Wrapper for Clustal Omega.

[jabaws.git] / binaries / src / clustalo / src / hhalign / hhfullalignment.h

diff --git a/binaries/src/clustalo/src/hhalign/hhfullalignment.h b/binaries/src/clustalo/src/hhalign/hhfullalignment.h
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+++ b/binaries/src/clustalo/src/hhalign/hhfullalignment.h
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+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhfullalignment.h 243 2011-05-31 13:49:19Z fabian $
+ */
+
+//////////////////////////////////////////////////////////////////////////////
+// Class for output alignment of query against template sequences
+//////////////////////////////////////////////////////////////////////////////
+
+class FullAlignment
+{
+public:
+  FullAlignment(int maxseqdis=MAXSEQDIS);
+  ~FullAlignment();
+  void FreeMemory();
+  int Build(HMM& q, Hit& hit);
+  void PrintHeader(FILE* outf, HMM& q, Hit& hit);
+  void PrintHHR(FILE* outf, Hit& hit);
+  void PrintA2M(FILE* outf, Hit& hit);
+  void PrintFASTA(FILE* outf, Hit& hit);
+  void PrintA3M(FILE* outf, Hit& hit);
+  void OverWriteSeqs(char **ppcFirstProf, char **ppcSecndProf);
+  int identities;      // number of identical residues in query and template sequence
+  float score_sim;     // substitution matrix similarity score between query and template
+
+private:
+  HalfAlignment* qa; //query and template parts of the alignment
+  HalfAlignment* ta; //query and template parts of the alignment
+  char symbol[LINELEN];         //symbol[h] = symbol (= - . + |) indicating match score for col h of alignment    
+  void ClearSymbols()      {for (int h=0; h<LINELEN-1; h++) symbol[h]=' ';}
+  void AddColumns(int i, int j, char prev_state, char state, float S);
+  void AddGaps();
+  int ScoreChr(float S) {return (S<-1.5?'=':(S<-0.5?'-':(S<0.5?'.':(S<1.5?'+':'|'))));}
+};