removing chime source files from mother project.

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 16348c8d324a962ca336c82a2ad303f156cde9e3..528f71c11c24f7a47133bef2d60a6906249abe92 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -11,6 +11,7 @@
 #include "readphylip.h"
 #include "readcolumn.h"
 #include "readmatrix.hpp"
+#include "clusterdoturcommand.h"
 
 //**********************************************************************************************************************
 vector<string> ClusterCommand::setParameters(){        
@@ -135,16 +136,17 @@ ClusterCommand::ClusterCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { phylipfile = ""; abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  distfile = phylipfile;  format = "phylip";      }
+                       else {  distfile = phylipfile;  format = "phylip";      m->setPhylipFile(phylipfile); }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { columnfile = ""; abort = true; }        
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  distfile = columnfile; format = "column";       }
+                       else {  distfile = columnfile; format = "column"; m->setColumnFile(columnfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        if ((phylipfile == "") && (columnfile == "")) { 
                                //is there are current file available for either of these?
@@ -181,7 +183,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
@@ -191,7 +193,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
                        method = validParameter.validFile(parameters, "method", false);
@@ -206,7 +208,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        timing = validParameter.validFile(parameters, "timing", false);
                        if (timing == "not found") { timing = "F"; }
                        
-                       }
+               }
        }
        catch(exception& e) {
                m->errorOut(e, "ClusterCommand", "ClusterCommand");
@@ -222,6 +224,34 @@ int ClusterCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
+               //phylip file given and cutoff not given - use cluster.classic because it uses less memory and is faster
+               if ((format == "phylip") && (cutoff > 10.0)) {
+                       m->mothurOutEndLine(); m->mothurOut("You are using a phylip file and no cutoff.  I will run cluster.classic to save memory and time."); m->mothurOutEndLine();
+                       
+                       //run unique.seqs for deconvolute results
+                       string inputString = "phylip=" + distfile;
+                       if (namefile != "") { inputString += ", name=" + namefile; }
+                       inputString += ", precision=" + toString(precision);
+                       inputString += ", method=" + method;
+                       if (hard)       { inputString += ", hard=T";    }
+                       else            { inputString += ", hard=F";    }
+                       if (sim)        { inputString += ", sim=T";             }
+                       else            { inputString += ", sim=F";             }
+
+                       
+                       m->mothurOutEndLine(); 
+                       m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine(); 
+                       m->mothurOut("Running command: cluster.classic(" + inputString + ")"); m->mothurOutEndLine(); 
+                       
+                       Command* clusterClassicCommand = new ClusterDoturCommand(inputString);
+                       clusterClassicCommand->execute();
+                       delete clusterClassicCommand;
+                       
+                       m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine();  
+
+                       return 0;
+               }
+               
                ReadMatrix* read;
                if (format == "column") { read = new ReadColumnMatrix(columnfile, sim); }       //sim indicates whether its a similarity matrix
                else if (format == "phylip") { read = new ReadPhylipMatrix(phylipfile, sim); }
@@ -243,7 +273,7 @@ int ClusterCommand::execute(){
                if (m->control_pressed) { //clean up
                        delete list; delete matrix; delete rabund;
                        sabundFile.close();rabundFile.close();listFile.close();
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
                        return 0;
                }
                
@@ -282,7 +312,7 @@ int ClusterCommand::execute(){
                        if (m->control_pressed) { //clean up
                                delete list; delete matrix; delete rabund; delete cluster;
                                sabundFile.close();rabundFile.close();listFile.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear();
                                return 0;
                        }
                
@@ -325,7 +355,7 @@ int ClusterCommand::execute(){
                        cout.flush();
                        print_start = false;
                }
-       
+               
                if(previousDist <= 0.0000){
                        printData("unique");
                }