1 // ==========================================================================
2 // SeqAn - The Library for Sequence Analysis
3 // ==========================================================================
4 // Copyright (c) 2006-2010, Knut Reinert, FU Berlin
5 // All rights reserved.
6 //
7 // Redistribution and use in source and binary forms, with or without
8 // modification, are permitted provided that the following conditions are met:
9 //
10 // * Redistributions of source code must retain the above copyright
11 // notice, this list of conditions and the following disclaimer.
12 // * Redistributions in binary form must reproduce the above copyright
13 // notice, this list of conditions and the following disclaimer in the
14 // documentation and/or other materials provided with the distribution.
15 // * Neither the name of Knut Reinert or the FU Berlin nor the names of
16 // its contributors may be used to endorse or promote products derived
17 // from this software without specific prior written permission.
18 //
19 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
23 // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25 // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
27 // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
28 // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
29 // DAMAGE.
30 //
31 // ==========================================================================
32
33 #ifndef SEQAN_HEADER_GRAPH_ALIGN_TCOFFEE_PROGRESSIVE_H
34 #define SEQAN_HEADER_GRAPH_ALIGN_TCOFFEE_PROGRESSIVE_H
35
36 namespace SEQAN_NAMESPACE_MAIN
37 {
38
39 //////////////////////////////////////////////////////////////////////////////
40 // Progressive Alignment
41 //////////////////////////////////////////////////////////////////////////////
42
43 //////////////////////////////////////////////////////////////////////////////
44
45 template<typename TStringSet, typename TCargo, typename TSpec, typename TPosition, typename TSequence>
46 inline void
_buildLeafString(Graph<Alignment<TStringSet,TCargo,TSpec>> const & g,TPosition const pos,TSequence & alignSeq)47 _buildLeafString(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
48 TPosition const pos,
49 TSequence& alignSeq)
50 {
51 SEQAN_CHECKPOINT
52 typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
53 typedef typename Size<TGraph>::Type TSize;
54 typedef typename Id<TGraph>::Type TId;
55 typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
56 typedef typename Value<TSequence>::Type TVertexString;
57
58 //TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
59 TStringSet& str = stringSet(g);
60 TId seqId = positionToId(str, pos);
61 TSize lenRoot = length(str[pos]);
62 TSize i = 0;
63 while(i<lenRoot) {
64 TVertexDescriptor nextVertex = findVertex(const_cast<TGraph&>(g), seqId, i);
65 //SEQAN_ASSERT_TRUE(nextVertex != nilVertex);
66 //if (nextVertex == nilVertex) {
67 // std::cout << "Warning: Nil Vertex" << std::endl;
68 // TSize j = i + 1;
69 // while ((j < lenRoot) && (findVertex(const_cast<TGraph&>(g), seqId, j) == nilVertex)) ++j;
70 // nextVertex = addVertex(const_cast<TGraph&>(g), seqId, i, j-i);
71 //}
72 appendValue(alignSeq, TVertexString(nextVertex), Generous());
73 i += fragmentLength(g, nextVertex);
74 }
75 }
76
77 //////////////////////////////////////////////////////////////////////////////
78
79 template<typename TStringSet, typename TCargo, typename TSpec, typename TSegmentString, typename TOutGraph>
80 inline void
_createAlignmentGraph(Graph<Alignment<TStringSet,TCargo,TSpec>> const & g,TSegmentString & alignSeq,TOutGraph & gOut)81 _createAlignmentGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
82 TSegmentString& alignSeq,
83 TOutGraph& gOut)
84 {
85 SEQAN_CHECKPOINT
86 typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
87 typedef typename Size<TGraph>::Type TSize;
88 typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
89 typedef String<TVertexDescriptor> TVertexString;
90
91 // Create the alignment graph
92 TSize alignSeqLen = length(alignSeq);
93 for(TSize i = 0; i<alignSeqLen;++i) {
94 TVertexString& alignSeq_i = alignSeq[i];
95 TSize len_i = length(alignSeq_i);
96 for(TSize j=0; j<len_i; ++j) {
97 TVertexDescriptor v = alignSeq_i[j];
98 SEQAN_ASSERT_TRUE(fragmentBegin(g,v) < length(getValueById(stringSet(g), sequenceId(g,v))));
99 SEQAN_ASSERT_TRUE(fragmentLength(g,v) > 0);
100 SEQAN_ASSERT_TRUE(fragmentBegin(g,v) + fragmentLength(g,v) <= length(getValueById(stringSet(g), sequenceId(g,v))));
101 TVertexDescriptor l = addVertex(gOut, sequenceId(g, v), fragmentBegin(g,v), fragmentLength(g,v));
102 //std::cout << l << label(gOut, l) << ',';
103 TSize count = 1;
104 for(TSize k = j; k>0; --k) {
105 SEQAN_ASSERT_TRUE(fragmentLength(gOut,l) == fragmentLength(gOut,l - count));
106 addEdge(gOut, (TVertexDescriptor) (l - count), (TVertexDescriptor) l);
107 ++count;
108 }
109 }
110 //std::cout << std::endl;
111 }
112 }
113
114 //////////////////////////////////////////////////////////////////////////////
115
116 /**
117 .Function.progressiveAlignment:
118 ..summary:Performs a progressive alignment.
119 ..cat:Graph
120 ..signature:
121 progressiveAlignment(inputGraph, guideTree, outputGraph)
122 ..param.inputGraph:The alignment graph with multiple sequence information.
123 ...type:Spec.Alignment Graph
124 ..param.guideTree:A guide tree.
125 ...type:Spec.Tree
126 ..param.outputGraph:An alignment graph for the final MSA.
127 ...type:Spec.Alignment Graph
128 ..returns:void
129 ..include:seqan/graph_msa.h
130 */
131 template<typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TOutGraph>
132 inline void
progressiveAlignment(Graph<Alignment<TStringSet,TCargo,TSpec>> & g,TGuideTree & tree,TOutGraph & gOut)133 progressiveAlignment(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
134 TGuideTree& tree,
135 TOutGraph& gOut)
136 {
137 SEQAN_CHECKPOINT
138 typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
139 typedef typename Size<TGraph>::Type TSize;
140 typedef typename VertexDescriptor<TGuideTree>::Type TVertexDescriptor;
141 typedef typename Iterator<TGuideTree, BfsIterator>::Type TBfsIterator;
142 typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjacencyIterator;
143 typedef String<TVertexDescriptor> TVertexString;
144 typedef String<TVertexString> TSegmentString;
145
146 // Initialization
147 TVertexDescriptor rootVertex = getRoot(tree);
148 TSize nVertices = numVertices(tree);
149
150 // Vertices in reversed bfs order
151 TVertexString vertices;
152 resize(vertices, nVertices);
153
154 // All Strings of Strings of vertices for each node of the guide tree
155 String<TSegmentString> segString;
156 resize(segString, nVertices);
157
158 // Walk through the tree in bfs order
159 typedef typename Iterator<TVertexString, Standard>::Type TVertexIter;
160 TVertexIter itVert = begin(vertices, Standard());
161 TVertexIter itVertEnd = end(vertices, Standard());
162 --itVertEnd;
163 TBfsIterator bfsIt(tree, rootVertex);
164 for(;!atEnd(bfsIt);goNext(bfsIt), --itVertEnd)
165 *itVertEnd = *bfsIt;
166
167 // Progressive alignment
168 itVert = begin(vertices, Standard());
169 itVertEnd = end(vertices, Standard());
170 for(;itVert != itVertEnd; ++itVert) {
171 if(isLeaf(tree, *itVert)) _buildLeafString(g, *itVert, segString[*itVert]);
172 else {
173 // Align the two children (Binary tree)
174 TAdjacencyIterator adjIt(tree, *itVert);
175 TVertexDescriptor child1 = *adjIt; goNext(adjIt);
176 heaviestCommonSubsequence(g, segString[child1], segString[*adjIt], segString[*itVert]);
177 clear(segString[child1]);
178 clear(segString[*adjIt]);
179 }
180 }
181
182 // Create the alignment graph
183 _createAlignmentGraph(g, segString[rootVertex], gOut);
184 }
185
186
187
188 //////////////////////////////////////////////////////////////////////////////
189 // Progressive Matching, just for testing purposes
190 //////////////////////////////////////////////////////////////////////////////
191
192
193 //////////////////////////////////////////////////////////////////////////////
194
195 template<typename TStringSet, typename TCargo, typename TSpec, typename TSegmentString, typename TEdgeMap, typename TOutGraph>
196 inline void
_createMatchingGraph(Graph<Alignment<TStringSet,TCargo,TSpec>> const & g,TSegmentString & alignSeq,TEdgeMap & edgeMap,TOutGraph & gOut,TEdgeMap & edgeMapOut)197 _createMatchingGraph(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
198 TSegmentString& alignSeq,
199 TEdgeMap& edgeMap,
200 TOutGraph& gOut,
201 TEdgeMap& edgeMapOut)
202 {
203 typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
204 typedef typename Size<TGraph>::Type TSize;
205 typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
206 typedef typename EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
207 typedef String<TVertexDescriptor> TVertexString;
208
209 // Initialization
210 TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
211
212 // Create the matching graph
213 clear(edgeMapOut);
214 TSize alignSeqLen = length(alignSeq);
215 for(TSize i = 0; i<alignSeqLen;++i) {
216 TVertexString& alignSeq_i = alignSeq[i];
217 TSize len_i = length(alignSeq_i);
218 for(TSize j=0; j<len_i - 1; ++j) {
219 for(TSize k=j+1; k<len_i; ++k) {
220 TVertexDescriptor v1 = getValue(alignSeq_i, j);
221 TVertexDescriptor v2 = getValue(alignSeq_i, k);
222 if ((v1 == nilVertex) || (v2 == nilVertex)) continue;
223
224 TVertexDescriptor v1New = findVertex(gOut, sequenceId(g, v1), fragmentBegin(g,v1));
225 if (v1New == nilVertex) v1New = addVertex(gOut, sequenceId(g, v1), fragmentBegin(g,v1), fragmentLength(g,v1));
226 TVertexDescriptor v2New = findVertex(gOut, sequenceId(g, v2), fragmentBegin(g,v2));
227 if (v2New == nilVertex) v2New = addVertex(gOut, sequenceId(g, v2), fragmentBegin(g,v2), fragmentLength(g,v2));
228
229 TEdgeDescriptor e = findEdge(g, v1, v2);
230 addEdge(gOut, v1New, v2New, cargo(e));
231 appendValue(edgeMapOut, property(edgeMap, e));
232 }
233 }
234 }
235 }
236
237 //////////////////////////////////////////////////////////////////////////////
238
239 template<typename TStringSet, typename TCargo, typename TSpec, typename TString, typename TOutString>
240 inline TCargo
heaviestMatching(Graph<Alignment<TStringSet,TCargo,TSpec>> const & g,TString const & str1,TString const & str2,TOutString & align)241 heaviestMatching(Graph<Alignment<TStringSet, TCargo, TSpec> > const& g,
242 TString const& str1,
243 TString const& str2,
244 TOutString& align)
245 {
246 typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
247 typedef __int64 TLargeSize;
248 typedef typename Size<TStringSet>::Type TSize;
249 typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
250 typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
251 typedef typename Value<TString>::Type TVertexSet;
252
253 TSize m = length(str1); // How many sets of vertex descriptors in seq1
254 TSize n = length(str2); // How many sets of vertex descriptors in seq1
255
256 // Size of the sequences
257 // Note for profile alignments every member of the sequence is a String!!! of vertex descriptors
258 TCargo divider = (TCargo) length(str1[0]) * (TCargo) length(str2[0]);
259 TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
260
261 // Fill the vertex to position map for str1
262 // Remember for each vertex descriptor the position in the sequence
263 typedef std::map<TVertexDescriptor, TSize> TVertexToPosMap;
264 typedef typename TVertexToPosMap::const_iterator TVertexToPosMapIter;
265 TVertexToPosMap map;
266 typedef typename Iterator<TString const>::Type TStringIterConst;
267 typedef typename Iterator<TVertexSet const>::Type TVertexSetIterConst;
268 TStringIterConst itStrEnd1 = end(str1);
269 TSize pos = 0;
270 for(TStringIterConst itStr1 = begin(str1);itStr1 != itStrEnd1;++itStr1, ++pos) {
271 TVertexSetIterConst itVEnd = end(getValue(itStr1));
272 for(TVertexSetIterConst itV = begin(getValue(itStr1));itV != itVEnd;++itV) {
273 if (*itV != nilVertex) map.insert(std::make_pair(*itV, pos));
274 }
275 }
276
277 // Given a full graph, what positions are occupied?
278 typedef std::set<TLargeSize> TOccupiedPositions;
279 TOccupiedPositions occupiedPositions;
280 TStringIterConst itStrEnd2 = end(str2);
281 TSize posItStr2 = 0;
282 for(TStringIterConst itStr2 = begin(str2);itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
283 TVertexSetIterConst itVEnd = end(getValue(itStr2));
284 for(TVertexSetIterConst itV = begin(getValue(itStr2));itV != itVEnd;++itV) {
285 if (*itV != nilVertex) {
286 TOutEdgeIterator itOut(g, *itV);
287 for(;!atEnd(itOut); ++itOut) {
288 // Target vertex must be in the map
289 TVertexToPosMapIter pPos = map.find(targetVertex(itOut));
290 if (pPos != map.end()) occupiedPositions.insert( (TLargeSize) (pPos->second) * (TLargeSize) n + (TLargeSize) (n - posItStr2 - 1) );
291 }
292 }
293 }
294 }
295 // Map the occupied positions to slots
296 typedef std::map<TLargeSize, TSize> TPositionToSlotMap;
297 TPositionToSlotMap posToSlotMap;
298 TSize counter = 0;
299 for(typename TOccupiedPositions::const_iterator setIt = occupiedPositions.begin();setIt != occupiedPositions.end(); ++setIt, ++counter) {
300 posToSlotMap.insert(std::make_pair(*setIt, counter));
301 }
302 occupiedPositions.clear();
303
304 // Walk through str2 and fill in the weights of the actual edges
305 typedef String<TCargo> TWeights;
306 typedef typename Iterator<TWeights>::Type TWeightsIter;
307 TWeights weights;
308 resize(weights, posToSlotMap.size(),0);
309 posItStr2 = 0;
310 for(TStringIterConst itStr2 = begin(str2);itStr2 != itStrEnd2;++itStr2, ++posItStr2) {
311 TVertexSetIterConst itVEnd = end(getValue(itStr2));
312 for(TVertexSetIterConst itV = begin(getValue(itStr2));itV != itVEnd;++itV) {
313 if (*itV != nilVertex) {
314 TOutEdgeIterator itOut(g, *itV);
315 for(;!atEnd(itOut); ++itOut) {
316 // Target vertex must be in the map
317 TVertexToPosMapIter pPos = map.find(targetVertex(itOut));
318 if (pPos != map.end()) weights[posToSlotMap[ (TLargeSize) (pPos->second) * (TLargeSize) n + (TLargeSize) (n - posItStr2 - 1) ]] += (TCargo) cargo(*itOut);
319 }
320 }
321 }
322 }
323 map.clear();
324 // Average weights
325 TWeightsIter itWeights = begin(weights);
326 TWeightsIter itWeightsEnd = begin(weights);
327 for(;itWeights != itWeightsEnd; ++itWeights) *itWeights /= divider;
328
329 // Create the match graph
330 Graph<Undirected<void> > matchGraph;
331 typedef typename VertexDescriptor<Graph<Undirected<void> > >::Type TVD;
332 String<bool> vertexMap;
333 resize(vertexMap, m + n, false);
334 for(TSize i = 0; i < m; ++i) addVertex(matchGraph);
335 for(TSize i = 0; i < n; ++i) value(vertexMap, addVertex(matchGraph)) = true;
336 for(typename TPositionToSlotMap::const_iterator mapIt = posToSlotMap.begin();mapIt != posToSlotMap.end(); ++mapIt) {
337 TLargeSize pos = mapIt->first;
338 TSize i = (TSize) (pos / (TLargeSize) n); // Get the index in str1
339 TSize j = n - 1 - (TSize) (pos % (TLargeSize) n); // Get the index in str2
340 addEdge(matchGraph, i, m+j);
341 }
342
343 // Compute the best matching
344 typedef String<Pair<TVD, TVD> > TEdges;
345 TEdges edges;
346
347 //std::fstream strm;
348 //strm.open("Z:\\my_graph.dot", std::ios_base::out | std::ios_base::trunc);
349 //write(strm,matchGraph,DotDrawing());
350 //strm.close();
351
352 TCargo val = weightedBipartiteMatching(matchGraph, vertexMap, weights, edges);
353
354 // Retrieve the aligned segments
355 TSize seqsInStr1 = length(str1[0]);
356 TSize seqsInStr2 = length(str2[0]);
357 typedef typename Value<TString>::Type TVertexSet;
358 typedef typename Iterator<TString const, Rooted>::Type TStringIter;
359 typedef typename Iterator<TString, Rooted>::Type TSIter;
360 typedef typename Iterator<TVertexSet const, Rooted>::Type TVertexSetIter;
361 typedef typename Iterator<TVertexSet, Rooted>::Type TIter;
362 clear(align);
363 // Retrieve all matches
364 String<bool> matchedVertices;
365 resize(matchedVertices, n + m, false);
366 typedef typename Iterator<TEdges>::Type TEdgesIter;
367 TEdgesIter itEdges = begin(edges);
368 TEdgesIter itEdgesEnd = end(edges);
369 for(;itEdges != itEdgesEnd; ++itEdges) {
370 TSize i = (value(itEdges)).i1;
371 TSize j = (value(itEdges)).i2 - m;
372 value(matchedVertices, i) = true;
373 value(matchedVertices, m+j) = true;
374 TVertexSet tmp;
375 resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
376 TVertexSetIter itVEnd = end(value(str1,i));
377 TSize count = 0;
378 for(TVertexSetIter itV = begin(value(str1,i));itV != itVEnd;++itV) {
379 tmp[count] = *itV;
380 ++count;
381 }
382 TVertexSetIter itVEnd2 = end(value(str2,j));
383 for(TVertexSetIter itV2 = begin(value(str2,j));itV2 != itVEnd2;++itV2) {
384 tmp[count] = *itV2;
385 ++count;
386 }
387 appendValue(align, tmp);
388 }
389 typedef typename Iterator<Graph<Undirected<void> >, VertexIterator>::Type TVertexIterator;
390 TVertexIterator itVertex(matchGraph);
391 for(;!atEnd(itVertex);++itVertex) {
392 if (getProperty(matchedVertices, *itVertex) == true) continue;
393 if (*itVertex < m) {
394 TSize i = *itVertex;
395 TVertexSet tmp;
396 resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
397 TVertexSetIter itVEnd = end(value(str1, i));
398 TSize count = 0;
399 for(TVertexSetIter itV = begin(value(str1, i));itV != itVEnd;++itV) {
400 tmp[count] = *itV;
401 ++count;
402 }
403 appendValue(align, tmp);
404 } else {
405 TSize j = *itVertex - m;
406 TVertexSet tmp;
407 resize(tmp, (seqsInStr1 + seqsInStr2), nilVertex);
408 TVertexSetIter itVEnd = end(value(str2, j));
409 TSize count = 0;
410 for(TVertexSetIter itV = begin(value(str2, j));itV != itVEnd;++itV) {
411 tmp[count] = *itV;
412 ++count;
413 }
414 appendValue(align, tmp);
415 }
416 }
417
418 return val;
419 }
420
421 //////////////////////////////////////////////////////////////////////////////
422
423 template<typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TVertexDescriptor, typename TSequence>
424 inline void
_recursiveProgressiveMatching(Graph<Alignment<TStringSet,TCargo,TSpec>> & g,TGuideTree & tree,TVertexDescriptor const root,TSequence & alignSeq)425 _recursiveProgressiveMatching(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
426 TGuideTree& tree,
427 TVertexDescriptor const root,
428 TSequence& alignSeq)
429 {
430 typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
431 typedef typename Size<TGraph>::Type TSize;
432 typedef typename Id<TGraph>::Type TId;
433 typedef typename Iterator<TGuideTree, AdjacencyIterator>::Type TAdjacencyIterator;
434 typedef typename Iterator<TGuideTree, DfsPreorder>::Type TDfsPreorderIterator;
435
436 if(isLeaf(tree, root)) {
437 _buildLeafString(g, root, alignSeq);
438 } else {
439 // Align the two children (Binary tree)
440 typedef String<String<TVertexDescriptor> > TSegmentString;
441 TSegmentString seq1;
442 TSegmentString seq2;
443 TAdjacencyIterator adjIt(tree, root);
444 _recursiveProgressiveMatching(g,tree, *adjIt, seq1);
445 goNext(adjIt);
446 _recursiveProgressiveMatching(g,tree, *adjIt, seq2);
447
448 heaviestMatching(g, seq1, seq2, alignSeq);
449
450 //// Debug Code
451 //for(TSize i = 0; i<length(alignSeq);++i) {
452 // std::cout << '(';
453 // for(TSize j=0; j<length(alignSeq[i]);++j) {
454 // std::cout << getValue(alignSeq[i], j) << ',';
455 // }
456 // std::cout << ')' << ',';
457 //}
458 //std::cout << std::endl;
459 }
460 }
461
462 //////////////////////////////////////////////////////////////////////////////
463
464 template<typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TEdgeMap, typename TOutGraph>
465 inline void
progressiveMatching(Graph<Alignment<TStringSet,TCargo,TSpec>> & g,TGuideTree & tree,TEdgeMap & edgeMap,TOutGraph & gOut,TEdgeMap & edgeMapOut)466 progressiveMatching(Graph<Alignment<TStringSet, TCargo, TSpec> >& g,
467 TGuideTree& tree,
468 TEdgeMap& edgeMap,
469 TOutGraph& gOut,
470 TEdgeMap& edgeMapOut)
471 {
472 typedef Graph<Alignment<TStringSet, TCargo, TSpec> > TGraph;
473 typedef typename Size<TGraph>::Type TSize;
474 typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
475 typedef String<TVertexDescriptor> TVertexString;
476 typedef String<TVertexString> TSegmentString;
477
478 // Perform progressive alignment
479 TSegmentString alignSeq;
480 _recursiveProgressiveMatching(g,tree,getRoot(tree),alignSeq);
481
482 // Create the alignment graph
483 _createMatchingGraph(g, alignSeq, edgeMap, gOut, edgeMapOut);
484 }
485
486
487 }// namespace SEQAN_NAMESPACE_MAIN
488
489 #endif //#ifndef SEQAN_HEADER_...
490