moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
deleted file mode 100644 (file)
index 481fd1d..0000000
--- a/groupmap.cpp
+++ /dev/null
@@ -1,195 +0,0 @@
-/*
- *  groupmap.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 12/1/08.
- *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "groupmap.h"
-
-/************************************************************/
-
- GroupMap::GroupMap(string filename) {
-       m = MothurOut::getInstance();
-       groupFileName = filename;
-       m->openInputFile(filename, fileHandle);
-       index = 0;
-}
-
-/************************************************************/
- GroupMap::~GroupMap(){}
-
-/************************************************************/
-int GroupMap::readMap() {
-               string seqName, seqGroup;
-               int error = 0;
-
-               while(fileHandle){
-                       fileHandle >> seqName;  m->gobble(fileHandle);          //read from first column
-                       fileHandle >> seqGroup;                 //read from second column
-                       
-                       if (m->control_pressed) {  fileHandle.close();  return 1; }
-       
-                       setNamesOfGroups(seqGroup);
-                       
-                       it = groupmap.find(seqName);
-                       
-                       if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
-                       else {
-                               groupmap[seqName] = seqGroup;   //store data in map
-                               seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
-                       }
-                       m->gobble(fileHandle);
-               }
-               fileHandle.close();
-               m->setAllGroups(namesOfGroups);
-               return error;
-}
-/************************************************************/
-int GroupMap::readDesignMap() {
-               string seqName, seqGroup;
-               int error = 0;
-
-               while(fileHandle){
-                       fileHandle >> seqName;  m->gobble(fileHandle);          //read from first column
-                       fileHandle >> seqGroup;                 //read from second column
-                       
-                       if (m->control_pressed) {  fileHandle.close();  return 1; }
-       
-                       setNamesOfGroups(seqGroup);
-                       
-                       it = groupmap.find(seqName);
-                       
-                       if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group names must be unique. Please correct."); m->mothurOutEndLine();  }
-                       else {
-                               groupmap[seqName] = seqGroup;   //store data in map
-                               seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
-                       }
-                       m->gobble(fileHandle);
-               }
-               fileHandle.close();
-               m->setAllGroups(namesOfGroups);
-               return error;
-}
-
-/************************************************************/
-int GroupMap::getNumGroups() { return namesOfGroups.size();    }
-/************************************************************/
-
-string GroupMap::getGroup(string sequenceName) {
-                       
-       it = groupmap.find(sequenceName);
-       if (it != groupmap.end()) { //sequence name was in group file
-               return it->second;      
-       }else {
-               return "not found";
-       }
-}
-
-/************************************************************/
-
-void GroupMap::setGroup(string sequenceName, string groupN) {
-       setNamesOfGroups(groupN);
-       
-       it = groupmap.find(sequenceName);
-       
-       if (it != groupmap.end()) {  m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
-       else {
-               groupmap[sequenceName] = groupN;        //store data in map
-               seqsPerGroup[groupN]++;  //increment number of seqs in that group
-       }
-}
-
-/************************************************************/
-void GroupMap::setNamesOfGroups(string seqGroup) {
-       int i, count;
-       count = 0;
-       for (i=0; i<namesOfGroups.size(); i++) {
-               if (namesOfGroups[i] != seqGroup) {
-                       count++; //you have not found this group
-               }else {
-                       break; //you already have it
-               }
-       }
-       if (count == namesOfGroups.size()) {
-               namesOfGroups.push_back(seqGroup); //new group
-               seqsPerGroup[seqGroup] = 0;
-               groupIndex[seqGroup] = index;
-               index++;
-       }
-}
-/************************************************************/
-bool GroupMap::isValidGroup(string groupname) {
-       try {
-               for (int i = 0; i < namesOfGroups.size(); i++) {
-                       if (groupname == namesOfGroups[i]) { return true; }
-               }
-               
-               return false;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "GroupMap", "isValidGroup");
-               exit(1);
-       }
-}
-/************************************************************/
-int GroupMap::getNumSeqs(string group) {
-       try {
-               
-               map<string, int>::iterator itNum;
-               
-               itNum = seqsPerGroup.find(group);
-               
-               if (itNum == seqsPerGroup.end()) { return 0; }
-               
-               return seqsPerGroup[group];
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "GroupMap", "getNumSeqs");
-               exit(1);
-       }
-}
-
-/************************************************************/
-vector<string> GroupMap::getNamesSeqs(){
-       try {
-       
-               vector<string> names;
-               
-               for (it = groupmap.begin(); it != groupmap.end(); it++) {
-                       names.push_back(it->first);
-               }
-               
-               return names;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "GroupMap", "getNamesSeqs");
-               exit(1);
-       }
-}
-/************************************************************/
-vector<string> GroupMap::getNamesSeqs(vector<string> picked){
-       try {
-               
-               vector<string> names;
-               
-               for (it = groupmap.begin(); it != groupmap.end(); it++) {
-                       //if you are belong to one the the groups in the picked vector add you
-                       if (m->inUsersGroups(it->second, picked)) {
-                               names.push_back(it->first);
-                       }
-               }
-               
-               return names;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "GroupMap", "getNamesSeqs");
-               exit(1);
-       }
-}
-
-/************************************************************/
-