X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;h=c228162aab1d511af3fc5318aaf3e5eb5b39610c;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=e472570895414a4ec535e10c5f02bee10dfea982;hpb=219104a887d4725af80487729f4c34a030fe4358;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index e472570..c228162 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -12,36 +12,99 @@
 /************************************************************/
 
  TreeMap::TreeMap(string filename) {
+	m = MothurOut::getInstance();
 	groupFileName = filename;
-	openInputFile(filename, fileHandle);
+	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);
-			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) {
@@ -49,7 +112,7 @@ 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);
+			namesOfSeqs.erase(namesOfSeqs.begin()+i);
 			break;
 		}
 	}
@@ -61,8 +124,6 @@ void TreeMap::removeSeq(string seqName) {
 	//remove seq from treemap
 	it = treemap.find(seqName);
 	treemap.erase(it);
-	
-
 }
 /************************************************************/
 
@@ -137,7 +198,7 @@ bool TreeMap::isValidGroup(string groupname) {
 		return false;
 	}
 	catch(exception& e) {
-		errorOut(e, "TreeMap", "isValidGroup");
+		m->errorOut(e, "TreeMap", "isValidGroup");
 		exit(1);
 	}
 }
@@ -151,19 +212,19 @@ void TreeMap::print(ostream& output){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "TreeMap", "print");
+		m->errorOut(e, "TreeMap", "print");
 		exit(1);
 	}
 }
 
 /************************************************************/
-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++) {
@@ -175,7 +236,7 @@ void TreeMap::makeSim(GroupMap* groupmap) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "TreeMap", "makeSim");
+		m->errorOut(e, "TreeMap", "makeSim");
 		exit(1);
 	}
 }
@@ -201,7 +262,61 @@ void TreeMap::makeSim(ListVector* list) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "TreeMap", "makeSim");
+		m->errorOut(e, "TreeMap", "makeSim");
+		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);
 	}
 }