X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;h=c228162aab1d511af3fc5318aaf3e5eb5b39610c;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=52a90031d380fedddd275bd5ebbb6a3f8600964c;hpb=e03de8796670a0c747aed63483daa09c8b86aea0;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index 52a9003..c228162 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -12,36 +12,84 @@
 /************************************************************/
 
  TreeMap::TreeMap(string filename) {
+	m = MothurOut::getInstance();
 	groupFileName = filename;
 	m->openInputFile(filename, fileHandle);
 }
 
 /************************************************************/
  TreeMap::~TreeMap(){}
+/************************************************************/
+int TreeMap::readMap(string gf) {
+    
+    groupFileName = gf;
+	m->openInputFile(gf, fileHandle);
+    
+    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);
+        
+        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]++;
+            }				
+        }
+        
+        m->gobble(fileHandle);
+    }
+    fileHandle.close();
+    
+    return error;
+}
 
 /************************************************************/
-void TreeMap::readMap() {
+int TreeMap::readMap() {
 		string seqName, seqGroup;
-	
+		int error = 0;
+		
 		while(fileHandle){
-			fileHandle >> seqName;			//read from first column
+			fileHandle >> seqName;      	 m->gobble(fileHandle); //read from first column
 			fileHandle >> seqGroup;			//read from second column
-
-			namesOfSeqs.push_back(seqName);
+			
+			if (m->control_pressed) {  fileHandle.close();  return 1; }
+			
 			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]++;
+			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]++;
+				}				
 			}
-
+			
 			m->gobble(fileHandle);
 		}
 		fileHandle.close();
+	
+
+		return error;
 }
 /************************************************************/
 void TreeMap::addSeq(string seqName, string seqGroup) {
@@ -170,13 +218,13 @@ void TreeMap::print(ostream& output){
 }
 
 /************************************************************/
-void TreeMap::makeSim(GroupMap* groupmap) {
+void TreeMap::makeSim(vector<string> ThisnamesOfGroups) {
 	try {
 		//set names of groups
-		namesOfGroups = groupmap->namesOfGroups;
+		namesOfGroups = ThisnamesOfGroups;
 		
 		//set names of seqs to names of groups
-		namesOfSeqs = groupmap->namesOfGroups;
+		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++) {
@@ -218,6 +266,60 @@ void TreeMap::makeSim(ListVector* list) {
 		exit(1);
 	}
 }
+/************************************************************/
+int TreeMap::getCopy(TreeMap& copy){
+	try {
+         
+        namesOfGroups = copy.getNamesOfGroups();
+		numGroups = copy.getNumGroups();
+        namesOfSeqs = copy.namesOfSeqs;
+        seqsPerGroup = copy.seqsPerGroup;
+        treemap = copy.treemap;
+        
+        return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeMap", "getCopy");
+		exit(1);
+	}
+}
+/************************************************************/
+vector<string> TreeMap::getNamesSeqs(){
+	try {
+        
+		vector<string> names;
+		
+        for(it = treemap.begin(); it != treemap.end(); it++){
+            names.push_back(it->first);
+		}
+		
+		return names;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeMap", "getNamesSeqs");
+		exit(1);
+	}
+}
+/************************************************************/
+vector<string> TreeMap::getNamesSeqs(vector<string> picked){
+	try {
+		
+		vector<string> names;
+		
+		for(it = treemap.begin(); it != treemap.end(); it++){
+			//if you are belong to one the the groups in the picked vector add you
+			if (m->inUsersGroups(it->second.groupname, picked)) {
+				names.push_back(it->first);
+			}
+		}
+		
+		return names;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeMap", "getNamesSeqs");
+		exit(1);
+	}
+}
 
 /************************************************************/