-											//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{
-								if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
-				
-								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 = nameMap->get(matrixNames[i]);
-											int col = nameMap->get(matrixNames[j]);
-											
-											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; }
-										}
-										index++;
-										reading->update(index);
-								}
-						}
-				}
-		}
-		
-		if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
-		
-		reading->finish();
-		delete reading;
-
-		list->setLabel("0");
-		rabund = new RAbundVector(list->getRAbundVector());
-		
-		fileHandle.close();
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ClusterClassic", "readPhylipFile");
-		exit(1);
-	}
-
-}
-/***********************************************************************/
-//sets smallCol and smallRow, returns distance
-double ClusterClassic::getSmallCell() {
-	try {
-			
-		smallDist = aboveCutoff;
-		smallRow = 1;
-		smallCol = 0;
-		
-		vector<colDist> mins;
-		
-		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 (mins.size() > 0) {
-			int zrand = 0;
-			if (mins.size() > 1) {
-				//pick random number between 0 and mins.size()
-				zrand = (int)((float)(rand()) / (RAND_MAX / (mins.size()-1) + 1));
-			}
-			
-			smallRow = mins[zrand].row;
-			smallCol = mins[zrand].col;
-		
-		}
-	//cout << smallRow << '\t' << smallCol << '\t' << smallDist << endl;
-		//eliminate smallCell
-		if (smallRow < smallCol) { dMatrix[smallCol][smallRow] = aboveCutoff; }
-		else { dMatrix[smallRow][smallCol] = aboveCutoff; }
-		
-		return smallDist;
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ClusterClassic", "getSmallCell");
-		exit(1);
-	}
-}
-/***********************************************************************/
-void ClusterClassic::clusterBins(){
-	try {
-	//	cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol);
-
-		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;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ClusterClassic", "clusterBins");
-		exit(1);
-	}
-}
-/***********************************************************************/
-void ClusterClassic::clusterNames(){
-	try {
-	//	cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << list->get(smallRow) << '\t' << list->get(smallCol);
-		if (mapWanted) {  updateMap();  }
-		
-		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;
-    }
-	catch(exception& e) {
-		m->errorOut(e, "ClusterClassic", "clusterNames");
-		exit(1);
-	}
-}
-/***********************************************************************/
-void ClusterClassic::update(double& cutOFF){
-	try {
-//print();		
-		getSmallCell();
-		
-		int r, c;
-		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(method == "furthest"){
-					newDist = max(distRow, distCol);
-				}
-				else if (method == "average"){
-					int rowBin = rabund->get(r);
-					int colBin = rabund->get(c);
-					newDist = (colBin * distCol + rowBin * distRow) / (rowBin + colBin);
-				}
-				else if (method == "weighted"){
-					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; }
-				
-			}
-		}
-			
-		clusterBins();
-		clusterNames();
-		
-		//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];
-			}
-		}			
-		
-		//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");
-		exit(1);
-	}
-}
-/***********************************************************************/
-void ClusterClassic::setMapWanted(bool f)  {  
-	try {
-		mapWanted = f;
-		
-		//initialize map
-		for (int i = 0; i < list->getNumBins(); i++) {
-			
-			//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(','));
-				//save name and bin number
-				seq2Bin[name] = i;
-				names = names.substr(names.find_first_of(',')+1, names.length());
-			}
-			
-			//get last name
-			seq2Bin[names] = i;
-		}
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ClusterClassic", "setMapWanted");
-		exit(1);
-	}
-}
-/***********************************************************************/
-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;
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ClusterClassic", "updateMap");
-		exit(1);
-	}
-}
-/***********************************************************************/
-void ClusterClassic::print() {
-try {
-		//update location of seqs in smallRow since they move to smallCol now
-		for (int i = 0; i < dMatrix.size(); i++) {
-			m->mothurOut("row = " + toString(i) + "\t");
-			for (int j = 0; j < dMatrix[i].size(); j++) {
-				m->mothurOut(toString(dMatrix[i][j]) + "\t");
-			}
-			m->mothurOutEndLine();
-		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ClusterClassic", "updateMap");
-		exit(1);
-	}
-}
-/***********************************************************************/
-