added alignment code

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 4dfcbc1cf7129a6a9044b74f3ffb76671a0fd059..b4239f36bebb2fce5544cb171d6493c0d4a86aaf 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -85,10 +85,14 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "scale")                     { scale = value;                }
                                if (key == "ends" )                     { ends = value;                 }
                                if (key == "processors" )       { processors = value;   }
-                               
-
-                               
-
+                               if (key == "template")          { templatefile = value; }
+                               if (key == "search")            { search = value;               }
+                               if (key == "ksize")                     { ksize = value;                }
+                               if (key == "align")                 { align = value;            }
+                               if (key == "match")                     { match = value;                }
+                               if (key == "mismatch")          { mismatch = value;         }
+                               if (key == "gapopen")           { gapopen = value;              }
+                               if (key == "gapextend" )        { gapextend = value;    }
                                
                                if (key == "line") {//stores lines to be used in a set
                                        lines.clear();
@@ -151,7 +155,14 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "scale")                     { scale = value;                }
                        if (key == "ends" )                     { ends = value;                 }
                        if (key == "processors" )       { processors = value;   }
-
+                       if (key == "template")          { templatefile = value; }
+                       if (key == "search")            { search = value;               }
+                       if (key == "ksize")                     { ksize = value;                }
+                       if (key == "align")                 { align = value;            }
+                       if (key == "match")                     { match = value;                }
+                       if (key == "mismatch")          { mismatch = value;         }
+                       if (key == "gapopen")           { gapopen = value;              }
+                       if (key == "gapextend" )        { gapextend = value;    }
 
                        if (key == "line") {//stores lines to be used in a vector
                                lines.clear();
@@ -289,6 +300,14 @@ string GlobalData::getFilter()                     {   return filter;              }
 string GlobalData::getScale()                  {       return scale;           }
 string GlobalData::getEnds()                   {   return ends;                }
 string GlobalData::getProcessors()             {       return processors;      }
+string GlobalData::getTemplateFile()   {       return templatefile;}
+string GlobalData::getSearch()                 {       return search;          }
+string GlobalData::getKSize()                  {       return ksize;           }
+string GlobalData::getAlign()                  {       return align;           }
+string GlobalData::getMatch()                  {       return match;           }
+string GlobalData::getMismatch()               {       return mismatch;        }
+string GlobalData::getGapopen()                        {       return gapopen;         }
+string GlobalData::getGapextend()              {       return gapextend;       }
 
 void GlobalData::setListFile(string file)              {       listfile = file;        inputFileName = file;}
 void GlobalData::setGroupFile(string file)             {       groupfile = file;       }
@@ -334,6 +353,7 @@ void GlobalData::clear() {
        clustalfile             =   "";
        treefile                =       "";
        sharedfile              =       "";
+       templatefile    =       "";
        cutoff                  =       "10.00";
        format                  =       "";
        precision               =       "100";
@@ -357,6 +377,14 @@ void GlobalData::clear() {
        scale                   =       "log10";
        ends                    =   "T";  //yes
        processors              =       "1";
+       search                  =       "suffix";
+       ksize                   =       "7";
+       align                   =       "blast";
+       match                   =       "1.0";
+       mismatch                =       "-1.0";
+       gapopen                 =       "-5.0";
+       gapextend               =       "-2.0";
+       
 
 }
 
@@ -379,6 +407,13 @@ void GlobalData::reset() {
        form                    =       "integral";
        ends                    =   "T";
        processors              =       "1";
+       search                  =       "suffix";
+       ksize                   =       "7";
+       align                   =       "blast";
+       match                   =       "1.0";
+       mismatch                =       "-1.0";
+       gapopen                 =       "-5.0";
+       gapextend               =       "-2.0";
 }
 /*******************************************************/