intervalSorter = new RangeComparator(true);
/**
* Constructor given a list of things that are each located on a contiguous
* interval. Note that the constructor may reorder the list.
*
* We assume here that for each range, start <= end. Behaviour for reverse
* ordered ranges is undefined.
*
* @param ranges
*/
public NCList(List ranges)
{
build(ranges);
}
/**
* @param ranges
*/
protected void build(List ranges)
{
/*
* sort by start ascending so that contained intervals
* follow their containing interval
*/
Collections.sort(ranges, intervalSorter);
List sublists = findSubranges(ranges);
subranges = new ArrayList>();
/*
* convert each subrange to an NCNode consisting of a range and
* (possibly) its contained NCList
*/
for (SubList sublist : sublists)
{
subranges.add(new NCNode(ranges.subList(sublist.startIndex,
sublist.endIndex + 1)));
}
sublists.clear();
}
public NCList(T entry)
{
List ranges = new ArrayList();
ranges.add(entry);
build(ranges);
}
/**
* Traverses the sorted ranges to identify sublists, within which each
* interval contains the one that follows it
*
* @param ranges
* @return
*/
protected List findSubranges(List ranges)
{
List sublists = new ArrayList();
int listStartIndex = 0;
long lastEndPos = Long.MAX_VALUE;
for (int i = 0; i < ranges.size(); i++)
{
ContiguousI nextInterval = ranges.get(i);
long nextStart = nextInterval.getBegin();
long nextEnd = nextInterval.getEnd();
if (nextStart > lastEndPos || nextEnd > lastEndPos)
{
/*
* this interval is not contained in the preceding one
* close off the last sublist
*/
sublists.add(new SubList(listStartIndex, i - 1));
listStartIndex = i;
}
lastEndPos = nextEnd;
}
sublists.add(new SubList(listStartIndex, ranges.size() - 1));
return sublists;
}
/**
* Adds one entry to the stored set
*
* @param entry
*/
public synchronized void add(T entry)
{
long start = entry.getBegin();
long end = entry.getEnd();
/*
* cases:
* - precedes all subranges: add as NCNode on front of list
* - follows all subranges: add as NCNode on end of list
* - enclosed by a subrange - add recursively to subrange
* - encloses one or more subranges - push them inside it
* - none of the above - add as a new node and resort nodes list (?)
*/
/*
* find the first subrange whose end does not precede entry's start
*/
int candidateIndex = findFirstOverlap(start);
if (candidateIndex == -1)
{
/*
* all subranges precede this one - add it on the end
*/
subranges.add(new NCNode(entry));
return;
}
/*
* search for maximal span of subranges i-k that the new entry
* encloses; or a subrange that encloses the new entry
*/
int i = candidateIndex;
boolean enclosing = false;
boolean overlapping = false;
for (int j = candidateIndex; j < subranges.size(); j++)
{
NCNode subrange = subranges.get(j);
if (end < subrange.getStart() && !overlapping)
{
/*
* new entry lies between subranges j-1 j
*/
subranges.add(j, new NCNode(entry));
return;
}
if (subrange.getStart() <= start && subrange.getEnd() >= end)
{
/*
* push new entry inside this subrange as it encloses it
*/
subrange.add(entry);
return;
}
if (start <= subrange.getStart())
{
if (end >= subrange.getEnd())
{
/*
* new entry encloses this subrange (and possibly preceding ones);
* continue to find the maximal list it encloses
*/
enclosing = true;
continue;
}
else
{
/*
* entry spans from before this subrange to inside it
*/
if (enclosing)
{
/*
* entry encloses one or more preceding subranges
*/
addEnclosingRange(entry, i, j - 1);
return;
}
else
{
/*
* entry spans two subranges but doesn't enclose any
* so just add it
*/
subranges.add(j, new NCNode(entry));
return;
}
}
}
}
}
/**
* Update the tree so that the range of the new entry encloses subranges i to
* j (inclusive). That is, replace subranges i-j with a new subrange that
* contains them.
*
* @param entry
* @param i
* @param j
*/
protected synchronized void addEnclosingRange(T entry, int i, int j)
{
// TODO how to rebuild the subranges as an NCList?
}
/**
* Returns a (possibly empty) list of items whose extent overlaps the given
* range
*
* @param from
* start of overlap range (inclusive)
* @param to
* end of overlap range (inclusive)
* @return
*/
public List findOverlaps(long from, long to)
{
List result = new ArrayList();
findOverlaps(from, to, result);
return result;
}
/**
* Recursively searches the NCList adding any items that overlap the from-to
* range to the result list
*
* @param from
* @param to
* @param result
*/
protected void findOverlaps(long from, long to,
List result)
{
/*
* find the first sublist that might overlap, i.e.
* the first whose end position is >= from
*/
int candidateIndex = findFirstOverlap(from);
if (candidateIndex == -1)
{
return;
}
for (int i = candidateIndex; i < subranges.size(); i++)
{
NCNode candidate = subranges.get(i);
if (candidate.getStart() > to)
{
/*
* we are past the end of our target range
*/
break;
}
candidate.addOverlaps(from, to, result);
}
}
/**
* Search subranges for the first one whose end position is not before the
* target range's start position, i.e. the first one that may overlap the
* target range. Returns the index in the list of the first such range found,
* or -1 if none found.
*
* @param from
* @return
*/
protected int findFirstOverlap(long from)
{
// TODO binary search
// for now quick cheat linear search
int i = 0;
if (subranges != null)
{
for (NCNode subrange : subranges)
{
if (subrange.getEnd() >= from)
{
return i;
}
i++;
}
}
return -1;
}
/**
* Formats the tree as a bracketed list e.g.
*
*
* [1-100 [10-30 [10-20]], 15-30 [20-20]]
*
*/
@Override
public String toString()
{
return subranges.toString();
}
}