VALUE MethodResultJni::enumerateRubyObjects(VALUE klass)
{
RAWTRACE("enumerateRubyObjects");
JNIEnv *env = jniInit();
if (!env) {
RAWLOG_ERROR("JNI initialization failed");
rb_raise(rb_eRuntimeError,"JNI initialization failed");
return Qnil;;
}
if(getResultType(env) == typeList)
{
CHoldRubyValue valArray(rho_ruby_create_array());
HStringVector pIDs = rho_cast<HStringVector>(env, getListResult(env));
for(HStringVector::element_type::size_type i = 0; i < pIDs->size(); ++i)
{
VALUE valObj = rho_ruby_create_object_with_id( klass, (*pIDs)[i].c_str() );
rho_ruby_add_to_array(valArray, valObj);
}
RAWTRACE("has enumerated");
reset(env);
return valArray;
} else
{
return toRuby();
}
}
void MultAlignmentFormat::fill(
const HMultAlignment & src,
const HStringVector & sequences,
const ExpansionType & expansion_type )
{
debug_func_cerr( 5 );
if (sequences->size() != src->getNumSequences())
throw AlignlibException("MultAlignmentFormat.cpp: number of sequences in src and sequences do not match");
for (int x = 0; x < src->getNumSequences(); ++x )
if ( (*src)[x]->getColTo() > 0 && (*src)[x]->getColTo() > (*sequences)[x].size())
throw AlignlibException("MultAlignmentFormat.cpp: sequence length in mali longer than in provided sequence");
mData.clear();
}
void writeNewHampshire(
std::ostream & output,
const HTree & tree,
const HStringVector & labels )
{
debug_func_cerr( 5 );
Node node;
std::vector<Node> node_stack;
Node root = tree->getRoot();
node_stack.push_back( root ); // push root on stack
bool docomma = false;
Node numleaves = tree->getNumLeaves();
if (labels->size() > 0 && labels->size() != numleaves)
throw AlignlibException( "writeNewHampshire: number of leaves and number of labels are different");
Node last_interior_node = 2 * numleaves - 1;
TreeWeight weight = 0;
debug_cerr( 5, "starting traversal from root " << root << " with " << numleaves << " leaves" );
while (!node_stack.empty())
{
node = node_stack.back();
node_stack.pop_back();
debug_cerr( 5, "Processing node " << node << " root=" << root );
if (node != root && node < last_interior_node )
weight = tree->getWeight( node, tree->getParent( node ));
if (node < numleaves)
{ // process leaves: print name:branchlength
if (docomma)
output << ",";
if (labels->size() > 0)
{
output << (*labels)[node];
} else
{
output << node;
}
output << ":" << weight;
docomma = true;
}
else
{
if (node <= last_interior_node)
{ // process interior nodes
if (docomma) output << "," << endl;
// 1) print a '('
output << "(";
// 2) push on stack: ), right child, left child
node_stack.push_back( node + numleaves );
node_stack.push_back( tree->getRightChild(node) );
node_stack.push_back( tree->getLeftChild(node) );
// 3) record branch lengths
docomma = false;
}
else
{ // close interior node
// print a ):branchlength (if root, just print ")" )
if (node == root + numleaves)
{
output << ")\n";
}
else
{
node = node - numleaves;
output << "):" << tree->getWeight( node, tree->getParent(node) );
}
docomma = true;
}
}
}
}