trim.seqs fix of gobble

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 0ba5ef1f28261307e91d678a73b4993ff38fa0ec..0d3bc33e2e406e1a811598fee620a92f3cedc3e2 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -23,10 +23,10 @@
 //**********************************************************************************************************************
 vector<string> HeatMapSimCommand::setParameters(){     
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);    
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
+               CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);        
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
-               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);              
+               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);          
                CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
@@ -512,8 +512,8 @@ int HeatMapSimCommand::runCommandDist() {
                                map<string, int>::iterator itA = nameMap->find(first);
                                map<string, int>::iterator itB = nameMap->find(second);
                                
-                               if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << first << "' was not found in the names file, please correct\n"; exit(1);  }
-                               if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << second << "' was not found in the names file, please correct\n"; exit(1);  }
+                               if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1);  }
+                               if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1);  }
                                
                                //save distance
                                matrix[itA->second][itB->second] = dist;