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//![INCLUDE]
#include <seqan/store.h>
//![INCLUDE]
//![MAIN]
#include <iostream>
#include <seqan/sequence.h>
#include <seqan/stream.h>
using namespace seqan2;
int main()
{
//![MAIN]
//![SIGNATURE]
FragmentStore<> store;
//![SIGNATURE]
//![LOAD]
CharString fileName = getAbsolutePath("demos/tutorial/genome_annotations/example.gtf");
GffFileIn file(toCString(fileName));
readRecords(store, file);
//![LOAD]
//![ITERATOR]
Iterator<FragmentStore<>, AnnotationTree<> >::Type it;
it = begin(store, AnnotationTree<>());
//![ITERATOR]
//![MOVE]
// Move the iterator down to a leaf
while (goDown(it))
{}
// Create a new iterator and if possible move it to the right sibling of the first iterator
Iterator<FragmentStore<>, AnnotationTree<> >::Type it2;
if (isLastChild(it))
it2 = nodeRight(it);
//![MOVE]
//![DFS]
// Move the iterator back to the beginning
goBegin(it);
// Iterate over the nodes in preorder DFS while the end is not reached and
// output if the current node is a leaf
while (!atEnd(it))
{
if (isLeaf(it))
std::cout << " current node is leaf" << std::endl;
goNext(it);
}
//![DFS]
//![ACCESS]
// Move the iterator to the begin of the annotation tree
it = begin(store, AnnotationTree<>());
// Go down to exon level
while (goDown(it)) ;
std::cout << "type: " << getType(it) << std::endl;
std::cout << "id: " << value(it) << std::endl;
std::cout << "begin position: " << getAnnotation(it).beginPos << std::endl;
//![ACCESS]
//![CREATE]
Iterator<FragmentStore<>, AnnotationTree<> >::Type it3;
// Create a right sibling of the current node and return an iterator to this new node
it3 = createSibling(it);
//![CREATE]
//![OUT]
// Open output stream
GffFileOut fileOut("example_out.gtf");
// Write annotations to GTF file
writeRecords(fileOut, store);
//![OUT]
return 0;
}
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