From e03de8796670a0c747aed63483daa09c8b86aea0 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Fri, 27 Aug 2010 15:21:38 +0000
Subject: [PATCH] made read.tree not require a groupfile, if one is not given
 all seqs are assumed to be from one group

---
 readtreecommand.cpp | 18 +++++++++++++++---
 tree.cpp            | 14 +++++++++++++-
 tree.h              |  6 ++++--
 treemap.cpp         | 15 +++++++++++++++
 treemap.h           |  1 +
 5 files changed, 48 insertions(+), 6 deletions(-)

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index fdfdb05..89efc9a 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -76,8 +76,20 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }	
-			else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;	}
-			else {  
+			else if (groupfile == "not found") { 
+				groupfile = ""; 
+				
+				m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine(); 	
+				
+				if (treefile != "") {  Tree* tree = new Tree(treefile); delete tree;  } //extracts names from tree to make faked out groupmap
+				
+				globaldata->setGroupFile(groupfile); 
+				//read in group map info.
+				treeMap = new TreeMap();
+				for (int i = 0; i < globaldata->Treenames.size(); i++) { treeMap->addSeq(globaldata->Treenames[i], "Group1"); }
+				globaldata->gTreemap = treeMap;
+					
+			}else {  
 				globaldata->setGroupFile(groupfile); 
 				//read in group map info.
 				treeMap = new TreeMap(groupfile);
@@ -227,7 +239,7 @@ int ReadTreeCommand::readNamesFile() {
 				vector<string> dupNames;
 				m->splitAtComma(second, dupNames);
 				
-				for (int i = 0; i < dupNames.size(); i++) {	nameMap[dupNames[i]] = dupNames[i];  }
+				for (int i = 0; i < dupNames.size(); i++) {	nameMap[dupNames[i]] = dupNames[i];  if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); }  }
 			}else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; }			
 		}
 		in.close();
diff --git a/tree.cpp b/tree.cpp
index dbb3f44..3cb2611 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -9,7 +9,19 @@
 
 #include "tree.h"
 
-
+/*****************************************************************/
+Tree::Tree(string g) {
+	try {
+		globaldata = GlobalData::getInstance();
+		m = MothurOut::getInstance();
+		
+		parseTreeFile();  globaldata->runParse = false;  
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "Tree - just parse");
+		exit(1);
+	}
+}
 /*****************************************************************/
 Tree::Tree() {
 	try {
diff --git a/tree.h b/tree.h
index 603f1c3..59343d5 100644
--- a/tree.h
+++ b/tree.h
@@ -18,6 +18,7 @@ class GlobalData;
 
 class Tree {
 public: 
+	Tree(string); 
 	Tree();		//to generate a tree from a file
 	~Tree();
 	
@@ -40,7 +41,8 @@ public:
 	int assembleTree();	
 	
 	vector<Node> tree;		//the first n nodes are the leaves, where n is the number of sequences.
-		
+	
+			
 private:
 	GlobalData* globaldata;
 	int numNodes, numLeaves;
@@ -64,7 +66,7 @@ private:
 	int readTreeString(ifstream&);
 		
 	MothurOut* m;
-	
+		
 };
 
 #endif
diff --git a/treemap.cpp b/treemap.cpp
index b2fc591..52a9003 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -44,6 +44,21 @@ void TreeMap::readMap() {
 		fileHandle.close();
 }
 /************************************************************/
+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
diff --git a/treemap.h b/treemap.h
index bda6926..d4b506e 100644
--- a/treemap.h
+++ b/treemap.h
@@ -36,6 +36,7 @@ public:
 	bool isValidGroup(string);  //return true if string is a valid group
 	void removeSeq(string);  //removes a sequence, this is to accomadate trees that do not contain all the seqs in your groupfile
 	string getGroup(string);
+	void addSeq(string, string);
 	vector<string> namesOfGroups;
 	vector<string> namesOfSeqs;
     map<string,int> seqsPerGroup;	//groupname, number of seqs in that group.
-- 
2.39.2