9 * Created by Pat Schloss on 12/19/08.
10 * Copyright 2008 Patrick D. Schloss. All rights reserved.
16 /******************************************************************************************************************/
24 void setCandidate(Sequence*);
25 void setTemplate(Sequence*);
26 void setSearchParameters(string, float);
27 void setAlignmentParameters(string, Alignment*);
28 void setNastParameters(Nast);
41 string alignmentMethod;
42 int candidateStartPosition, candidateEndPosition;
43 int templateStartPosition, templateEndPosition;
45 int pairwiseAlignmentLength;
47 int totalGapsInQuery, totalGapsInTemplate;
48 float similarityToTemplate;
49 ofstream candidateReportFile;
53 /******************************************************************************************************************/