[Seqan-dev] parseString funktion in a Trie

[Jakob Schulze <jakob.schulze@fu-berlin.de>]

Hi,
I constructed a Trie with createTrie and then I tried to call 
parseString. The following error message came up:
seqan-trunk/core/include/seqan/graph_types/graph_impl_automaton.h:905 
Assertion failed : idInUse(g.data_id_managerV, vertex) should be true 
but was 0

When I broke my program down, I saw that my parseString call does not 
work at all. (But the error message vanished mysteriously) It should 
store the final Vertex, but it doesn't.

Regards,
Jakob



Here my little code example: (without error message)

#include <iostream>
#include <seqan/graph_algorithms.h>
#include <seqan/graph_types.h>
using namespace seqan;
using namespace std;

int main() {

    typedef Graph<Automaton<Dna> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    String<String<unsigned int> > terminalStateMap;
    TGraph g;
    String<CharString> sequenceList;

    appendValue(sequenceList, "aat");
    appendValue(sequenceList, "aac");
    createTrie(g, terminalStateMap, sequenceList);

    DnaString str;
    appendValue(str, 'c');
    appendValue(str, 'a');
    appendValue(str, 'a');
    appendValue(str, 'c');
    Iterator<Dna>::Type itBegin = begin(str) + 1;
    Iterator<Dna>::Type itEnd = end(str);
    TVertexDescriptor finalVertex = getRoot(g);

    parseString(g, finalVertex, itBegin, itEnd);
    cout << "finalVertex = " << finalVertex << endl;
    cout << "finalVertex == root" << "\t" << isRoot(g, finalVertex) << 
endl;
    return 0;
}

Output:
finalVertex = 0
finalVertex == root    1

#include <iostream>
#include <seqan/graph_algorithms.h>
#include <seqan/graph_types.h>
using namespace seqan;
using namespace std;

int main() {

	typedef Graph<Automaton<Dna> > TGraph;
	typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
	String<String<unsigned int> > terminalStateMap;
	TGraph g;
	String<CharString> sequenceList;

	appendValue(sequenceList, "aat");
	appendValue(sequenceList, "aac");
	createTrie(g, terminalStateMap, sequenceList);

	DnaString str;
	appendValue(str, 'c');
	appendValue(str, 'a');
	appendValue(str, 'a');
	appendValue(str, 'c');
	Iterator<Dna>::Type itBegin = begin(str) + 1;
	Iterator<Dna>::Type itEnd = end(str);
	TVertexDescriptor finalVertex = getRoot(g);

	parseString(g, finalVertex, itBegin, itEnd);
	cout << "finalVertex = " << finalVertex << endl;
	cout << "finalVertex == root" << "\t" << isRoot(g, finalVertex) << endl;
	return 0;
}