pat's changes to seq.error command

[mothur.git] / reportfile.h

diff --git a/reportfile.h b/reportfile.h
new file mode 100644 (file)
index 0000000..1bd2c94
--- /dev/null
+++ b/reportfile.h
@@ -0,0 +1,57 @@
+#ifndef REPORTFILE
+#define REPORTFILE
+
+/*
+ *  reportfile.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 7/12/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "mothur.h"
+#include "mothurout.h"
+
+/**************************************************************************************************/
+
+class ReportFile {
+public:
+       ReportFile();
+       ReportFile(ifstream&);
+       ReportFile(ifstream&, string);
+       
+       string getQueryName()                           {       return queryName;                               }
+       string getTemplateName()                        {       return templateName;                    }
+       string getSearchMethod()                        {       return searchMethod;                    }
+       string getAlignmentMethod()                     {       return alignmentMethod;                 }
+       
+       int getQueryLength()                            {       return queryLength;                             }
+       int getTemplateLength()                         {       return templateLength;                  }
+       int getQueryStart()                                     {       return queryStart;                              }
+       int getQueryEnd()                                       {       return queryEnd;                                }
+       int getTemplateStart()                          {       return templateStart;                   }
+       int getTemplateEnd()                            {       return templateEnd;                             }
+       int getPairwiseAlignmentLength()        {       return pairwiseAlignmentLength; }
+       int getGapsInQuery()                            {       return gapsInQuery;                             }
+       int getGapsInTemplate()                         {       return gapsInTemplate;                  }
+       int getLongestInsert()                          {       return longestInsert;                   }
+       
+       float getSearchScore()                          {       return searchScore;                             }
+       float getSimBtwnQueryAndTemplate()      {       return simBtwnQueryAndTemplate; }
+       
+
+private:
+       
+       MothurOut* m;
+               
+       string queryName, templateName, searchMethod, alignmentMethod;
+       int queryLength, templateLength, queryStart, queryEnd, templateStart, templateEnd, pairwiseAlignmentLength, gapsInQuery, gapsInTemplate, longestInsert;
+       float searchScore, simBtwnQueryAndTemplate;
+       
+};
+
+/**************************************************************************************************/
+
+#endif