- mothurOut("The hcluster command parameter options are cutoff, precision, method, showabund, timing, phylip, column, name and sorted. Phylip or column and name are required.\n");
+ mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
mothurOut("The hcluster command should be in the following format: \n");
mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
mothurOut("The hcluster command should be in the following format: \n");
@@ -161,7+161,7 @@ int HClusterCommand::execute(){
mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); mothurOutEndLine();
estart = time(NULL);
mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); mothurOutEndLine();
estart = time(NULL);
-
+
//list vector made by read contains all sequence names
if(list != NULL){
rabund = new RAbundVector(list->getRAbundVector());
//list vector made by read contains all sequence names
if(list != NULL){
rabund = new RAbundVector(list->getRAbundVector());
@@ -177,7+177,7 @@ int HClusterCommand::execute(){
print_start = true;
start = time(NULL);
print_start = true;
start = time(NULL);
-//cout << "here" << endl;
+
ifstream in;
openInputFile(distfile, in);
string firstName, secondName;
ifstream in;
openInputFile(distfile, in);
string firstName, secondName;
@@ -187,7+187,7 @@ int HClusterCommand::execute(){
bool clusteredSomething;
vector<seqDist> seqs; seqs.resize(1); // to start loop
exitedBreak = false; //lets you know if there is a distance stored in next
bool clusteredSomething;
vector<seqDist> seqs; seqs.resize(1); // to start loop
exitedBreak = false; //lets you know if there is a distance stored in next