X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=formatphylip.cpp;fp=formatphylip.cpp;h=4a7878a54a19fb6a63ad32c00d359c7b490e5216;hb=e1cf60b82a48d4d96e3a696a2d221c56cfb0b298;hp=0000000000000000000000000000000000000000;hpb=92f998cc7debc4bf3e8594848586b8153d96db16;p=mothur.git

diff --git a/formatphylip.cpp b/formatphylip.cpp
new file mode 100644
index 0000000..4a7878a
--- /dev/null
+++ b/formatphylip.cpp
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+/*
+ *  formatphylip.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 1/13/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "formatphylip.h"
+#include "progress.hpp"
+
+/***********************************************************************/
+FormatPhylipMatrix::FormatPhylipMatrix(string df) : filename(df) {
+        openInputFile(filename, fileHandle);
+}
+/***********************************************************************/
+//not using nameMap
+void FormatPhylipMatrix::read(NameAssignment* nameMap){
+	try {
+        
+			float distance;
+			int square, nseqs;
+			string name;
+			ofstream out;
+			
+			fileHandle >> nseqs >> name;
+						
+			list = new ListVector(nseqs);
+			list->set(0, name);
+			
+			char d;
+			while((d=fileHandle.get()) != EOF){
+                
+				if(isalnum(d)){  //you are square
+					square = 1;
+					fileHandle.close();  //reset file
+					
+					//open and get through numSeqs, code below formats rest of file
+					openInputFile(filename, fileHandle);
+					fileHandle >> nseqs; gobble(fileHandle);
+					
+					distFile = filename + ".rowFormatted";
+					openOutputFile(distFile, out);
+					break;
+				}
+				if(d == '\n'){
+					square = 0;
+					break;
+				}
+			}
+			
+			Progress* reading;
+			reading = new Progress("Formatting matrix:     ", nseqs * nseqs);
+			
+			//lower triangle, so must go to column then formatted row file
+			if(square == 0){
+				int  index = 0;
+				
+				ofstream outTemp;
+				string tempFile = filename + ".temp";
+				openOutputFile(tempFile, outTemp);
+                
+				//convert to square column matrix
+				for(int i=1;i<nseqs;i++){
+					fileHandle >> name;
+					
+					list->set(i, name);
+					
+					for(int j=0;j<i;j++){
+						fileHandle >> distance;
+						
+						if (distance == -1) { distance = 1000000; }
+						
+						if(distance < cutoff){
+							outTemp << i << '\t' << j << '\t' << distance << endl;
+							outTemp << j << '\t' << i << '\t' << distance << endl;
+						}
+						index++;
+						reading->update(index);
+					}
+				}
+				outTemp.close();
+				
+				//format from square column to rowFormatted
+				//sort file by first column so the distances for each row are together
+				string outfile = getRootName(tempFile) + "sorted.dist.temp";
+				
+				//use the unix sort 
+				#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+					string command = "sort -n " + tempFile + " -o " + outfile;
+					system(command.c_str());
+				#else //sort using windows sort
+					string command = "sort " + tempFile + " /O " + outfile;
+					system(command.c_str());
+				#endif
+				
+
+				//output to new file distance for each row and save positions in file where new row begins
+				ifstream in;
+				openInputFile(outfile, in);
+				
+				distFile = outfile + ".rowFormatted";
+				openOutputFile(distFile, out);
+				
+				rowPos.resize(nseqs, -1);
+				int currentRow;
+				int first, second;
+				float dist;
+				map<int, float> rowMap;
+				map<int, float>::iterator itRow;
+				
+				//get first currentRow
+				in >> first;
+				currentRow = first;
+				
+				string firstString = toString(first);
+				for(int k = 0; k < firstString.length(); k++)  {   in.putback(firstString[k]);  }
+				
+				while(!in.eof()) {
+					in >> first >> second >> dist; gobble(in);
+					
+					if (first != currentRow) {
+						//save position in file of each new row
+						rowPos[currentRow] = out.tellp();
+						
+						out << currentRow << '\t' << rowMap.size() << '\t';
+						
+						for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
+							out << itRow->first << '\t' << itRow->second << '\t';
+						}
+						out << endl;
+						
+						currentRow = first;
+						rowMap.clear();
+						
+						//save row you just read
+						rowMap[second] = dist;
+						
+						index++;
+						reading->update(index);
+					}else{
+						rowMap[second] = dist;
+					}
+				}
+				
+				//print last Row
+				//save position in file of each new row
+				rowPos[currentRow] = out.tellp();
+				
+				out << currentRow << '\t' << rowMap.size() << '\t';
+				
+				for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
+					out << itRow->first << '\t' << itRow->second << '\t';
+				}
+				out << endl;
+				
+				in.close();
+				out.close();
+				
+				remove(tempFile.c_str());
+				remove(outfile.c_str());
+			}
+			else{ //square matrix convert directly to formatted row file
+				int index = nseqs;
+				map<int, float> rowMap;
+				map<int, float>::iterator itRow;
+
+                
+				for(int i=0;i<nseqs;i++){
+					fileHandle >> name;                
+										
+					list->set(i, name);
+					
+					for(int j=0;j<nseqs;j++){
+						fileHandle >> distance;
+						
+						if (distance == -1) { distance = 1000000; }
+						
+						if((distance < cutoff) && (j != i)){
+							rowMap[j] = distance;
+						}
+						index++;
+						reading->update(index);
+					}
+					
+					//save position in file of each new row
+					rowPos[i] = out.tellp();
+
+					//output row to file
+					out << i << '\t' << rowMap.size() << '\t';
+					for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
+						out << itRow->first << '\t' << itRow->second << '\t';
+					}
+					out << endl;
+					
+					//clear map for new row's info
+					rowMap.clear();
+				}
+			}
+			reading->finish();
+			delete reading;
+			
+			list->setLabel("0");
+			fileHandle.close();
+			out.close();
+			
+	}
+	catch(exception& e) {
+               errorOut(e, "FormatPhylipMatrix", "read");
+                exit(1);
+	}
+}
+/***********************************************************************/
+FormatPhylipMatrix::~FormatPhylipMatrix(){}
+/***********************************************************************/
+
+