Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalo/src/hhalign/hhfullalignment.h b/website/archive/binaries/mac/src/clustalo/src/hhalign/hhfullalignment.h
deleted file mode 100644 (file)
index 43c1cbd..0000000
--- a/website/archive/binaries/mac/src/clustalo/src/hhalign/hhfullalignment.h
+++ /dev/null
@@ -1,49 +0,0 @@
-/* -*- 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?'+':'|'))));}
-};