X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;fp=groupmap.cpp;h=481fd1decfc4516eb5e1cf618c6b4d40cffbc8a9;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
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index 0000000..481fd1d
--- /dev/null
+++ b/groupmap.cpp
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+/*
+ *  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);
+	}
+}
+
+/************************************************************/
+