1.18.0

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 221646700817bdddf61c1f2b968328a1af590ac1..cdcc6ca9745d8bdf3509c3505ef5c15dc61fd991 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -20,11 +20,11 @@ vector<string> ClusterCommand::setParameters(){
                CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);              
                CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
+               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
                CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
                CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
                CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -44,7 +44,7 @@ string ClusterCommand::getHelpString(){
                helpString += "The cluster command parameter options are phylip, column, name, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
                helpString += "The cluster command should be in the following format: \n";
                helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
-               helpString += "The acceptable cluster methods are furthest, nearest, average and weighted.  If no method is provided then furthest is assumed.\n";      
+               helpString += "The acceptable cluster methods are furthest, nearest, average and weighted.  If no method is provided then average is assumed.\n";       
                return helpString;
        }
        catch(exception& e) {
@@ -182,7 +182,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        length = temp.length();
                        convert(temp, precision); 
                        
-                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
@@ -194,7 +194,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        cutoff += (5 / (precision * 10.0));  
                        
                        method = validParameter.validFile(parameters, "method", false);
-                       if (method == "not found") { method = "furthest"; }
+                       if (method == "not found") { method = "average"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, and weighted."); m->mothurOutEndLine(); abort = true; }

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 4471b357d268490a2c22ff7d44e9172be392512b..2b7b02b63a3a97d683d16a01b4514c5aa2671626 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -17,8 +17,8 @@ vector<string> ClusterDoturCommand::setParameters(){
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
                CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
@@ -40,7 +40,7 @@ string ClusterDoturCommand::getHelpString(){
                helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
                helpString += "The cluster.classic command should be in the following format: \n";
                helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
-               helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then furthest is assumed.\n";      
+               helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then average is assumed.\n";       
                return helpString;
        }
        catch(exception& e) {
@@ -151,14 +151,14 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
-                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
                        sim = m->isTrue(temp); 
                        
                        method = validParameter.validFile(parameters, "method", false);
-                       if (method == "not found") { method = "furthest"; }
+                       if (method == "not found") { method = "average"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { 
                                if (method == "furthest") { tag = "fn"; }

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 6d908c61c94eb0917730479cf76a7f34cc102d15..a695a6a750eefc5620e83bb5b9a294b9921495fc 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -32,8 +32,8 @@ vector<string> ClusterSplitCommand::setParameters(){
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                        
@@ -62,7 +62,7 @@ string ClusterSplitCommand::getHelpString(){
                helpString += "The name parameter allows you to enter your name file and is required if your distance file is in column format. \n";
                helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 10.0. \n";
                helpString += "The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n";
-               helpString += "The method allows you to specify what clustering algorythm you want to use, default=furthest, option furthest, nearest, or average. \n";
+               helpString += "The method allows you to specify what clustering algorythm you want to use, default=average, option furthest, nearest, or average. \n";
                helpString += "The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance, classify or fasta. \n";
                helpString += "The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n";
                helpString += "The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list. \n";
@@ -263,7 +263,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        length = temp.length();
                        convert(temp, precision); 
                        
-                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "large", false);                    if (temp == "not found") { temp = "F"; }
@@ -286,7 +286,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        temp = validParameter.validFile(parameters, "taxlevel", false);         if (temp == "not found")  { temp = "1"; }
                        convert(temp, taxLevelCutoff); 
                        
-                       method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "furthest"; }
+                       method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "average"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 310ad376733be3baa142f3bc1b110edbfc19e04d..12f1f9e0b33904639cca446f0b0d698e9f64f625 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -17,8 +17,8 @@ vector<string> HClusterCommand::setParameters(){
                CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
                CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter psorted("sorted", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psorted);
                CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
                CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);          
@@ -182,7 +182,7 @@ HClusterCommand::HClusterCommand(string option)  {
                        length = temp.length();
                        convert(temp, precision); 
                        
-                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
@@ -191,7 +191,7 @@ HClusterCommand::HClusterCommand(string option)  {
                        cutoff += (5 / (precision * 10.0)); 
                        
                        method = validParameter.validFile(parameters, "method", false);
-                       if (method == "not found") { method = "furthest"; }
+                       if (method == "not found") { method = "average"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average or weighted."); m->mothurOutEndLine(); abort = true; }

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 10932bc065ca69f6546503e3c0d402571d27cdc2..945d116c035d663eff0a3bc2317fda9ba643b908 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -18,8 +18,8 @@ vector<string> MGClusterCommand::setParameters(){
                CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
                CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "",false,false); parameters.push_back(pmethod);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter pmin("min", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmin);
                CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmerge);
                CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phcluster);
@@ -44,7 +44,7 @@ string MGClusterCommand::getHelpString(){
                helpString += "This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n";
                helpString += "The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n";
                helpString += "The precision parameter's default value is 100. \n";
-               helpString += "The acceptable mgcluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n";      
+               helpString += "The acceptable mgcluster methods are furthest, nearest and average.  If no method is provided then average is assumed.\n";       
                helpString += "The min parameter allows you to specify is you want the minimum or maximum blast score ratio used in calculating the distance. The default is true, meaning you want the minimum.\n";
                helpString += "The length parameter is used to specify the minimum overlap required.  The default is 5.\n";
                helpString += "The penalty parameter is used to adjust the error rate.  The default is 0.10.\n";
@@ -154,7 +154,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                        cutoff += (5 / (precision * 10.0));
                        
                        method = validParameter.validFile(parameters, "method", false);
-                       if (method == "not found") { method = "furthest"; }
+                       if (method == "not found") { method = "average"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
@@ -174,7 +174,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                        temp = validParameter.validFile(parameters, "hcluster", false);                 if (temp == "not found") { temp = "false"; }
                        hclusterWanted = m->isTrue(temp); 
                        
-                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                }