Adjusts cutoff for agc and dgc methods

cluster and cluster.split #254
mothur · fc821b8c4a333be95e9ccd5a48fc14f4de077ea3 · mothur-westcott committed Jul 20, 2016 · Jul 20, 2016 · fc821b8
1 parent 5ddcbf3
commit fc821b8c4a333be95e9ccd5a48fc14f4de077ea3
Unified Split

Showing with 13 additions and 12 deletions.

+8 −7 source/commands/clustercommand.cpp

+5 −5 source/commands/clustersplitcommand.cpp
diff --git a/source/commands/clustercommand.cpp b/source/commands/clustercommand.cpp
@@ -257,13 +257,6 @@ ClusterCommand::ClusterCommand(string option)  {
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
 			
-            //bool cutoffSet = false;
-			temp = validParameter.validFile(parameters, "cutoff", false);
-			if (temp == "not found") { temp = "10"; }
-            //else { cutoffSet = true; }
-			m->mothurConvert(temp, cutoff); 
-			cutoff += (5 / (precision * 10.0));
-            
             //temp = validParameter.validFile(parameters, "adjust", false);				if (temp == "not found") { temp = "F"; }
             //if (m->isNumeric1(temp))    { m->mothurConvert(temp, adjust);   }
             //else if (m->isTrue(temp))   { adjust = 1.0;                     }
@@ -283,6 +276,14 @@ ClusterCommand::ClusterCommand(string option)  {
 #else
             if ((method == "agc") || (method == "dgc")) { m->mothurOut("[ERROR]: The agc and dgc clustering methods are not available for Windows, aborting\n."); abort = true; }
 #endif
+            
+            //bool cutoffSet = false;
+            temp = validParameter.validFile(parameters, "cutoff", false);
+            if (temp == "not found") { temp = "10"; }
+            //else { cutoffSet = true; }
+            m->mothurConvert(temp, cutoff);
+            if ((method != "agc") && (method != "dgc")) { cutoff += (5 / (precision * 10.0)); }
+            
 			showabund = validParameter.validFile(parameters, "showabund", false);
 			if (showabund == "not found") { showabund = "T"; }
 
diff --git a/source/commands/clustersplitcommand.cpp b/source/commands/clustersplitcommand.cpp
@@ -346,11 +346,6 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
             
             //not using file option and don't have fasta method with classic
             if (((splitmethod != "fasta") && classic) && (file == "")) { m->mothurOut("[ERROR]: splitmethod must be fasta to use cluster.classic, or you must use the file option.\n"); abort=true; }
-            
-            cutoffNotSet = false;
-            temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found")  { cutoffNotSet = true; temp = "0.25"; }
-			m->mothurConvert(temp, cutoff); 
-			cutoff += (5 / (precision * 10.0));  
 			
 			temp = validParameter.validFile(parameters, "taxlevel", false);		if (temp == "not found")  { temp = "3"; }
 			m->mothurConvert(temp, taxLevelCutoff); 
@@ -369,6 +364,11 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
             if ((method == "agc") || (method == "dgc")) { m->mothurOut("[ERROR]: The agc and dgc clustering methods are not available for Windows, aborting\n."); abort = true; }
             #endif
             
+            cutoffNotSet = false;
+            temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found")  { cutoffNotSet = true; temp = "0.25"; }
+            m->mothurConvert(temp, cutoff);
+            if ((method != "agc") && (method != "dgc")) { cutoff += (5 / (precision * 10.0)); }
+            
 			if ((splitmethod == "distance") || (splitmethod == "classify") || (splitmethod == "fasta")) { }
 			else { m->mothurOut("[ERROR]: " + splitmethod + " is not a valid splitting method.  Valid splitting algorithms are distance, classify or fasta."); m->mothurOutEndLine(); abort = true; }