static void reConnectAnnotation(IDnum * currentPreNodeID, Annotation * annot,
Coordinate * currentPosition,
IDnum sequenceIndex,
PreGraph * preGraph,
PreMarker ** previous)
{
IDnum nextPreNodeID = getStartID(annot);
*previous = addPreMarker_pg(preGraph,
nextPreNodeID,
sequenceIndex,
currentPosition,
*previous);
while (*currentPreNodeID != getFinishID(annot)) {
nextPreNodeID = (*currentPreNodeID) + 1;
*previous = addPreMarker_pg(preGraph,
nextPreNodeID,
sequenceIndex,
currentPosition,
*previous);
*currentPreNodeID = nextPreNodeID;
}
}
static void convertInsertionMarkers(InsertionMarker * insertionMarkers,
InsertionMarker * veryLastMarker,
IDnum * chains)
{
InsertionMarker *marker;
Annotation *annot;
for (marker = insertionMarkers; marker != veryLastMarker; marker++) {
annot = marker->annot;
if (getAnnotSequenceID(annot) > 0) {
if (marker->isStart) {
if (getStartID(annot) == 0)
setStartID(annot,
chains
[getAnnotSequenceID
(annot)]);
else
setStartID(annot,
getStartID(annot) + 1);
}
} else {
if (marker->isStart)
setStartID(annot, -getStartID(annot));
else {
if (getFinishID(annot) == 0)
setFinishID(annot,
-chains
[-getAnnotSequenceID
(annot)]);
else
setFinishID(annot,
-getFinishID(annot) -
1);
}
}
}
free(insertionMarkers);
}
static void connectAnnotation(IDnum * currentPreNodeID, Annotation * annot,
Coordinate * currentPosition,
IDnum sequenceIndex, boolean isReference,
PreGraph * preGraph)
{
IDnum nextPreNodeID = getStartID(annot);
connectPreNodeToTheNext(currentPreNodeID, nextPreNodeID,
currentPosition,
sequenceIndex, isReference, preGraph);
while (*currentPreNodeID != getFinishID(annot)) {
nextPreNodeID = (*currentPreNodeID) + 1;
connectPreNodeToTheNext(currentPreNodeID, nextPreNodeID,
currentPosition,
sequenceIndex,
isReference,
preGraph);
}
}