readseqsphylip.cpp

   1 /*
   2  *  readphylip.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/24/09.
   6  *  Copyright 2009 __MyCompanyName__. All rights reserved.
   7  *
   8  */
   9
  10 #include "readseqsphylip.h"
  11 #include <iostream>
  12 #include <fstream>
  13
  14 /*******************************************************************************/
  15 bool ReadPhylip::isSeq(string seq) {
  16         string validChars[] = {"A","G","C","T","U","N","-"};
  17
  18         for(int i = 0; i < seq.length(); i++) {
  19                 bool valid = false;
  20                 string c = seq.substr(i,1);
  21                 for(int k = 0; k < 7; k++)
  22                         if(c.compare(validChars[k]) == 0) {
  23                                 valid = true;
  24                                 k = 7;
  25                         }
  26                 if(!valid)
  27                         return false;
  28         }
  29
  30         return true;
  31 }
  32
  33 /*******************************************************************************/
  34 ReadPhylip::ReadPhylip(string file) {
  35         try {
  36                 openInputFile(file, filehandle);
  37                 phylipFile = file;
  38                 globaldata = GlobalData::getInstance();
  39         }
  40         catch(exception& e) {
  41                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44         catch(...) {
  45                 cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  46                 exit(1);
  47         }
  48 }
  49 /*******************************************************************************/
  50 ReadPhylip::~ReadPhylip(){
  51 //      for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  52 //              delete sequencedb.get(i);
  53 }
  54 /*******************************************************************************/
  55 void ReadPhylip::read() {
  56         string temp;
  57         string name;
  58         string sequence;
  59
  60         int count = 0;
  61         int letterCount = 0;
  62         int numCols = 0;
  63         filehandle >> temp;
  64         int numSeqs = atoi(temp.c_str());
  65         filehandle >> temp;
  66         int numLetters = atoi(temp.c_str());
  67
  68         bool firstDone = false;
  69         bool last = false;
  70         filehandle >> name;
  71
  72         while(!filehandle.eof()) {
  73                 if(!firstDone) {
  74                         sequence = "";
  75                         if(count == 0) {
  76                                 filehandle >> temp;
  77                                 while(isSeq(temp)) {
  78                                         sequence += temp;
  79                                         numCols++;
  80                                         filehandle >> temp;
  81                                 }
  82                                 letterCount += sequence.length();
  83                         }
  84                         else {
  85                                 for(int i = 0; i < numCols; i++) {
  86                                         filehandle >> temp;
  87                                         sequence += temp;
  88                                 }
  89                                 if(count < numSeqs-1)
  90                                         filehandle >> temp;
  91                         }
  92                         Sequence newSeq(name, sequence);
  93                         sequencedb.add(newSeq);
  94                         if(count < numSeqs-1)
  95                                 name = temp;
  96                 }
  97                 else {
  98                         sequence = "";
  99                         for(int i = 0; i < numCols; i++) {
 100                                 filehandle >> temp;
 101                                 sequence += temp;
 102                                 if(count == 0)
 103                                         letterCount += temp.length();
 104                                 if(letterCount == numLetters && count == 0) {
 105                                         numCols = i + 1;
 106                                         i = numCols;
 107                                 }
 108                         }
 109                         if(!(last && count == 0))
 110                                 sequencedb.set(count, sequencedb.get(count).getAligned() + sequence);
 111                         if(letterCount == numLetters && count == 0)
 112                                 last = true;
 113                 }
 114
 115                 count++;
 116
 117                 if(count == numSeqs) {
 118                         firstDone = true;
 119                         count = 0;
 120                 }
 121         }
 122         filehandle.close();
 123 }
 124
 125 /*********************************************************************************/
 126 SequenceDB* ReadPhylip::getDB() {
 127         return &sequencedb;
 128 }