5 * Created by Sarah Westcott on 4/21/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 /***********************************************************************/
14 ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
16 //openInputFile(philFile, fileHandle);
19 /***********************************************************************/
20 //This function reads the list, rabund or sabund files to be used by collect and rarefact command.
21 void ReadOTUFile::read(GlobalData* globaldata){
24 if (globaldata->getOrderFile() == "") {
25 //you have two inputs because in the next if statement if you only have one then it moves ahead in the same file.
26 //So when you run the collect or summary commands you miss a line.
27 input = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
28 inputList = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund.
29 inputSabund = new InputData(philFile, globaldata->getFormat()); //format tells you whether philFile is list, rabund, sabund or shared.
30 inputRabund = new InputData(philFile, globaldata->getFormat());
31 }else {//there is an orderfile
32 input = new InputData(philFile, globaldata->getOrderFile(), globaldata->getFormat());
35 //memory leak prevention
36 //if (globaldata->ginput != NULL) { delete globaldata->ginput; }
37 globaldata->ginput = input; //saving to be used by collector and rarefact commands.
39 if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
40 order = input->getOrderVector();
41 //memory leak prevention
42 //if (globaldata->gorder != NULL) { delete globaldata->gorder; }
43 globaldata->gorder = order; //saving to be used by collect and rarefact commands.
44 sabund = inputSabund->getSAbundVector();
45 //if (globaldata->sabund != NULL) { delete globaldata->sabund; }
46 globaldata->sabund = sabund; //saving to be used by summary command.
48 rabund = inputRabund->getRAbundVector();
49 //if (globaldata->rabund != NULL) { delete globaldata->rabund; }
50 globaldata->rabund = rabund; //saving to be used by heatmap.bin command.
52 list = inputList->getListVector();
53 //if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
54 globaldata->gListVector = list;
57 }else if (globaldata->getFormat() == "shared") {
58 SharedList = input->getSharedListVector(); //you are reading for collect.shared, rarefaction.shared, summary.shared, parselist command, or shared commands.
59 //memory leak prevention
60 //if (globaldata->gSharedList != NULL) { delete globaldata->gSharedList; }
61 globaldata->gSharedList = SharedList;
65 errorOut(e, "ReadOTUFile", "read");
70 /***********************************************************************/
72 ReadOTUFile::~ReadOTUFile(){
77 /***********************************************************************/