SeqAn-1.1/seqan/file/file_format_cgviz.h

   1  /*==========================================================================
   2                 SeqAn - The Library for Sequence Analysis
   3                           http://www.seqan.de
   4  ============================================================================
   5   Copyright (C) 2007
   6
   7   This library is free software; you can redistribute it and/or
   8   modify it under the terms of the GNU Lesser General Public
   9   License as published by the Free Software Foundation; either
  10   version 3 of the License, or (at your option) any later version.
  11
  12   This library is distributed in the hope that it will be useful,
  13   but WITHOUT ANY WARRANTY; without even the implied warranty of
  14   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  15   Lesser General Public License for more details.
  16
  17  ============================================================================
  18   $Id: file_format_cgviz.h,v 1.1 2008/08/25 16:20:03 langmead Exp $
  19  ==========================================================================*/
  20
  21 #ifndef SEQAN_HEADER_FILE_CGVIZ_H
  22 #define SEQAN_HEADER_FILE_CGVIZ_H
  23
  24 namespace SEQAN_NAMESPACE_MAIN
  25 {
  26
  27 //////////////////////////////////////////////////////////////////////////////
  28 // File Formats - CGViz
  29 //////////////////////////////////////////////////////////////////////////////
  30
  31
  32 /**
  33 .Tag.File Format.tag.CGViz:
  34         CGViz file format for sequences. Only output.
  35 */
  36 struct TagCGViz_;
  37 typedef Tag<TagCGViz_> const CGViz;
  38
  39 /////////////////////////////////////////////////////////////////////////
  40
  41
  42
  43 //////////////////////////////////////////////////////////////////////////////
  44 // goNext
  45 //////////////////////////////////////////////////////////////////////////////
  46
  47 template <typename TFile>
  48 void goNext(TFile & file, CGViz) {
  49         SEQAN_CHECKPOINT
  50         SEQAN_ASSERT(!_streamEOF(file))
  51
  52         return;
  53 }
  54
  55
  56
  57 //////////////////////////////////////////////////////////////////////////////
  58 // write
  59 //////////////////////////////////////////////////////////////////////////////
  60
  61 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
  62 void _write_impl(TFile& target, Align<TSource, TSpec>& align, TStringContainer& ids, CGViz) {
  63         SEQAN_CHECKPOINT
  64
  65         typedef Align<TSource, TSpec> const TAlign;
  66         typedef typename Row<TAlign>::Type TRow;
  67         typedef typename Position<typename Rows<TAlign>::Type>::Type TRowsPosition;
  68         typedef typename Position<TAlign>::Type TPosition;
  69         TRowsPosition row_count = length(rows(align));
  70         if (row_count < 2) return;
  71
  72         unsigned int pair=1;
  73         unsigned int count=0;
  74         for(TRowsPosition i=0;i<row_count-1;++i) {
  75                 for(TRowsPosition j=i+1;j<row_count;++j) {
  76
  77                         // Print header
  78                         _streamWrite(target, "{DATA dat");
  79                         _streamPutInt(target, pair);
  80                         _streamPut(target, '\n');
  81                         _streamWrite(target, "[__GLOBAL__] dimension=2:\n");
  82
  83                         TPosition begin_ = beginPosition(cols(align));
  84                         TPosition end_ = endPosition(cols(align));
  85
  86                         bool match = false;
  87                         while(begin_ < end_) {
  88                                 if ((row(align, i)[begin_]==row(align, j)[begin_]) && (row(align, i)[begin_]!='-')) {
  89                                         if (!match) {
  90                                                 match=true;
  91                                                 _streamPutInt(target, toSourcePosition(row(align,i),begin_+1));
  92                                                 _streamPut(target, ' ');
  93                                                 _streamPutInt(target, toSourcePosition(row(align,j),begin_+1));
  94                                                 _streamPut(target, ' ');
  95                                         }
  96                                 }
  97                                 if ((row(align, i)[begin_]!=row(align, j)[begin_]) || (row(align, i)[begin_]=='-') || (row(align, j)[begin_]=='-')) {
  98                                         if (match) {
  99                                                 _streamPutInt(target, toSourcePosition(row(align,i),begin_));
 100                                                 _streamPut(target, ' ');
 101                                                 _streamPutInt(target, toSourcePosition(row(align,j),begin_));
 102                                                 _streamPut(target, '\n');
 103                                                 match=false;
 104                                         }
 105                                 }
 106                                 begin_++;
 107                         }
 108                         if (match) {
 109                                 _streamPutInt(target, toSourcePosition(row(align,i),begin_));
 110                                 _streamPut(target, ' ');
 111                                 _streamPutInt(target, toSourcePosition(row(align,j),begin_));
 112                                 _streamPut(target, '\n');
 113                                 match=false;
 114                         }
 115                         _streamPut(target, '}');
 116                         _streamPut(target, '\n');
 117
 118                         // Write footer
 119                         _streamWrite(target, "{GLYPH Glyph");
 120                         _streamPutInt(target, pair);
 121                         _streamPut(target, '\n');
 122                         _streamWrite(target, "drawerName=Lines\n");
 123                         _streamWrite(target, "lineWidth=3\n");
 124                         _streamPut(target, '}');
 125                         _streamPut(target, '\n');
 126                         _streamWrite(target, "{PANE Pane");
 127                         _streamPutInt(target, pair);
 128                         _streamPut(target, '\n');
 129                         _streamWrite(target, "uLabel=");
 130                         _streamWrite(target, getValue(ids,i));
 131                         _streamPut(target, '\n');
 132                         _streamWrite(target, "uStop=");
 133                         _streamPutInt(target, length(source(row(align,i))));
 134                         _streamPut(target, '\n');
 135                         _streamWrite(target, "vLabel=");
 136                         _streamWrite(target, getValue(ids,j));
 137                         _streamPut(target, '\n');
 138                         _streamWrite(target, "vStop=");
 139                         _streamPutInt(target, length(source(row(align,j))));
 140                         _streamPut(target, '\n');
 141                         _streamPut(target, '}');
 142                         _streamPut(target, '\n');
 143                         _streamWrite(target, "{WINDOW Window");
 144                         _streamPutInt(target, pair);
 145                         _streamPut(target, '\n');
 146                         _streamPut(target, '}');
 147                         _streamPut(target, '\n');
 148                         _streamWrite(target, "{FEEDER Feeder<");
 149                         _streamPutInt(target, pair);
 150                         _streamPut(target, '>');
 151                         _streamPut(target, ' ');
 152                         _streamPutInt(target, count);
 153                         _streamPut(target, ' ');
 154                         _streamPutInt(target, count+1);
 155                         _streamPut(target, '\n');
 156                         _streamPut(target, '}');
 157                         _streamPut(target, '\n');
 158                         ++count;
 159                         _streamWrite(target, "{THREADER Threader<");
 160                         _streamPutInt(target, pair);
 161                         _streamPut(target, '>');
 162                         _streamPut(target, ' ');
 163                         _streamPutInt(target, count);
 164                         _streamPut(target, ' ');
 165                         _streamPutInt(target, count+1);
 166                         _streamPut(target, '\n');
 167                         _streamPut(target, '}');
 168                         _streamPut(target, '\n');
 169                         ++count;
 170                         _streamWrite(target, "{ANCHOR Anchor<");
 171                         _streamPutInt(target, pair);
 172                         _streamPut(target, '>');
 173                         _streamPut(target, ' ');
 174                         _streamPutInt(target, count);
 175                         _streamPut(target, ' ');
 176                         _streamPutInt(target, count+1);
 177                         _streamPut(target, '\n');
 178                         _streamPut(target, '}');
 179                         _streamPut(target, '\n');
 180                         count+=2;
 181                         ++pair;
 182                 }
 183         }
 184 }
 185
 186
 187 //____________________________________________________________________________
 188
 189 template <typename TFile, typename TSource, typename TSpec>
 190 void write(TFile & file, Align<TSource, TSpec>& align, CGViz) {
 191         SEQAN_CHECKPOINT
 192         _write_impl(file, align, String<String<char> >(), CGViz());
 193 }
 194
 195 //____________________________________________________________________________
 196
 197 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
 198 void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, CGViz) {
 199         SEQAN_CHECKPOINT
 200         _write_impl(file, align, ids, CGViz());
 201 }
 202
 203
 204 //VisualC++ const array bug workaround
 205 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec>
 206 void write(TFile & file, Align<TSource, TSpec>* align, TStringContainer & ids, CGViz) {
 207         SEQAN_CHECKPOINT
 208         _write_impl(file, align, ids, CGViz());
 209 }
 210
 211 //____________________________________________________________________________
 212
 213 template <typename TFile, typename TStringContainer, typename TSource, typename TSpec, typename TMeta>
 214 void write(TFile & file, Align<TSource, TSpec> & align, TStringContainer& ids, TMeta &, CGViz) {
 215         SEQAN_CHECKPOINT
 216         _write_impl(file, align, ids, CGViz());
 217 }
 218
 219
 220
 221 //////////////////////////////////////////////////////////////////////////////
 222 } //namespace SEQAN_NAMESPACE_MAIN
 223
 224 //////////////////////////////////////////////////////////////////////////////
 225
 226 #endif //#ifndef SEQAN_HEADER_...