X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treereader.cpp;fp=treereader.cpp;h=b385d214fbf4043d5b32b58ec23673b3e9136438;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/treereader.cpp b/treereader.cpp
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index 0000000..b385d21
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+++ b/treereader.cpp
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+//
+//  treereader.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 4/11/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "treereader.h"
+#include "readtree.h"
+
+/***********************************************************************/
+
+TreeReader::TreeReader(string tf) : treefile(tf)  { 
+    try {
+        m = MothurOut::getInstance();
+        namefile = "";
+        groupfile = "";
+        readTrees();
+    }
+	catch(exception& e) {
+		m->errorOut(e, "TreeReader", "TreeReader");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+TreeReader::TreeReader(string tf, string gf) : treefile(tf),  groupfile(gf)  { 
+    try {
+        m = MothurOut::getInstance();
+        namefile = "";
+        readTrees();
+    }
+	catch(exception& e) {
+		m->errorOut(e, "TreeReader", "TreeReader");
+		exit(1);
+	}
+}
+/***********************************************************************/
+TreeReader::TreeReader(string tf, string gf, string nf) : treefile(tf),  groupfile(gf), namefile(nf)  { 
+    try {
+        m = MothurOut::getInstance();
+        readTrees();
+    }
+	catch(exception& e) {
+		m->errorOut(e, "TreeReader", "TreeReader");
+		exit(1);
+	}
+}
+/***********************************************************************/
+bool TreeReader::readTrees()  { 
+    try {
+        
+        tmap = new TreeMap();
+        if (groupfile != "") {      tmap->readMap(groupfile);        }
+		else{ //fake out by putting everyone in one group
+			Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
+			for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+		}
+		
+        int numUniquesInName = 0;
+		if (namefile != "") { numUniquesInName = readNamesFile(); }
+		
+		ReadTree* read = new ReadNewickTree(treefile);
+		int readOk = read->read(tmap); 
+		
+		if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine();  delete read; m->control_pressed=true; return 0; }
+		
+		read->AssembleTrees(names);
+		trees = read->getTrees();
+		delete read;
+        
+		//make sure all files match
+		//if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
+		int numNamesInTree;
+		if (namefile != "")  {  
+			if (numUniquesInName == m->Treenames.size()) {  numNamesInTree = nameMap.size();  }
+			else {   numNamesInTree = m->Treenames.size();  }
+		}else {  numNamesInTree = m->Treenames.size();  }
+		
+		
+		//output any names that are in group file but not in tree
+		if (numNamesInTree < tmap->getNumSeqs()) {
+			for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
+				//is that name in the tree?
+				int count = 0;
+				for (int j = 0; j < m->Treenames.size(); j++) {
+					if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
+					count++;
+				}
+				
+				if (m->control_pressed) { for (int i = 0; i < trees.size(); i++) { delete trees[i]; } return 0; }
+				
+				//then you did not find it so report it 
+				if (count == m->Treenames.size()) { 
+					//if it is in your namefile then don't remove
+					map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
+					
+					if (it == nameMap.end()) {
+						m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
+						tmap->removeSeq(tmap->namesOfSeqs[i]);
+						i--; //need this because removeSeq removes name from namesOfSeqs
+					}
+				}
+			}
+		}
+        
+        return true;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "TreeReader", "readTrees");
+		exit(1);
+	}
+}
+/*****************************************************************/
+int TreeReader::readNamesFile() {
+	try {
+		nameMap.clear();
+        names.clear();
+		int numUniquesInName = 0;
+		
+		ifstream in;
+		m->openInputFile(namefile, in);
+		
+		string first, second;
+		map<string, string>::iterator itNames;
+		
+		while(!in.eof()) {
+			in >> first >> second; m->gobble(in);
+			
+			numUniquesInName++;
+			
+			itNames = nameMap.find(first);
+			if (itNames == nameMap.end()) {  
+				names[first] = second; 
+				
+				//we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
+				vector<string> dupNames;
+				m->splitAtComma(second, dupNames);
+				
+				for (int i = 0; i < dupNames.size(); i++) {	
+					nameMap[dupNames[i]] = first; 
+					if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); } 
+				}
+			}else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); nameMap.clear(); names.clear(); namefile = ""; return 1; }			
+		}
+		in.close();
+		
+		return numUniquesInName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeReader", "readNamesFile");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+