modified trim.seqs to speed up the append with multiple processors

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 21c70324611794f0574eb07cd97f2d10980a8bef..9f96f35e95c5b5f74d58690e8d485cb0987114a8 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -301,8 +301,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
                ofstream out;
                m->openOutputFile(outputFileName, out);
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-               out << "Node\tOTU#\tIndVal" << endl;
-               
+                               
                string treeOutputDir = outputDir;
                if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
                string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
@@ -335,13 +334,6 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
                        if (sharedfile != "") {
                                vector< vector<SharedRAbundVector*> > groupings;
                                
-                               /*groupings.resize(1);
-                               groupings[0].push_back(lookup[0]);
-                               groupings[0].push_back(lookup[1]);
-                               groupings[0].push_back(lookup[2]);
-                               groupings[0].push_back(lookup[3]);
-                               groupings[0].push_back(lookup[4]);*/
-                               
                                //get nodes that will be a valid grouping
                                //you are valid if you are not one of my descendants
                                //AND your distToLeaf is <= mine
@@ -444,15 +436,18 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
                        
                        if (m->control_pressed) { out.close(); return 0; }
                        
+                       
                        /******************************************************/
                        //output indicator values to table form + label tree  //
                        /*****************************************************/
+                       out << (i+1) << '\t';
                        for (int j = 0; j < indicatorValues.size(); j++) {
                                
                                if (m->control_pressed) { out.close(); return 0; }
                                
-                               out << (i+1) << '\t' << (j+1) << '\t' << indicatorValues[j] << endl;
+                               out << indicatorValues[j] << '\t';
                        }
+                       out << endl;
                        
                        T->tree[i].setLabel((i+1));
                        
@@ -587,14 +582,18 @@ map<int, float> IndicatorCommand::getLengthToLeaf(Tree*& T){
        try {
                map<int, float> dists;
                
+               bool hasBranchLengths = false;
+               for (int i = 0; i < T->getNumNodes(); i++) { 
+                       if (T->tree[i].getBranchLength() > 0.0) {  hasBranchLengths = true; break; }
+               }
+               
                for (int i = 0; i < T->getNumNodes(); i++) {
                        
                        int lc = T->tree[i].getLChild();
                        int rc = T->tree[i].getRChild();
                                 
                        //if you have no branch length, set it then calc
-                       if (T->tree[i].getBranchLength() <= 0.0) {
-                               
+                       if (!hasBranchLengths) {
                                if (lc == -1) { // you are a leaf
                                        //if you are a leaf set you priliminary length to 1.0, this may adjust later
                                        T->tree[i].setBranchLength(1.0);
@@ -605,8 +604,8 @@ map<int, float> IndicatorCommand::getLengthToLeaf(Tree*& T){
                                        float rdist = dists[rc];
                                        
                                        float greater = ldist;
-                                       if (rdist > greater) { greater = rdist; dists[i] = ldist; }
-                                       else { dists[i] = rdist; }
+                                       if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0; }
+                                       else { dists[i] = rdist + 1.0; }
                                        
                                        //branch length = difference + 1
                                        T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));