import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
+import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
float nonPositionalMaxScore;
+ private ArrayList<SequenceFeature> featuresList;
+
/**
* Constructor
*/
public FeatureStore()
{
features = new IntervalStore<>();
+ featuresList = new ArrayList<>();
positionalFeatureGroups = new HashSet<>();
nonPositionalFeatureGroups = new HashSet<>();
positionalMinScore = Float.NaN;
*
* @param feature
*/
+
public boolean addFeature(SequenceFeature feature)
{
if (contains(feature))
{
if (feature.isNonPositional())
{
- return nonPositionalFeatures == null ? false : nonPositionalFeatures
- .contains(feature);
+ return nonPositionalFeatures == null ? false
+ : nonPositionalFeatures.contains(feature);
}
if (feature.isContactFeature())
{
- return contactFeatureStarts == null ? false : listContains(
- contactFeatureStarts, feature);
+ return contactFeatureStarts == null ? false
+ : listContains(contactFeatureStarts, feature);
}
- return features == null ? false : features
- .contains(feature);
+ return features == null ? false : features.contains(feature);
}
/**
features = new IntervalStore<>();
}
features.add(feature);
+ featuresList.add(feature);
}
/**
f -> f.getBegin() >= feature.getBegin());
contactFeatureStarts.add(insertPosition, feature);
-
/*
* insert into list sorted by end (second contact position):
* binary search the sorted list to find the insertion point
* end position of overlap range (inclusive)
* @return
*/
+
public List<SequenceFeature> findOverlappingFeatures(long start, long end)
{
List<SequenceFeature> result = new ArrayList<>();
SequenceFeature sf = contactFeatureEnds.get(index);
if (!sf.isContactFeature())
{
- System.err.println("Error! non-contact feature type "
- + sf.getType() + " in contact features list");
+ System.err.println("Error! non-contact feature type " + sf.getType()
+ + " in contact features list");
index++;
continue;
}
*
* @return
*/
+
public List<SequenceFeature> getPositionalFeatures()
{
List<SequenceFeature> result = new ArrayList<>();
*
* @return
*/
+
public List<SequenceFeature> getContactFeatures()
{
if (contactFeatureStarts == null)
*
* @return
*/
+
public List<SequenceFeature> getNonPositionalFeatures()
{
if (nonPositionalFeatures == null)
*
* @param sf
*/
+
public synchronized boolean delete(SequenceFeature sf)
{
boolean removed = false;
if (!removed && features != null)
{
removed = features.remove(sf);
+ featuresList.remove(sf);
}
if (removed)
positionalMaxScore = Float.NaN;
nonPositionalMinScore = Float.NaN;
nonPositionalMaxScore = Float.NaN;
-
/*
* scan non-positional features for groups and scores
*/
*
* @return
*/
+
public boolean isEmpty()
{
boolean hasFeatures = (contactFeatureStarts != null
- && !contactFeatureStarts
- .isEmpty())
- || (nonPositionalFeatures != null && !nonPositionalFeatures
- .isEmpty())
+ && !contactFeatureStarts.isEmpty())
+ || (nonPositionalFeatures != null
+ && !nonPositionalFeatures.isEmpty())
|| (features != null && features.size() > 0);
return !hasFeatures;
* @param positionalFeatures
* @return
*/
+
public Set<String> getFeatureGroups(boolean positionalFeatures)
{
if (positionalFeatures)
}
else
{
- return nonPositionalFeatureGroups == null ? Collections
- .<String> emptySet() : Collections
- .unmodifiableSet(nonPositionalFeatureGroups);
+ return nonPositionalFeatureGroups == null
+ ? Collections.<String> emptySet()
+ : Collections.unmodifiableSet(nonPositionalFeatureGroups);
}
}
* @param positional
* @return
*/
+
public int getFeatureCount(boolean positional)
{
if (!positional)
{
- return nonPositionalFeatures == null ? 0 : nonPositionalFeatures
- .size();
+ return nonPositionalFeatures == null ? 0
+ : nonPositionalFeatures.size();
}
int size = 0;
*
* @return
*/
+
public int getTotalFeatureLength()
{
return totalExtent;
* @param positional
* @return
*/
+
public float getMinimumScore(boolean positional)
{
return positional ? positionalMinScore : nonPositionalMinScore;
* @param positional
* @return
*/
+
public float getMaximumScore(boolean positional)
{
return positional ? positionalMaxScore : nonPositionalMaxScore;
* @param group
* @return
*/
+
public List<SequenceFeature> getFeaturesForGroup(boolean positional,
String group)
{
for (SequenceFeature sf : sfs)
{
String featureGroup = sf.getFeatureGroup();
- if (group == null && featureGroup == null || group != null
- && group.equals(featureGroup))
+ if (group == null && featureGroup == null
+ || group != null && group.equals(featureGroup))
{
result.add(sf);
}
}
/**
- * Adds the shift value to the start and end of all positional features.
- * Returns true if at least one feature was updated, else false.
+ * Adds the shift amount to the start and end of all positional features whose
+ * start position is at or after fromPosition. Returns true if at least one
+ * feature was shifted, else false.
*
- * @param shift
+ * @param fromPosition
+ * @param shiftBy
* @return
*/
- public synchronized boolean shiftFeatures(int shift)
+
+ public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
{
/*
* Because begin and end are final fields (to ensure the data store's
boolean modified = false;
for (SequenceFeature sf : getPositionalFeatures())
{
- modified = true;
- int newBegin = sf.getBegin() + shift;
- int newEnd = sf.getEnd() + shift;
-
- /*
- * sanity check: don't shift left of the first residue
- */
- if (newEnd > 0)
+ if (sf.getBegin() >= fromPosition)
{
- newBegin = Math.max(1, newBegin);
- SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
- sf.getFeatureGroup(), sf.getScore());
- addFeature(sf2);
+ modified = true;
+ int newBegin = sf.getBegin() + shiftBy;
+ int newEnd = sf.getEnd() + shiftBy;
+
+ /*
+ * sanity check: don't shift left of the first residue
+ */
+ if (newEnd > 0)
+ {
+ newBegin = Math.max(1, newBegin);
+ SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
+ sf.getFeatureGroup(), sf.getScore());
+ addFeature(sf2);
+ }
+ delete(sf);
}
- delete(sf);
}
return modified;
}
+
+ /////////////////////// added by Bob Hanson ///////////////////////
+
+ // The following methods use a linked list of containment in features
+ // rather than IntervalStore. Implemented only for OverviewPanel, because
+ // only that makes calls for start == end in feature overlap requests.
+ //
+ //
+ // There are two parts --- initialization, and overlap searching.
+ //
+ // Initialization involves two steps:
+ //
+ // (1) sorting of features by start position using a standard Array.sort with
+ // Comparator.
+ // (2) linking of features, effectively nesting them.
+ //
+ // Searching also involves two steps:
+ //
+ // (1) binary search for a position within the sorted features array.
+ // (2) traversing the linked lists with an end check to read out the
+ // overlapped features at this position.
+ //
+ // All of this is done with very simple standard methods.
+
+ // single public method:
+
+ /**
+ * Find all features containing this position.
+ *
+ * @param pos
+ * @return list of SequenceFeatures
+ * @author Bob Hanson 2019.07.30
+ */
+
+ public List<SequenceFeature> findOverlappingFeatures(int pos,
+ List<SequenceFeature> result)
+ {
+ if (result == null)
+ {
+ result = new ArrayList<>();
+ }
+
+ if (contactFeatureStarts != null)
+ {
+ findContacts(contactFeatureStarts, pos, result, true);
+ findContacts(contactFeatureEnds, pos, result, false);
+ }
+ if (featuresList != null)
+ {
+ findOverlaps(featuresList, pos, result);
+ }
+ return result;
+ }
+
+ // Initialization
+
+ /*
+ * contact features ordered by first contact position
+ */
+ private SequenceFeature[] orderedFeatureStarts;
+
+ private void rebuildArrays(int n)
+ {
+ if (startComp == null)
+ {
+ startComp = new StartComparator();
+ }
+ orderedFeatureStarts = new SequenceFeature[n];
+ for (int i = n; --i >= 0;)
+ {
+ SequenceFeature sf = featuresList.get(i);
+ sf.index = i; // for debugging only
+ orderedFeatureStarts[i] = sf;
+ }
+ Arrays.sort(orderedFeatureStarts, startComp);
+ linkFeatures(orderedFeatureStarts);
+ }
+
+ /**
+ * just a standard Comparator
+ */
+ private static StartComparator startComp;
+
+ class StartComparator implements Comparator<SequenceFeature>
+ {
+
+ @Override
+ public int compare(SequenceFeature o1, SequenceFeature o2)
+ {
+ int p1 = o1.begin;
+ int p2 = o2.begin;
+ return (p1 < p2 ? -1 : p1 > p2 ? 1 : 0);
+ }
+
+ }
+
+ /**
+ *
+ * @param intervals
+ */
+ private void linkFeatures(SequenceFeature[] intervals)
+ {
+ if (intervals.length < 2)
+ {
+ return;
+ }
+ int maxEnd = intervals[0].end;
+ for (int i = 1, n = intervals.length; i < n; i++)
+ {
+ SequenceFeature ithis = intervals[i];
+ if (ithis.begin <= maxEnd)
+ {
+ ithis.containedBy = getContainedBy(intervals[i - 1], ithis);
+ }
+ if (ithis.end > maxEnd)
+ {
+ maxEnd = ithis.end;
+ }
+ }
+ }
+
+ /**
+ * Since we are traversing the sorted feature array, all elements prior to the
+ * one we are working on have been fully linked. All we are doing is following
+ * those links until we find the first array feature with a containedBy
+ * element that has an end >= our begin point. It is generally a very short
+ * list -- maybe one or two depths. But it might be more than that.
+ *
+ * @param sf
+ * @param sf0
+ * @return
+ */
+ private SequenceFeature getContainedBy(SequenceFeature sf,
+ SequenceFeature sf0)
+ {
+ int begin = sf0.begin;
+ while (sf != null)
+ {
+ if (begin <= sf.end)
+ {
+ System.out.println("\nFS found " + sf0.index + ":" + sf0
+ + "\nFS in " + sf.index + ":" + sf);
+ return sf;
+ }
+ sf = sf.containedBy;
+ }
+ return null;
+ }
+
+ // Searching for overlapping features at a given position:
+
+ /**
+ * Binary search for contact start or end at a given (Overview) position.
+ *
+ * @param l
+ * @param pos
+ * @param result
+ * @param isStart
+ *
+ * @author Bob Hanson 2019.07.30
+ */
+ private static void findContacts(List<SequenceFeature> l, int pos,
+ List<SequenceFeature> result, boolean isStart)
+ {
+ int low = 0;
+ int high = l.size() - 1;
+ while (low <= high)
+ {
+ int mid = (low + high) >>> 1;
+ SequenceFeature f = l.get(mid);
+ switch (Long.signum((isStart ? f.begin : f.end) - pos))
+ {
+ case -1:
+ low = mid + 1;
+ continue;
+ case 1:
+ high = mid - 1;
+ continue;
+ case 0:
+ int m = mid;
+ result.add(f);
+ // could be "5" in 12345556788 ?
+ while (++mid <= high && (f = l.get(mid)) != null
+ && (isStart ? f.begin : f.end) == pos)
+ {
+ result.add(f);
+ }
+ while (--m >= low && (f = l.get(m)) != null
+ && (isStart ? f.begin : f.end) == pos)
+ {
+ result.add(f);
+ }
+ return;
+ }
+ }
+ }
+
+ /**
+ * Find all overlaps; special case when there is only one feature. The
+ * required array of start-sorted SequenceFeature is created lazily.
+ *
+ * @param features
+ * @param pos
+ * @param result
+ */
+ private void findOverlaps(List<SequenceFeature> features, int pos,
+ List<SequenceFeature> result)
+ {
+ int n = featuresList.size();
+ if (n == 1)
+ {
+ checkOne(featuresList.get(0), pos, result);
+ return;
+ }
+ if (orderedFeatureStarts == null)
+ {
+ rebuildArrays(n);
+ }
+
+ // (1) Find the closest feature to this position.
+
+ SequenceFeature sf = findClosestFeature(orderedFeatureStarts, pos);
+
+ // (2) Traverse the containedBy field, checking for overlap.
+
+ while (sf != null)
+ {
+ if (sf.end >= pos)
+ {
+ result.add(sf);
+ }
+ sf = sf.containedBy;
+ }
+ }
+
+ /**
+ * Quick check when we only have one feature.
+ *
+ * @param sf
+ * @param pos
+ * @param result
+ */
+ private void checkOne(SequenceFeature sf, int pos,
+ List<SequenceFeature> result)
+ {
+ if (sf.begin <= pos && sf.end >= pos)
+ {
+ result.add(sf);
+ }
+ return;
+ }
+
+ /**
+ * A binary search identical to the one used for contact start/end, but here
+ * we return the feature itself.
+ *
+ * @param l
+ * @param pos
+ * @return
+ */
+ private SequenceFeature findClosestFeature(SequenceFeature[] l, int pos)
+ {
+ int low = 0;
+ int high = l.length - 1;
+ while (low <= high)
+ {
+ int mid = (low + high) >>> 1;
+ SequenceFeature f = l[mid];
+ switch (Long.signum(f.begin - pos))
+ {
+ case -1:
+ low = mid + 1;
+ continue;
+ case 1:
+ high = mid - 1;
+ continue;
+ case 0:
+
+ while (++mid <= high && l[mid].begin == pos)
+ {
+ ;
+ }
+ mid--;
+ return l[mid];
+ }
+ }
+ // -1 here?
+ return (high < 0 || low >= l.length ? null : l[high]);
+ }
+
+
}
git://source.jalview.org / jalview.git / blobdiff