final fixes for 1.7

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 6e3ec243addd289a6d44226adeddd6a3fccbb0d2..38559500b0a81f25716b983b2274b88332e3ff56 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -53,8 +53,8 @@ HClusterCommand::HClusterCommand(string option){
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
                        
-                       if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a cluster command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
-                       else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a cluster command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
+                       if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a hcluster command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
+                       else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
                
                        if (columnfile != "") {
                                if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
@@ -114,11 +114,12 @@ HClusterCommand::HClusterCommand(string option){
 
 void HClusterCommand::help(){
        try {
-               mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
-               mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n");
-               mothurOut("The cluster command should be in the following format: \n");
-               mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
-               mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n"); 
+               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 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("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
+               mothurOut("The acceptable hcluster methods is furthest, but we hope to add nearest and average in the future.\n\n");    
        }
        catch(exception& e) {
                errorOut(e, "HClusterCommand", "help");
@@ -168,8 +169,6 @@ int HClusterCommand::execute(){
                        mothurOut("Error: no list vector!"); mothurOutEndLine(); return 0;
                }
                
-               
-               
                float previousDist = 0.00000;
                float rndPreviousDist = 0.00000;
                oldRAbund = *rabund;
@@ -260,6 +259,7 @@ int HClusterCommand::execute(){
                rabundFile.close();
                listFile.close();
                
+               delete cluster;
                //if (isTrue(timing)) {
                        mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); mothurOutEndLine();
                //}
@@ -330,10 +330,10 @@ vector<seqDist> HClusterCommand::getSeqs(ifstream& filehandle){
                        map<string,int>::iterator itB = globaldata->nameMap->find(secondName);
                        
                        if(itA == globaldata->nameMap->end()){
-                               cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
+                               cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);
                        }
                        if(itB == globaldata->nameMap->end()){
-                               cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
+                               cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
                        }
                        
                        //using cutoff