9 * Created by Pat Schloss on 12/19/08.
10 * Copyright 2008 Patrick D. Schloss. All rights reserved.
16 /******************************************************************************************************************/
23 void setCandidate(Sequence*);
24 void setTemplate(Sequence*);
25 void setSearchParameters(string, float);
26 void setAlignmentParameters(string, Alignment*);
27 void setNastParameters(Nast);
37 string alignmentMethod;
38 int candidateStartPosition, candidateEndPosition;
39 int templateStartPosition, templateEndPosition;
41 int pairwiseAlignmentLength;
43 int totalGapsInQuery, totalGapsInTemplate;
44 float similarityToTemplate;
45 ofstream candidateReportFile;
48 /******************************************************************************************************************/