some changes while testing 1.9

[mothur.git] / phylotree.cpp

diff --git a/phylotree.cpp b/phylotree.cpp
index 1001542ea36548742a2c92b809875fd4e7ec4f89..3cdd6acb2a33c38daf4af882253ad2c34acc39a6 100644 (file)
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -29,6 +29,7 @@ PhyloTree::PhyloTree(){
 
 PhyloTree::PhyloTree(string tfile){
        try {
+               m = MothurOut::getInstance();
                numNodes = 1;
                numSeqs = 0;
                tree.push_back(TaxNode("Root"));
@@ -61,8 +62,10 @@ string PhyloTree::getNextTaxon(string& heirarchy){
        try {
                string currentLevel = "";
                if(heirarchy != ""){
-                       currentLevel=heirarchy.substr(0,heirarchy.find_first_of(';'));
-                       heirarchy=heirarchy.substr(heirarchy.find_first_of(';')+1);
+                       int pos = heirarchy.find_first_of(';');
+                       currentLevel=heirarchy.substr(0,pos);
+                       if (pos != (heirarchy.length()-1)) {  heirarchy=heirarchy.substr(pos+1);  }
+                       else { heirarchy = ""; }
                }
                return currentLevel;
        }
@@ -74,7 +77,7 @@ string PhyloTree::getNextTaxon(string& heirarchy){
 
 /**************************************************************************************************/
 
-void PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
+int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
        try {
                numSeqs++;
                
@@ -90,6 +93,8 @@ void PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
                        
                        level++;
                        
+                       if (m->control_pressed) { return 0; }
+                       
                        //somehow the parent is getting one too many accnos
                        //use print to reassign the taxa id
                        taxon = getNextTaxon(seqTaxonomy);
@@ -154,7 +159,7 @@ void PhyloTree::assignHeirarchyIDs(int index){
                        tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
                        counter++;
                        tree[it->second].level = tree[index].level + 1;
-                       
+                                               
                        //save maxLevel for binning the unclassified seqs
                        if (tree[it->second].level > maxLevel) { maxLevel = tree[it->second].level; }