X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;h=1fc5c01b796a67bd948a70147fa4dead9320ea08;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=6314eb04d04006ba5c57808f6927bddec89d6a00;hpb=b2dca66a02f8f82aa5528e531eace60fbbd2967b;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index 6314eb0..1fc5c01 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -12,42 +12,87 @@
 /************************************************************/
 
  TreeMap::TreeMap(string filename) {
+	m = MothurOut::getInstance();
 	groupFileName = filename;
-	openInputFile(filename, fileHandle);
+	m->openInputFile(filename, fileHandle);
 }
 
 /************************************************************/
- TreeMap::~TreeMap(){};
+ TreeMap::~TreeMap(){}
 
 /************************************************************/
-void TreeMap::readMap() {
+int TreeMap::readMap() {
 		string seqName, seqGroup;
-	
+		int error = 0;
+		
 		while(fileHandle){
-			fileHandle >> seqName;			//read from first column
+			fileHandle >> seqName;      	//read from first column
 			fileHandle >> seqGroup;			//read from second column
 			
-			namesOfSeqs.push_back(seqName);
-			setNamesOfGroups(seqGroup);
-						
-			treemap[seqName].groupname = seqGroup;	//store data in map
+			if (m->control_pressed) {  fileHandle.close();  return 1; }
 			
-			it2 = seqsPerGroup.find(seqGroup);
-			if (it2 == seqsPerGroup.end()) { //if it's a new group
-				seqsPerGroup[seqGroup] = 1;
-			}else {//it's a group we already have
-				seqsPerGroup[seqGroup]++;
+			setNamesOfGroups(seqGroup);
+					
+			map<string, GroupIndex>::iterator itCheck = treemap.find(seqName);
+			if (itCheck != treemap.end()) { error = 1; m->mothurOut("[WARNING]: Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
+			else {
+				namesOfSeqs.push_back(seqName);
+				treemap[seqName].groupname = seqGroup;	//store data in map
+				
+				it2 = seqsPerGroup.find(seqGroup);
+				if (it2 == seqsPerGroup.end()) { //if it's a new group
+					seqsPerGroup[seqGroup] = 1;
+				}else {//it's a group we already have
+					seqsPerGroup[seqGroup]++;
+				}				
 			}
-
-			gobble(fileHandle);
+			
+			m->gobble(fileHandle);
 		}
 		fileHandle.close();
+	
+
+		return error;
+}
+/************************************************************/
+void TreeMap::addSeq(string seqName, string seqGroup) {
+	
+		namesOfSeqs.push_back(seqName);
+		setNamesOfGroups(seqGroup);
+					
+		treemap[seqName].groupname = seqGroup;	//store data in map
+			
+		it2 = seqsPerGroup.find(seqGroup);
+		if (it2 == seqsPerGroup.end()) { //if it's a new group
+			seqsPerGroup[seqGroup] = 1;
+		}else {//it's a group we already have
+			seqsPerGroup[seqGroup]++;
+		}
+}
+/************************************************************/
+void TreeMap::removeSeq(string seqName) {
+	
+	//erase name from namesOfSeqs
+	for (int i = 0; i < namesOfSeqs.size(); i++) {
+		if (namesOfSeqs[i] == seqName)  {
+			namesOfSeqs.erase(namesOfSeqs.begin()+i);
+			break;
+		}
+	}
+	
+	//decrement sequences in this group
+	string group = treemap[seqName].groupname;
+	seqsPerGroup[group]--;
+	
+	//remove seq from treemap
+	it = treemap.find(seqName);
+	treemap.erase(it);
 }
 /************************************************************/
 
 int TreeMap::getNumGroups() {
 			
-	return seqsPerGroup.size();	
+	return namesOfGroups.size();	
 		
 }
 /************************************************************/
@@ -72,7 +117,13 @@ string TreeMap::getGroup(string sequenceName) {
 }
 /************************************************************/
 void TreeMap::setIndex(string seq, int index) {
-	treemap[seq].vectorIndex = index;
+	it = treemap.find(seq);
+	if (it != treemap.end()) { //sequence name was in group file
+		treemap[seq].vectorIndex = index;	
+	}else {
+		treemap[seq].vectorIndex = index;
+		treemap[seq].groupname = "not found";
+	}
 }
 /************************************************************/
 int TreeMap::getIndex(string seq) {
@@ -110,11 +161,7 @@ bool TreeMap::isValidGroup(string groupname) {
 		return false;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the TreeMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "TreeMap", "isValidGroup");
 		exit(1);
 	}
 }
@@ -128,13 +175,60 @@ void TreeMap::print(ostream& output){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "TreeMap", "print");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the TreeMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/************************************************************/
+void TreeMap::makeSim(vector<string> ThisnamesOfGroups) {
+	try {
+		//set names of groups
+		namesOfGroups = ThisnamesOfGroups;
+		
+		//set names of seqs to names of groups
+		namesOfSeqs = ThisnamesOfGroups;
+		
+		// make map where key and value are both the group name since that what the tree.shared command wants
+		for (int i = 0; i < namesOfGroups.size(); i++) {
+			treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
+			seqsPerGroup[namesOfGroups[i]] = 1;
+		}
+		
+		numGroups = namesOfGroups.size();
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeMap", "makeSim");
+		exit(1);
+	}
+}
+/************************************************************/
+void TreeMap::makeSim(ListVector* list) {
+	try {
+		//set names of groups
+		namesOfGroups.clear();
+		for(int i = 0; i < list->size(); i++) {
+			namesOfGroups.push_back(list->get(i));
+		}
+		
+		//set names of seqs to names of groups
+		namesOfSeqs = namesOfGroups;
+		
+		// make map where key and value are both the group name since that what the tree.shared command wants
+		for (int i = 0; i < namesOfGroups.size(); i++) {
+			treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
+			seqsPerGroup[namesOfGroups[i]] = 1;
+		}
+		
+		numGroups = namesOfGroups.size();
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeMap", "makeSim");
 		exit(1);
 	}
 }
 
 /************************************************************/
+