fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 029164452c49d2247bd97262369a649cfbd3d190..d3790df170ab0651c24987bc3541b62f48197c5f 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -100,11 +100,9 @@ float ReadTree::readBranchLength(istream& f) {
        }               
 }
 
-
 /***********************************************************************/
 /***********************************************************************/
 
-
 //Child Classes Below
 
 /***********************************************************************/
@@ -113,12 +111,25 @@ float ReadTree::readBranchLength(istream& f) {
 
 int ReadNewickTree::read() {
        try {
+               holder = "";
                int c, error;
                int comment = 0;
                
                //if you are not a nexus file 
                if ((c = filehandle.peek()) != '#') {  
                        while((c = filehandle.peek()) != EOF) { 
+                               while ((c = filehandle.peek()) != EOF) {
+                                       // get past comments
+                                       if(c == '[') {
+                                               comment = 1;
+                                       }
+                                       if(c == ']'){
+                                               comment = 0;
+                                       }
+                                       if((c == '(') && (comment != 1)){ break; }
+                                       filehandle.get();
+                               }
+
                                //make new tree
                                T = new Tree(); 
                                numNodes = T->getNumNodes();
@@ -164,6 +175,8 @@ int ReadNewickTree::read() {
                                globaldata->gTree.push_back(T); 
                        }
                }
+               
+               if (error != 0) { readOk = error; } 
                return readOk;
        }
        catch(exception& e) {
@@ -236,7 +249,7 @@ int ReadNewickTree::readTreeString() {
                        n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
 
                        lc = readNewickInt(filehandle, n, T);
-                       if (lc == -1) { return -1; } //reports an error in reading
+                       if (lc == -1) { cout << "error with lc" << endl; return -1; } //reports an error in reading
                
                        if(filehandle.peek()==','){                                                     
                                readSpecialChar(filehandle,',',"comma");
@@ -247,7 +260,7 @@ int ReadNewickTree::readTreeString() {
                        }                                                                                               
                        if(rooted != 1){                                                                
                                rc = readNewickInt(filehandle, n, T);
-                               if (rc == -1) { return -1; } //reports an error in reading
+                               if (rc == -1) { cout << "error with rc" << endl; return -1; } //reports an error in reading
                                if(filehandle.peek() == ')'){                                   
                                        readSpecialChar(filehandle,')',"right parenthesis");
                                }                                                                                       
@@ -331,7 +344,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        }
                
                        int blen = 0;
-                       if(d == ':')    {               blen = 1;                       }               
+                       if(d == ':')    {               blen = 1;       }               
                
                        f.putback(d);
                
@@ -342,27 +355,22 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        int n1 = T->getIndex(name);
                        
                        //adds sequence names that are not in group file to the "xxx" group
-                       if(n1 == -1) {
-                               cerr << "Name: " << name << " not found in your groupfile. \n"; readOk = -1; return n1;
+                       if(group == "not found") {
+                               cout << "Name: " << name << " is not in your groupfile, and will be disregarded. \n";  //readOk = -1; return n1;
                                
-                               //globaldata->gTreemap->namesOfSeqs.push_back(name);
-                               //globaldata->gTreemap->treemap[name].groupname = "xxx";
-                               //globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
+                               globaldata->gTreemap->namesOfSeqs.push_back(name);
+                               globaldata->gTreemap->treemap[name].groupname = "xxx";
                                
-                               //map<string, int>::iterator it;
-                               //it = globaldata->gTreemap->seqsPerGroup.find("xxx");
-                               //if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
-                               //      globaldata->gTreemap->namesOfGroups.push_back("xxx");
-                               //      globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
-                               //}else {
-                               //      globaldata->gTreemap->seqsPerGroup["xxx"]++;
-                               //}
+                               map<string, int>::iterator it;
+                               it = globaldata->gTreemap->seqsPerGroup.find("xxx");
+                               if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
+                                       globaldata->gTreemap->namesOfGroups.push_back("xxx");
+                                       globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
+                               }else {
+                                       globaldata->gTreemap->seqsPerGroup["xxx"]++;
+                               }
                                
-                               //find index in tree of name
-                               //n1 = T->getIndex(name);
-                               //group = "xxx";
-                               //numLeaves++;
-                               //numNodes = 2*numLeaves - 1;
+                               group = "xxx";
                        }
                        
                        T->tree[n1].setGroup(group);