9 * Created by Pat Schloss on 12/19/08.
10 * Copyright 2008 Patrick D. Schloss. All rights reserved.
16 /******************************************************************************************************************/
22 void setCandidate(Sequence*);
23 void setTemplate(Sequence*);
24 void setSearchParameters(string, float);
25 void setAlignmentParameters(string, Alignment*);
26 void setNastParameters(Nast);
36 string alignmentMethod;
37 int candidateStartPosition, candidateEndPosition;
38 int templateStartPosition, templateEndPosition;
40 int pairwiseAlignmentLength;
42 int totalGapsInQuery, totalGapsInTemplate;
43 float similarityToTemplate;
44 ofstream candidateReportFile;
47 /******************************************************************************************************************/