indicator command

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 173675e494a9ed8d328e5f634d5bdbc978869939..05ddaf6459959ad39bb83720547a1b458c7ae807 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -32,7 +32,7 @@ vector<string> ChimeraUchimeCommand::setParameters(){
                CommandParameter pchunks("chunks", "Number", "", "4", "", "", "",false,false); parameters.push_back(pchunks);
                CommandParameter pminchunk("minchunk", "Number", "", "64", "", "", "",false,false); parameters.push_back(pminchunk);
                CommandParameter pidsmoothwindow("idsmoothwindow", "Number", "", "32", "", "", "",false,false); parameters.push_back(pidsmoothwindow);
-               CommandParameter pminsmoothid("minsmoothid", "Number", "", "0.95", "", "", "",false,false); parameters.push_back(pminsmoothid);
+               //CommandParameter pminsmoothid("minsmoothid", "Number", "", "0.95", "", "", "",false,false); parameters.push_back(pminsmoothid);
                CommandParameter pmaxp("maxp", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmaxp);
                CommandParameter pskipgaps("skipgaps", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pskipgaps);
                CommandParameter pskipgaps2("skipgaps2", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pskipgaps2);
@@ -72,7 +72,7 @@ string ChimeraUchimeCommand::getHelpString(){
                helpString += "The chunks parameter is the number of chunks to extract from the query sequence when searching for parents. Default 4.\n";
                helpString += "The minchunk parameter is the minimum length of a chunk. Default 64.\n";
                helpString += "The idsmoothwindow parameter is the length of id smoothing window. Default 32.\n";
-               helpString += "The minsmoothid parameter - minimum factional identity over smoothed window of candidate parent. Default 0.95.\n";
+               //helpString += "The minsmoothid parameter - minimum factional identity over smoothed window of candidate parent. Default 0.95.\n";
                helpString += "The maxp parameter - maximum number of candidate parents to consider. Default 2. In tests so far, increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit.\n";
                helpString += "The skipgaps parameter controls how gapped columns affect counting of diffs. If skipgaps is set to T, columns containing gaps do not found as diffs. Default = T.\n";
                helpString += "The skipgaps2 parameter controls how gapped columns affect counting of diffs. If skipgaps2 is set to T, if column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default = T.\n";
@@ -337,7 +337,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        chunks = validParameter.validFile(parameters, "chunks", false);                                 if (chunks == "not found")                      { useChunks = false; chunks = "4";                                      }       else{ useChunks = true;                 }
                        minchunk = validParameter.validFile(parameters, "minchunk", false);                             if (minchunk == "not found")            { useMinchunk = false; minchunk = "64";                         }       else{ useMinchunk = true;               }
                        idsmoothwindow = validParameter.validFile(parameters, "idsmoothwindow", false); if (idsmoothwindow == "not found")      { useIdsmoothwindow = false; idsmoothwindow = "32";     }       else{ useIdsmoothwindow = true; }
-                       minsmoothid = validParameter.validFile(parameters, "minsmoothid", false);               if (minsmoothid == "not found")         { useMinsmoothid = false; minsmoothid = "0.95";         }       else{ useMinsmoothid = true;    }
+                       //minsmoothid = validParameter.validFile(parameters, "minsmoothid", false);             if (minsmoothid == "not found")         { useMinsmoothid = false; minsmoothid = "0.95";         }       else{ useMinsmoothid = true;    }
                        maxp = validParameter.validFile(parameters, "maxp", false);                                             if (maxp == "not found")                        { useMaxp = false; maxp = "2";                                          }       else{ useMaxp = true;                   }
                        minlen = validParameter.validFile(parameters, "minlen", false);                                 if (minlen == "not found")                      { useMinlen = false; minlen = "10";                                     }       else{ useMinlen = true;                 }
                        maxlen = validParameter.validFile(parameters, "maxlen", false);                                 if (maxlen == "not found")                      { useMaxlen = false; maxlen = "10000";                          }       else{ useMaxlen = true;                 }
@@ -650,7 +650,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                        cPara.push_back(tempIdsmoothwindow);
                }
                
-               if (useMinsmoothid) {
+               /*if (useMinsmoothid) {
                        char* tempminsmoothid = new char[14]; 
                        //strcpy(tempminsmoothid, "--minsmoothid"); 
                        *tempminsmoothid = '\0'; strncat(tempminsmoothid, "--minsmoothid", 13);
@@ -659,7 +659,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                        *tempMinsmoothid = '\0'; strncat(tempMinsmoothid, minsmoothid.c_str(), minsmoothid.length());
                        //strcpy(tempMinsmoothid, minsmoothid.c_str());
                        cPara.push_back(tempMinsmoothid);
-               }
+               }*/
                
                if (useMaxp) {
                        char* tempmaxp = new char[7]; 
@@ -673,16 +673,16 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                }
                
                if (!skipgaps) {
-                       char* tempskipgaps = new char[15]; 
+                       char* tempskipgaps = new char[13]; 
                        //strcpy(tempskipgaps, "--[no]skipgaps");
-                       *tempskipgaps = '\0'; strncat(tempskipgaps, "--[no]skipgaps", 14);
+                       *tempskipgaps = '\0'; strncat(tempskipgaps, "--noskipgaps", 12);
                        cPara.push_back(tempskipgaps);
                }
                
                if (!skipgaps2) {
-                       char* tempskipgaps2 = new char[16]; 
+                       char* tempskipgaps2 = new char[14]; 
                        //strcpy(tempskipgaps2, "--[no]skipgaps2"); 
-                       *tempskipgaps2 = '\0'; strncat(tempskipgaps2, "--[no]skipgaps2", 15);
+                       *tempskipgaps2 = '\0'; strncat(tempskipgaps2, "--noskipgaps2", 13);
                        cPara.push_back(tempskipgaps2);
                }