Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalo/src/hhalign/hhhalfalignment.h b/website/archive/binaries/mac/src/clustalo/src/hhalign/hhhalfalignment.h
deleted file mode 100644 (file)
index 5284e54..0000000
--- a/website/archive/binaries/mac/src/clustalo/src/hhalign/hhhalfalignment.h
+++ /dev/null
@@ -1,101 +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: hhhalfalignment.h 143 2010-10-14 13:11:14Z andreas $
- */
-
-/////////////////////////////////////////////////////////////////////////////////////
-// Class representing a2m/a3m-formatted alignment corresponding to one HMM
-/////////////////////////////////////////////////////////////////////////////////////
-
-
-class HalfAlignment
-{
-public:
-  HalfAlignment(int maxseqdis=MAXSEQDIS);
-  ~HalfAlignment();
-
-  // Initialize HalfAlignment; create index arrays s [],l[], m[]
-  void Set(char* name, char** seq_in, char** sname_in, int n_in, int L_in, int n1, int n2, int n3, int n4, int nc, int L_in2/*<--FS*/);
-
-  // Free memory in HalfAlignment arrays s[][], l[][], and m[][]
-  void Unset();
-
-  // Align query (HalfAlignment) to template (i.e. hit) match state structure
-  void AlignToTemplate(Hit& hit); 
-
-  // Write the a2m/a3m query alignment into alnfile 
-  void Print(char* outfile);
-
-  // Fill in insert states following match state i
-  void AddInserts(int i);
-
-  // Fill up alignment with gaps '.' to generate flush end (all h[k] equal)
-  void FillUpGaps();
-
-  // Fill in insert states following match state i and fill up gaps with '.' 
-  void AddInsertsAndFillUpGaps(int i);
-
-  // Add gap column '.' or character column
-  void AddChar(char c);
-
-  // Add match state column i as is
-  void AddColumn(int i);
-
-  // Add match state column i as insert state
-  void AddColumnAsInsert(int i);
-
-  // Build alignment in FASTA format
-  void BuildFASTA();
-
-  // Build alignment in A2M format
-  void BuildA2M();
-
-  // Build alignment in A3M format
-  void BuildA3M();
-
-  // Transform alignment sequences from A2M to FASTA ( lowercase to uppercase and '.' to '-')
-  void ToFASTA();
-
-  // Remove all characters c from template sequences
-  void RemoveChars(char c);
-
-private:
-  friend class FullAlignment;
-
-  int n;           //number of sequences in half-alignment
-  char** seq;      //sequences (in ASCII) in alignment
-  char** sname;    //names of sequences in alignment
-  int nss_dssp;    //index of sequence with dssp sec structure states
-  int nsa_dssp;    //index of sequence with dssp solvent accessiblity states
-  int nss_pred;    //index of sequence with predicted sec structure states
-  int nss_conf;    //index of sequence with prediction confidence values
-  int ncons;       //index of consensus sequence
-    
-  int pos;         //After FillUpGaps() all h[k] have value pos 
-  int L;           //number of match states in corresponding profile
-  int* h;          //h[k] = next position of sequence k to be written
-  char** s;        //s[k][h] = column h, sequence k of output alignment
-  int** l;         //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k 
-  int** m;         //counts positions:        m[k][i] = position of match state i in string seq[k]
-/*   int h[MAXSEQ];   //h[k] = next position of sequence k to be written */
-/*   char* s[MAXSEQ]; //s[k][h] = column h, sequence k of output alignment */
-/*   int* l[MAXSEQ];  //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k  */
-/*   int* m[MAXSEQ];  //counts positions:        m[k][i] = position of match state i in string seq[k] */
-};
-
-