import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
-import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import intervalstore.api.IntervalStoreI;
import intervalstore.impl.BinarySearcher;
-import intervalstore.impl.IntervalStore;
-/**
- * A data store for a set of sequence features that supports efficient lookup of
- * features overlapping a given range. Intended for (but not limited to) storage
- * of features for one sequence and feature type.
- *
- * @author gmcarstairs
- *
- */
-public class FeatureStore
+public abstract class FeatureStore implements FeatureStoreI
{
+
/*
* Non-positional features have no (zero) start/end position.
* Kept as a separate list in case this criterion changes in future.
* IntervalStore holds remaining features and provides efficient
* query for features overlapping any given interval
*/
- IntervalStoreI<SequenceFeature> features;
+ Collection<SequenceFeature> features;
+
+ @Override
+ public Collection<SequenceFeature> getFeatures()
+ {
+ return features;
+ }
/*
* Feature groups represented in stored positional features
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
*/
+ @Override
public boolean addFeature(SequenceFeature feature)
{
if (contains(feature))
* @param feature
* @return
*/
+ @Override
public boolean contains(SequenceFeature feature)
{
if (feature.isNonPositional())
if (feature.isContactFeature())
{
- return contactFeatureStarts == null ? false
- : listContains(contactFeatureStarts, feature);
+ return contactFeatureStarts != null
+ && listContains(contactFeatureStarts, feature);
}
return features == null ? false : features.contains(feature);
*/
protected synchronized void addNestedFeature(SequenceFeature feature)
{
- if (features == null)
- {
- features = new IntervalStore<>();
- }
features.add(feature);
- featuresList.add(feature);
}
-
/**
* Add a contact feature to the lists that hold them ordered by start (first
* contact) and by end (second contact) position, ensuring the lists remain
if (contactFeatureStarts == null)
{
contactFeatureStarts = new ArrayList<>();
- }
- if (contactFeatureEnds == null)
- {
contactFeatureEnds = new ArrayList<>();
}
return false;
}
- /**
- * Returns a (possibly empty) list of features whose extent overlaps the given
- * range. The returned list is not ordered. Contact features are included if
- * either of the contact points lies within the range.
- *
- * @param start
- * start position of overlap range (inclusive)
- * @param end
- * end position of overlap range (inclusive)
- * @return
- */
-
- public List<SequenceFeature> findOverlappingFeatures(long start, long end)
- {
- List<SequenceFeature> result = new ArrayList<>();
-
- findContactFeatures(start, end, result);
-
- if (features != null)
- {
- result.addAll(features.findOverlaps(start, end));
- }
-
- return result;
- }
-
- /**
- * Adds contact features to the result list where either the second or the
- * first contact position lies within the target range
- *
- * @param from
- * @param to
- * @param result
- */
- protected void findContactFeatures(long from, long to,
- List<SequenceFeature> result)
- {
- if (contactFeatureStarts != null)
- {
- findContactStartOverlaps(from, to, result);
- }
- if (contactFeatureEnds != null)
- {
- findContactEndOverlaps(from, to, result);
- }
- }
-
- /**
- * Adds to the result list any contact features whose end (second contact
- * point), but not start (first contact point), lies in the query from-to
- * range
- *
- * @param from
- * @param to
- * @param result
- */
- protected void findContactEndOverlaps(long from, long to,
- List<SequenceFeature> result)
- {
- /*
- * find the first contact feature (if any)
- * whose end point is not before the target range
- */
- int index = BinarySearcher.findFirst(contactFeatureEnds,
- f -> f.getEnd() >= from);
-
- while (index < contactFeatureEnds.size())
- {
- SequenceFeature sf = contactFeatureEnds.get(index);
- if (!sf.isContactFeature())
- {
- System.err.println("Error! non-contact feature type " + sf.getType()
- + " in contact features list");
- index++;
- continue;
- }
-
- int begin = sf.getBegin();
- if (begin >= from && begin <= to)
- {
- /*
- * this feature's first contact position lies in the search range
- * so we don't include it in results a second time
- */
- index++;
- continue;
- }
-
- if (sf.getEnd() > to)
- {
- /*
- * this feature (and all following) has end point after the target range
- */
- break;
- }
-
- /*
- * feature has end >= from and end <= to
- * i.e. contact end point lies within overlap search range
- */
- result.add(sf);
- index++;
- }
- }
-
- /**
- * Adds contact features whose start position lies in the from-to range to the
- * result list
- *
- * @param from
- * @param to
- * @param result
- */
- protected void findContactStartOverlaps(long from, long to,
- List<SequenceFeature> result)
- {
- int index = BinarySearcher.findFirst(contactFeatureStarts,
- f -> f.getBegin() >= from);
-
- while (index < contactFeatureStarts.size())
- {
- SequenceFeature sf = contactFeatureStarts.get(index);
- if (!sf.isContactFeature())
- {
- System.err.println("Error! non-contact feature " + sf.toString()
- + " in contact features list");
- index++;
- continue;
- }
- if (sf.getBegin() > to)
- {
- /*
- * this feature's start (and all following) follows the target range
- */
- break;
- }
-
- /*
- * feature has begin >= from and begin <= to
- * i.e. contact start point lies within overlap search range
- */
- result.add(sf);
- index++;
- }
- }
+ abstract protected void findContactFeatures(long from, long to,
+ List<SequenceFeature> result);
/**
* Answers a list of all positional features stored, in no guaranteed order
* @return
*/
- public List<SequenceFeature> getPositionalFeatures()
+ @Override
+ public List<SequenceFeature> getPositionalFeatures(
+ List<SequenceFeature> result)
{
- List<SequenceFeature> result = new ArrayList<>();
/*
* add any contact features - from the list by start position
* @return
*/
- public List<SequenceFeature> getContactFeatures()
+ @Override
+ public List<SequenceFeature> getContactFeatures(
+ List<SequenceFeature> result)
{
- if (contactFeatureStarts == null)
+ if (contactFeatureStarts != null)
{
- return Collections.emptyList();
+ result.addAll(contactFeatureStarts);
}
- return new ArrayList<>(contactFeatureStarts);
+ return result;
}
/**
* @return
*/
- public List<SequenceFeature> getNonPositionalFeatures()
+ @Override
+ public List<SequenceFeature> getNonPositionalFeatures(
+ List<SequenceFeature> result)
{
- if (nonPositionalFeatures == null)
+ if (nonPositionalFeatures != null)
{
- return Collections.emptyList();
+ result.addAll(nonPositionalFeatures);
}
- return new ArrayList<>(nonPositionalFeatures);
+ return result;
}
/**
* @param sf
*/
+ @Override
public synchronized boolean delete(SequenceFeature sf)
{
boolean removed = false;
if (!removed && features != null)
{
removed = features.remove(sf);
- featuresList.remove(sf);
}
if (removed)
/*
* scan non-positional features for groups and scores
*/
- for (SequenceFeature sf : getNonPositionalFeatures())
+ if (nonPositionalFeatures != null)
{
- nonPositionalFeatureGroups.add(sf.getFeatureGroup());
- float score = sf.getScore();
- nonPositionalMinScore = min(nonPositionalMinScore, score);
- nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ for (SequenceFeature sf : nonPositionalFeatures)
+ {
+ nonPositionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ nonPositionalMinScore = min(nonPositionalMinScore, score);
+ nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ }
}
/*
* scan positional features for groups, scores and extents
*/
- for (SequenceFeature sf : getPositionalFeatures())
+
+ rescanPositional(contactFeatureStarts);
+ rescanPositional(features);
+ }
+
+ private void rescanPositional(Collection<SequenceFeature> sfs)
+ {
+ if (sfs == null)
+ {
+ return;
+ }
+ for (SequenceFeature sf : sfs)
{
positionalFeatureGroups.add(sf.getFeatureGroup());
float score = sf.getScore();
}
}
+
/**
* Answers true if this store has no features, else false
*
* @return
*/
+ @Override
public boolean isEmpty()
{
boolean hasFeatures = (contactFeatureStarts != null
&& !contactFeatureStarts.isEmpty())
|| (nonPositionalFeatures != null
&& !nonPositionalFeatures.isEmpty())
- || (features != null && features.size() > 0);
+ || features.size() > 0;
return !hasFeatures;
}
* @return
*/
+ @Override
public Set<String> getFeatureGroups(boolean positionalFeatures)
{
if (positionalFeatures)
}
/**
- * Answers the number of positional (or non-positional) features stored.
- * Contact features count as 1.
+ * Answers a list of all either positional or non-positional features whose
+ * feature group matches the given group (which may be null)
*
* @param positional
+ * @param group
* @return
*/
- public int getFeatureCount(boolean positional)
+ @Override
+ public List<SequenceFeature> getFeaturesForGroup(boolean positional,
+ String group)
{
- if (!positional)
+ List<SequenceFeature> result = new ArrayList<>();
+
+ /*
+ * if we know features don't include the target group, no need
+ * to inspect them for matches
+ */
+ if (positional && !positionalFeatureGroups.contains(group)
+ || !positional && !nonPositionalFeatureGroups.contains(group))
{
- return nonPositionalFeatures == null ? 0
- : nonPositionalFeatures.size();
+ return result;
}
- int size = 0;
+ if (positional)
+ {
+ addFeaturesForGroup(group, contactFeatureStarts, result);
+ addFeaturesForGroup(group, features, result);
+ }
+ else
+ {
+ addFeaturesForGroup(group, nonPositionalFeatures, result);
+ }
+ return result;
+ }
- if (contactFeatureStarts != null)
+ private void addFeaturesForGroup(String group,
+ Collection<SequenceFeature> sfs, List<SequenceFeature> result)
+ {
+ if (sfs == null)
+ {
+ return;
+ }
+ for (SequenceFeature sf : sfs)
{
- // note a contact feature (start/end) counts as one
- size += contactFeatureStarts.size();
+ String featureGroup = sf.getFeatureGroup();
+ if (group == null && featureGroup == null
+ || group != null && group.equals(featureGroup))
+ {
+ result.add(sf);
+ }
}
+ }
- if (features != null)
+ /**
+ * Answers the number of positional (or non-positional) features stored.
+ * Contact features count as 1.
+ *
+ * @param positional
+ * @return
+ */
+
+ @Override
+ public int getFeatureCount(boolean positional)
+ {
+ if (!positional)
{
- size += features.size();
+ return nonPositionalFeatures == null ? 0
+ : nonPositionalFeatures.size();
}
- return size;
+ return (contactFeatureStarts == null ? 0 : contactFeatureStarts.size())
+ + features.size();
+
}
+
/**
* Answers the total length of positional features (or zero if there are
* none). Contact features contribute a value of 1 to the total.
* @return
*/
+ @Override
public int getTotalFeatureLength()
{
return totalExtent;
* @return
*/
+ @Override
public float getMinimumScore(boolean positional)
{
return positional ? positionalMinScore : nonPositionalMinScore;
* @return
*/
+ @Override
public float getMaximumScore(boolean positional)
{
return positional ? positionalMaxScore : nonPositionalMaxScore;
}
- /**
- * Answers a list of all either positional or non-positional features whose
- * feature group matches the given group (which may be null)
- *
- * @param positional
- * @param group
- * @return
- */
-
- public List<SequenceFeature> getFeaturesForGroup(boolean positional,
- String group)
- {
- List<SequenceFeature> result = new ArrayList<>();
-
- /*
- * if we know features don't include the target group, no need
- * to inspect them for matches
- */
- if (positional && !positionalFeatureGroups.contains(group)
- || !positional && !nonPositionalFeatureGroups.contains(group))
- {
- return result;
- }
-
- List<SequenceFeature> sfs = positional ? getPositionalFeatures()
- : getNonPositionalFeatures();
- for (SequenceFeature sf : sfs)
- {
- String featureGroup = sf.getFeatureGroup();
- if (group == null && featureGroup == null
- || group != null && group.equals(featureGroup))
- {
- result.add(sf);
- }
- }
- return result;
- }
/**
* Adds the shift amount to the start and end of all positional features whose
* @return
*/
+ @Override
public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
{
/*
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);
- }
-
- }
-
- /**
- * Run through the sorted sequence array once, building the containedBy linked
- * list references. Does a check first to make sure there is actually
- * something out there that is overlapping. A null for sf.containedBy means
- * there are no overlaps for this feature.
- *
- * @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 sf = intervals[i];
- if (sf.begin <= maxEnd)
- {
- sf.containedBy = getContainedBy(intervals[i - 1], sf);
- }
- if (sf.end > maxEnd)
- {
- maxEnd = sf.end;
- }
- }
- }
-
- /**
- * Since we are traversing the sorted feature array in a forward direction,
- * 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;
- }
-
- // search-stage methods
- /**
- * 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)
+ @Override
+ public List<SequenceFeature> findOverlappingFeatures(long start, long end)
{
- 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;
- }
- }
+ return findOverlappingFeatures(start, end, null);
}
- /**
- * 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)
+ @Override
+ public List<SequenceFeature> getPositionalFeatures()
{
- 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;
- }
+ return getPositionalFeatures(new ArrayList<>());
}
- /**
- * Quick check when we only have one feature.
- *
- * @param sf
- * @param pos
- * @param result
- */
- private void checkOne(SequenceFeature sf, int pos,
- List<SequenceFeature> result)
+ @Override
+ public List<SequenceFeature> getContactFeatures()
{
- if (sf.begin <= pos && sf.end >= pos)
- {
- result.add(sf);
- }
- return;
+ return getContactFeatures(new ArrayList<>());
}
- /**
- * A binary search identical to the one used for contact start/end, but here
- * we return the feature itself. Unlike Collection.BinarySearch, all we have
- * to be is close, not exact, and we make sure if there is a string of
- * identical starts, then we slide to the end so that we can check all of
- * them.
- *
- * @param l
- * @param pos
- * @return
- */
- private SequenceFeature findClosestFeature(SequenceFeature[] l, int pos)
+ @Override
+ public List<SequenceFeature> getNonPositionalFeatures()
{
- 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)
- {
- ;
- }
- return l[--mid];
- }
- }
- // -1 here?
- return (high < 0 || low >= l.length ? null : l[high]);
+ return getNonPositionalFeatures(new ArrayList<>());
}
-
}
--- /dev/null
+package jalview.datamodel.features;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+
+public interface FeatureStoreI
+{
+
+ boolean addFeature(SequenceFeature feature);
+
+ boolean contains(SequenceFeature feature);
+
+ boolean delete(SequenceFeature sf);
+
+ List<SequenceFeature> findOverlappingFeatures(long start, long end);
+
+ List<SequenceFeature> findOverlappingFeatures(long start, long end,
+ List<SequenceFeature> result);
+
+ List<SequenceFeature> getContactFeatures();
+
+ List<SequenceFeature> getContactFeatures(List<SequenceFeature> result);
+
+ int getFeatureCount(boolean positional);
+
+ Set<String> getFeatureGroups(boolean positionalFeatures);
+
+ Collection<SequenceFeature> getFeatures();
+
+ List<SequenceFeature> getFeaturesForGroup(boolean positional,
+ String group);
+
+ float getMaximumScore(boolean positional);
+
+ float getMinimumScore(boolean positional);
+
+ List<SequenceFeature> getNonPositionalFeatures();
+
+ List<SequenceFeature> getNonPositionalFeatures(
+ List<SequenceFeature> result);
+
+ List<SequenceFeature> getPositionalFeatures();
+
+ List<SequenceFeature> getPositionalFeatures(List<SequenceFeature> result);
+
+ int getTotalFeatureLength();
+
+ boolean isEmpty();
+
+ boolean shiftFeatures(int fromPosition, int shiftBy);
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel.features;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import intervalstore.api.IntervalStoreI;
+import intervalstore.impl.BinarySearcher;
+import intervalstore.impl.IntervalStore;
+
+/**
+ * A data store for a set of sequence features that supports efficient lookup of
+ * features overlapping a given range. Intended for (but not limited to) storage
+ * of features for one sequence and feature type.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class FeatureStoreImpl extends FeatureStore
+{
+
+ public FeatureStoreImpl()
+ {
+ features = new IntervalStore<>();
+ }
+
+ /**
+ * Adds contact features to the result list where either the second or the
+ * first contact position lies within the target range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ @Override
+ protected void findContactFeatures(long from, long to,
+ List<SequenceFeature> result)
+ {
+ if (contactFeatureStarts != null)
+ {
+ findContactStartOverlaps(from, to, result);
+ findContactEndOverlaps(from, to, result);
+ }
+ }
+
+ /**
+ * Adds to the result list any contact features whose end (second contact
+ * point), but not start (first contact point), lies in the query from-to
+ * range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+
+ private void findContactEndOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ /*
+ * find the first contact feature (if any)
+ * whose end point is not before the target range
+ */
+ int index = BinarySearcher.findFirst(contactFeatureEnds,
+ f -> f.getEnd() >= from);
+
+ int n = contactFeatureEnds.size();
+ while (index < n)
+ {
+ SequenceFeature sf = contactFeatureEnds.get(index);
+ if (!sf.isContactFeature())
+ {
+ System.err.println("Error! non-contact feature type " + sf.getType()
+ + " in contact features list");
+ index++;
+ continue;
+ }
+
+ int begin = sf.getBegin();
+ if (begin >= from && begin <= to)
+ {
+ /*
+ * this feature's first contact position lies in the search range
+ * so we don't include it in results a second time
+ */
+ index++;
+ continue;
+ }
+
+ if (sf.getEnd() > to)
+ {
+ /*
+ * this feature (and all following) has end point after the target range
+ */
+ break;
+ }
+
+ /*
+ * feature has end >= from and end <= to
+ * i.e. contact end point lies within overlap search range
+ */
+ result.add(sf);
+ index++;
+ }
+ }
+
+ /**
+ * Adds contact features whose start position lies in the from-to range to the
+ * result list
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+
+ private void findContactStartOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ int index = BinarySearcher.findFirst(contactFeatureStarts,
+ f -> f.getBegin() >= from);
+
+ while (index < contactFeatureStarts.size())
+ {
+ SequenceFeature sf = contactFeatureStarts.get(index);
+ if (!sf.isContactFeature())
+ {
+ System.err.println("Error! non-contact feature " + sf.toString()
+ + " in contact features list");
+ index++;
+ continue;
+ }
+ if (sf.getBegin() > to)
+ {
+ /*
+ * this feature's start (and all following) follows the target range
+ */
+ break;
+ }
+
+ /*
+ * feature has begin >= from and begin <= to
+ * i.e. contact start point lies within overlap search range
+ */
+ result.add(sf);
+ index++;
+ }
+ }
+
+ /**
+ * Returns a (possibly empty) list of features whose extent overlaps the given
+ * range. The returned list is not ordered. Contact features are included if
+ * either of the contact points lies within the range.
+ *
+ * @param start
+ * start position of overlap range (inclusive)
+ * @param end
+ * end position of overlap range (inclusive)
+ * @param result
+ * ignored
+ * @return
+ */
+
+ @Override
+ public List<SequenceFeature> findOverlappingFeatures(long start, long end,
+ List<SequenceFeature> result)
+ {
+ result = new ArrayList<>();
+ findContactFeatures(start, end, result);
+ findOverlaps(start, end, result);
+ return result;
+ }
+
+ private void findOverlaps(long start, long end,
+ List<SequenceFeature> result)
+ {
+ result.addAll(((IntervalStoreI<SequenceFeature>) features)
+ .findOverlaps(start, end));
+ // TODO Auto-generated method stub
+
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel.features;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+
+/**
+ * An adaption of FeatureStore that is efficient and lightweight, accelerating
+ * processing speed in JavaScript.
+ *
+ * @author gmcarstairs
+ * @author Bob Hanson 2019.08.03
+ *
+ */
+public class FeatureStoreJS extends FeatureStore
+{
+ boolean contactsTainted = true;
+
+ /**
+ * Constructor
+ */
+ public FeatureStoreJS()
+ {
+ features = new ArrayList<>();
+ }
+
+ /**
+ * Returns a (possibly empty) list of features whose extent overlaps the given
+ * range. The returned list is not ordered. Contact features are included if
+ * either of the contact points lies within the range.
+ *
+ * @param start
+ * start position of overlap range (inclusive)
+ * @param end
+ * end position of overlap range (inclusive)
+ * @return
+ */
+
+ @Override
+ public List<SequenceFeature> findOverlappingFeatures(long start, long end,
+ List<SequenceFeature> result)
+ {
+ if (result == null)
+ {
+ result = new ArrayList<>();
+ }
+ if (contactFeatureStarts != null)
+ {
+ if (start == end)
+ {
+ findContactPoints(contactFeatureStarts, start, result, true);
+ findContactPoints(contactFeatureEnds, start, result, false);
+ }
+ else
+ {
+ findContactFeatures(start, end, result);
+ }
+ }
+ if (features.size() > 0)
+ {
+ findOverlaps(start, end, result);
+ }
+ return result;
+ }
+
+ // The following methods use a linked list of containment in SequenceFeature
+ // rather than IntervalStore.
+ //
+ // 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 involves three steps:
+ //
+ // (1) binary search for a starting point within the sorted features array.
+ // (2) traverse the linked lists with an end check to read out the
+ // overlapped features at this position.
+ // (3) For an interval, find the last feature that starts in this interval,
+ // and add all features up through that feature.
+ //
+ // All of this is done with very simple standard methods.
+
+ // 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 = ((ArrayList<SequenceFeature>) features).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);
+ }
+
+ }
+
+ /**
+ * Run through the sorted sequence array once, building the containedBy linked
+ * list references. Does a check first to make sure there is actually
+ * something out there that is overlapping. A null for sf.containedBy means
+ * there are no overlaps for this feature.
+ *
+ * @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 sf = intervals[i];
+ if (sf.begin <= maxEnd)
+ {
+ sf.containedBy = getContainedBy(intervals[i - 1], sf);
+ }
+ if (sf.end > maxEnd)
+ {
+ maxEnd = sf.end;
+ }
+ }
+ }
+
+ /**
+ * Since we are traversing the sorted feature array in a forward direction,
+ * 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;
+ }
+
+ // search-stage methods
+
+ /**
+ * 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 findContactPoints(List<SequenceFeature> l, long 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(long start, long end,
+ List<SequenceFeature> result)
+ {
+ int n = features.size();
+ switch (n)
+ {
+ case 0:
+ return;
+ case 1:
+ checkOne(((ArrayList<SequenceFeature>) features).get(0), start, end,
+ result);
+ return;
+ default:
+ if (orderedFeatureStarts == null)
+ {
+ rebuildArrays(n);
+ }
+ break;
+ }
+
+ // (1) Find the closest feature to this position.
+
+ int index = findClosestFeature(orderedFeatureStarts, start);
+ SequenceFeature sf = (index < 0 ? null : orderedFeatureStarts[index]);
+
+ // (2) Traverse the containedBy field, checking for overlap.
+
+ while (sf != null)
+ {
+ if (sf.end >= start)
+ {
+ result.add(sf);
+ }
+ sf = sf.containedBy;
+ }
+
+ // (3) For an interval, find the last feature that starts in this interval,
+ // and add all features up through that feature.
+
+ if (end > start)
+ {
+ // fill in with all features that start within this interval, fully
+ // inclusive
+ int index2 = findClosestFeature(orderedFeatureStarts, end);
+ while (++index <= index2)
+ {
+ result.add(orderedFeatureStarts[index]);
+ }
+
+ }
+ }
+
+ /**
+ * Quick check when we only have one feature.
+ *
+ * @param sf
+ * @param start
+ * @param end
+ * @param result
+ */
+ private void checkOne(SequenceFeature sf, long start, long end,
+ List<SequenceFeature> result)
+ {
+ if (sf.begin <= end && sf.end >= start)
+ {
+ result.add(sf);
+ }
+ return;
+ }
+
+ /**
+ * A binary search identical to the one used for contact start/end, but here
+ * we return the feature itself. Unlike Collection.BinarySearch, all we have
+ * to be is close, not exact, and we make sure if there is a string of
+ * identical starts, then we slide to the end so that we can check all of
+ * them.
+ *
+ * @param l
+ * @param pos
+ * @return
+ */
+ private int findClosestFeature(SequenceFeature[] l, long 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)
+ {
+ ;
+ }
+ return --mid;
+ }
+ }
+ return (high < 0 ? -1 : high);
+ }
+
+ /**
+ * Adds contact features to the result list where either the second or the
+ * first contact position lies within the target range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+ @Override
+ protected void findContactFeatures(long from, long to,
+ List<SequenceFeature> result)
+ {
+ findContactStartOverlaps(from, to, result);
+ findContactEndOverlaps(from, to, result);
+ }
+
+ /**
+ * Adds to the result list any contact features whose end (second contact
+ * point), but not start (first contact point), lies in the query from-to
+ * range
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+
+ private void findContactEndOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ // find the first contact feature (if any)
+ // with end point not before the target range
+
+ for (int i = findFirstEnd(contactFeatureEnds,
+ from), n = contactFeatureEnds.size(); i < n; i++)
+ {
+ SequenceFeature sf = contactFeatureEnds.get(i);
+ if (sf.begin >= from && sf.begin <= to)
+ {
+ // this feature's first contact position lies in the search range
+ // so we don't include it in results a second time
+ continue;
+ }
+
+ if (sf.end > to)
+ {
+ // this feature (and all following) has end point after the target range
+ break;
+ }
+
+ // feature has end >= from and end <= to
+ // i.e. contact end point lies within overlap search range
+ result.add(sf);
+ }
+ }
+
+ /**
+ * Adds contact features whose start position lies in the from-to range to the
+ * result list
+ *
+ * @param from
+ * @param to
+ * @param result
+ */
+
+ private void findContactStartOverlaps(long from, long to,
+ List<SequenceFeature> result)
+ {
+ for (int i = findFirstBegin(contactFeatureStarts,
+ from), n = contactFeatureStarts.size(); i < n; i++)
+ {
+ SequenceFeature sf = contactFeatureStarts.get(i);
+ if (sf.begin > to)
+ {
+ break;
+ }
+ result.add(sf);
+ }
+ }
+
+ public static int findFirstBegin(List<SequenceFeature> list, long pos)
+ {
+ int start = 0;
+ int end = list.size() - 1;
+ int matched = list.size();
+
+ while (start <= end)
+ {
+ int mid = (start + end) / 2;
+ if (list.get(mid).begin >= pos)
+ {
+ matched = mid;
+ end = mid - 1;
+ }
+ else
+ {
+ start = mid + 1;
+ }
+ }
+ return matched;
+ }
+
+ public static int findFirstEnd(List<SequenceFeature> list, long pos)
+ {
+ int start = 0;
+ int end = list.size() - 1;
+ int matched = list.size();
+
+ while (start <= end)
+ {
+ int mid = (start + end) / 2;
+ if (list.get(mid).end >= pos)
+ {
+ matched = mid;
+ end = mid - 1;
+ }
+ else
+ {
+ start = mid + 1;
+ }
+ }
+ return matched;
+ }
+
+
+}
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Platform;
import java.util.ArrayList;
import java.util.Arrays;
* map from feature type to structured store of features for that type
* null types are permitted (but not a good idea!)
*/
- private Map<String, FeatureStore> featureStore;
+ private Map<String, FeatureStoreI> featureStore;
+
+ private static boolean useIntervalStore = !Platform.isJS();
/**
* Constructor
* ? wrap as a synchronized map for add and delete operations
*/
// featureStore = Collections
- // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
+ // .synchronizedSortedMap(new TreeMap<String, FeatureStoreI>());
featureStore = new TreeMap<>();
}
if (featureStore.get(type) == null)
{
- featureStore.put(type, new FeatureStore());
+ featureStore.put(type, newFeatureStore());
}
return featureStore.get(type).addFeature(sf);
}
+ private FeatureStoreI newFeatureStore()
+ {
+ // TODO Auto-generated method stub
+ return (useIntervalStore ? new FeatureStoreImpl() : new FeatureStoreJS());
+ }
+
/**
* {@inheritDoc}
*/
String... type)
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.findOverlappingFeatures(from, to));
+ result.addAll(featureSet.findOverlappingFeatures(from, to, null));
}
return result;
}
{
int result = 0;
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
result += featureSet.getFeatureCount(positional);
}
{
int result = 0;
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
result += featureSet.getTotalFeatureLength();
}
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getPositionalFeatures());
+ featureSet.getPositionalFeatures(result);
}
return result;
}
* @param type
* @return
*/
- protected Iterable<FeatureStore> varargToTypes(String... type)
+ protected Iterable<FeatureStoreI> varargToTypes(String... type)
{
if (type == null || type.length == 0)
{
}
- List<FeatureStore> types = new ArrayList<>();
+ List<FeatureStoreI> types = new ArrayList<>();
List<String> args = Arrays.asList(type);
- for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+ for (Entry<String, FeatureStoreI> featureType : featureStore.entrySet())
{
if (args.contains(featureType.getKey()))
{
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ featureSet.getContactFeatures(result);
}
return result;
}
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ featureSet.getNonPositionalFeatures(result);
}
return result;
}
@Override
public boolean delete(SequenceFeature sf)
{
- for (FeatureStore featureSet : featureStore.values())
+ for (FeatureStoreI featureSet : featureStore.values())
{
if (featureSet.delete(sf))
{
@Override
public boolean hasFeatures()
{
- for (FeatureStore featureSet : featureStore.values())
+ for (FeatureStoreI featureSet : featureStore.values())
{
if (!featureSet.isEmpty())
{
{
Set<String> groups = new HashSet<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
}
{
Set<String> result = new HashSet<>();
- for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+ for (Entry<String, FeatureStoreI> featureType : featureStore.entrySet())
{
Set<String> featureGroups = featureType.getValue().getFeatureGroups(
positionalFeatures);
public Set<String> getFeatureTypes(String... soTerm)
{
Set<String> types = new HashSet<>();
- for (Entry<String, FeatureStore> entry : featureStore.entrySet())
+ for (Entry<String, FeatureStoreI> entry : featureStore.entrySet())
{
String type = entry.getKey();
if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
String group, String... type)
{
List<SequenceFeature> result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
if (featureSet.getFeatureGroups(positional).contains(group))
{
public boolean shiftFeatures(int fromPosition, int shiftBy)
{
boolean modified = false;
- for (FeatureStore fs : featureStore.values())
+ for (FeatureStoreI fs : featureStore.values())
{
modified |= fs.shiftFeatures(fromPosition, shiftBy);
}
public List<SequenceFeature> findFeatures(int pos, String type,
List<SequenceFeature> list)
{
- FeatureStore fs = featureStore.get(type);
- boolean useIntervalStore = /**
- * @j2sNative false &&
- */
- true;
- return (useIntervalStore ? fs.findOverlappingFeatures(pos, pos)
- : fs.findOverlappingFeatures(pos, list));
+ FeatureStoreI fs = featureStore.get(type);
+ return fs.findOverlappingFeatures(pos, pos, list);
}
// Chrome; developer console closed
--- /dev/null
+package jalview.datamodel.features;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
+public class FeatureStoreJSTest
+{
+
+ @Test(groups = "Functional")
+ public void testFindFeatures_nonNested()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN,
+ null));
+ // same range different description
+ fs.addFeature(new SequenceFeature("", "desc", 10, 20, Float.NaN, null));
+ fs.addFeature(new SequenceFeature("", "", 15, 25, Float.NaN, null));
+ fs.addFeature(new SequenceFeature("", "", 20, 35, Float.NaN, null));
+
+ List<SequenceFeature> overlaps = fs.findOverlappingFeatures(1, 9);
+ assertTrue(overlaps.isEmpty());
+
+ overlaps = fs.findOverlappingFeatures(8, 10);
+ assertEquals(overlaps.size(), 2);
+ assertEquals(overlaps.get(0).getEnd(), 20);
+ assertEquals(overlaps.get(1).getEnd(), 20);
+
+ overlaps = fs.findOverlappingFeatures(12, 16);
+ assertEquals(overlaps.size(), 3);
+ assertEquals(overlaps.get(0).getEnd(), 20);
+ assertEquals(overlaps.get(1).getEnd(), 20);
+ assertEquals(overlaps.get(2).getEnd(), 25);
+
+ overlaps = fs.findOverlappingFeatures(33, 33);
+ assertEquals(overlaps.size(), 1);
+ assertEquals(overlaps.get(0).getEnd(), 35);
+ }
+
+ private FeatureStoreI newFeatureStore()
+ {
+ return new FeatureStoreJS();
+ // return new FeatureStoreImpl();
+ }
+
+ @Test(groups = "Functional")
+ public void testFindFeatures_nested()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ SequenceFeature sf1 = addFeature(fs, 10, 50);
+ SequenceFeature sf2 = addFeature(fs, 10, 40);
+ SequenceFeature sf3 = addFeature(fs, 20, 30);
+ // fudge feature at same location but different group (so is added)
+ SequenceFeature sf4 = new SequenceFeature("", "", 20, 30, Float.NaN,
+ "different group");
+ fs.addFeature(sf4);
+ SequenceFeature sf5 = addFeature(fs, 35, 36);
+
+ List<SequenceFeature> overlaps = fs.findOverlappingFeatures(1, 9);
+ assertTrue(overlaps.isEmpty());
+
+ overlaps = fs.findOverlappingFeatures(10, 15);
+ assertEquals(overlaps.size(), 2);
+ assertTrue(overlaps.contains(sf1));
+ assertTrue(overlaps.contains(sf2));
+
+ overlaps = fs.findOverlappingFeatures(45, 60);
+ assertEquals(overlaps.size(), 1);
+ assertTrue(overlaps.contains(sf1));
+
+ overlaps = fs.findOverlappingFeatures(32, 38);
+ assertEquals(overlaps.size(), 3);
+ assertTrue(overlaps.contains(sf1));
+ assertTrue(overlaps.contains(sf2));
+ assertTrue(overlaps.contains(sf5));
+
+ overlaps = fs.findOverlappingFeatures(15, 25);
+ assertEquals(overlaps.size(), 4);
+ assertTrue(overlaps.contains(sf1));
+ assertTrue(overlaps.contains(sf2));
+ assertTrue(overlaps.contains(sf3));
+ assertTrue(overlaps.contains(sf4));
+ }
+
+ @Test(groups = "Functional")
+ public void testFindFeatures_mixed()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ SequenceFeature sf1 = addFeature(fs, 10, 50);
+ SequenceFeature sf2 = addFeature(fs, 1, 15);
+ SequenceFeature sf3 = addFeature(fs, 20, 30);
+ SequenceFeature sf4 = addFeature(fs, 40, 100);
+ SequenceFeature sf5 = addFeature(fs, 60, 100);
+ SequenceFeature sf6 = addFeature(fs, 70, 70);
+
+ List<SequenceFeature> overlaps = fs.findOverlappingFeatures(200, 200);
+ assertTrue(overlaps.isEmpty());
+
+ overlaps = fs.findOverlappingFeatures(1, 9);
+ assertEquals(overlaps.size(), 1);
+ assertTrue(overlaps.contains(sf2));
+
+ overlaps = fs.findOverlappingFeatures(5, 18);
+ assertEquals(overlaps.size(), 2);
+ assertTrue(overlaps.contains(sf1));
+ assertTrue(overlaps.contains(sf2));
+
+ overlaps = fs.findOverlappingFeatures(30, 40);
+ assertEquals(overlaps.size(), 3);
+ assertTrue(overlaps.contains(sf1));
+ assertTrue(overlaps.contains(sf3));
+ assertTrue(overlaps.contains(sf4));
+
+ overlaps = fs.findOverlappingFeatures(80, 90);
+ assertEquals(overlaps.size(), 2);
+ assertTrue(overlaps.contains(sf4));
+ assertTrue(overlaps.contains(sf5));
+
+ overlaps = fs.findOverlappingFeatures(68, 70);
+ assertEquals(overlaps.size(), 3);
+ assertTrue(overlaps.contains(sf4));
+ assertTrue(overlaps.contains(sf5));
+ assertTrue(overlaps.contains(sf6));
+ }
+
+ /**
+ * Helper method to add a feature of no particular type
+ *
+ * @param fs
+ * @param from
+ * @param to
+ * @return
+ */
+ SequenceFeature addFeature(FeatureStoreI fs, int from, int to)
+ {
+ SequenceFeature sf1 = new SequenceFeature("", "", from, to, Float.NaN,
+ null);
+ fs.addFeature(sf1);
+ return sf1;
+ }
+
+ @Test(groups = "Functional")
+ public void testFindFeatures_contactFeatures()
+ {
+ FeatureStoreI fs = newFeatureStore();
+
+ SequenceFeature sf = new SequenceFeature("disulphide bond", "bond", 10,
+ 20, Float.NaN, null);
+ fs.addFeature(sf);
+
+ /*
+ * neither contact point in range
+ */
+ List<SequenceFeature> overlaps = fs.findOverlappingFeatures(1, 9);
+ assertTrue(overlaps.isEmpty());
+
+ /*
+ * neither contact point in range
+ */
+ overlaps = fs.findOverlappingFeatures(11, 19);
+ assertTrue(overlaps.isEmpty());
+
+ /*
+ * first contact point in range
+ */
+ overlaps = fs.findOverlappingFeatures(5, 15);
+ assertEquals(overlaps.size(), 1);
+ assertTrue(overlaps.contains(sf));
+
+ /*
+ * second contact point in range
+ */
+ overlaps = fs.findOverlappingFeatures(15, 25);
+ assertEquals(overlaps.size(), 1);
+ assertTrue(overlaps.contains(sf));
+
+ /*
+ * both contact points in range
+ */
+ overlaps = fs.findOverlappingFeatures(5, 25);
+ assertEquals(overlaps.size(), 1);
+ assertTrue(overlaps.contains(sf));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetPositionalFeatures()
+ {
+ FeatureStoreI store = newFeatureStore();
+ SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
+ Float.NaN, null);
+ store.addFeature(sf1);
+ // same range, different description
+ SequenceFeature sf2 = new SequenceFeature("Metal", "desc2", 10, 20,
+ Float.NaN, null);
+ store.addFeature(sf2);
+ // discontiguous range
+ SequenceFeature sf3 = new SequenceFeature("Metal", "desc", 30, 40,
+ Float.NaN, null);
+ store.addFeature(sf3);
+ // overlapping range
+ SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 15, 35,
+ Float.NaN, null);
+ store.addFeature(sf4);
+ // enclosing range
+ SequenceFeature sf5 = new SequenceFeature("Metal", "desc", 5, 50,
+ Float.NaN, null);
+ store.addFeature(sf5);
+ // non-positional feature
+ SequenceFeature sf6 = new SequenceFeature("Metal", "desc", 0, 0,
+ Float.NaN, null);
+ store.addFeature(sf6);
+ // contact feature
+ SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
+ 18, 45, Float.NaN, null);
+ store.addFeature(sf7);
+
+ List<SequenceFeature> features = store.getPositionalFeatures();
+ assertEquals(features.size(), 6);
+ assertTrue(features.contains(sf1));
+ assertTrue(features.contains(sf2));
+ assertTrue(features.contains(sf3));
+ assertTrue(features.contains(sf4));
+ assertTrue(features.contains(sf5));
+ assertFalse(features.contains(sf6));
+ assertTrue(features.contains(sf7));
+
+ features = store.getNonPositionalFeatures();
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf6));
+ }
+
+ @Test(groups = "Functional")
+ public void testDelete()
+ {
+ FeatureStoreI store = newFeatureStore();
+ SequenceFeature sf1 = addFeature(store, 10, 20);
+ assertTrue(store.getPositionalFeatures().contains(sf1));
+
+ /*
+ * simple deletion
+ */
+ assertTrue(store.delete(sf1));
+ assertTrue(store.getPositionalFeatures().isEmpty());
+
+ /*
+ * non-positional feature deletion
+ */
+ SequenceFeature sf2 = addFeature(store, 0, 0);
+ assertFalse(store.getPositionalFeatures().contains(sf2));
+ assertTrue(store.getNonPositionalFeatures().contains(sf2));
+ assertTrue(store.delete(sf2));
+ assertTrue(store.getNonPositionalFeatures().isEmpty());
+
+ /*
+ * contact feature deletion
+ */
+ SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11,
+ 23, Float.NaN, null);
+ store.addFeature(sf3);
+ assertEquals(store.getPositionalFeatures().size(), 1);
+ assertTrue(store.getPositionalFeatures().contains(sf3));
+ assertTrue(store.delete(sf3));
+ assertTrue(store.getPositionalFeatures().isEmpty());
+
+ /*
+ * nested feature deletion
+ */
+ SequenceFeature sf4 = addFeature(store, 20, 30);
+ SequenceFeature sf5 = addFeature(store, 22, 26); // to NCList
+ SequenceFeature sf6 = addFeature(store, 23, 24); // child of sf5
+ SequenceFeature sf7 = addFeature(store, 25, 25); // sibling of sf6
+ SequenceFeature sf8 = addFeature(store, 24, 24); // child of sf6
+ SequenceFeature sf9 = addFeature(store, 23, 23); // child of sf6
+ assertEquals(store.getPositionalFeatures().size(), 6);
+
+ // delete a node with children - they take its place
+ assertTrue(store.delete(sf6)); // sf8, sf9 should become children of sf5
+ assertEquals(store.getPositionalFeatures().size(), 5);
+ assertFalse(store.getPositionalFeatures().contains(sf6));
+
+ // delete a node with no children
+ assertTrue(store.delete(sf7));
+ assertEquals(store.getPositionalFeatures().size(), 4);
+ assertFalse(store.getPositionalFeatures().contains(sf7));
+
+ // delete root of NCList
+ assertTrue(store.delete(sf5));
+ assertEquals(store.getPositionalFeatures().size(), 3);
+ assertFalse(store.getPositionalFeatures().contains(sf5));
+
+ // continue the killing fields
+ assertTrue(store.delete(sf4));
+ assertEquals(store.getPositionalFeatures().size(), 2);
+ assertFalse(store.getPositionalFeatures().contains(sf4));
+
+ assertTrue(store.delete(sf9));
+ assertEquals(store.getPositionalFeatures().size(), 1);
+ assertFalse(store.getPositionalFeatures().contains(sf9));
+
+ assertTrue(store.delete(sf8));
+ assertTrue(store.getPositionalFeatures().isEmpty());
+ }
+
+ @Test(groups = "Functional")
+ public void testAddFeature()
+ {
+ FeatureStoreI fs = newFeatureStore();
+
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
+ Float.NaN, null);
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
+ Float.NaN, null);
+
+ assertTrue(fs.addFeature(sf1));
+ assertEquals(fs.getFeatureCount(true), 1); // positional
+ assertEquals(fs.getFeatureCount(false), 0); // non-positional
+
+ /*
+ * re-adding the same or an identical feature should fail
+ */
+ assertFalse(fs.addFeature(sf1));
+ assertEquals(fs.getFeatureCount(true), 1);
+ assertFalse(fs.addFeature(sf2));
+ assertEquals(fs.getFeatureCount(true), 1);
+
+ /*
+ * add non-positional
+ */
+ SequenceFeature sf3 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
+ null);
+ assertTrue(fs.addFeature(sf3));
+ assertEquals(fs.getFeatureCount(true), 1); // positional
+ assertEquals(fs.getFeatureCount(false), 1); // non-positional
+ SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
+ null);
+ assertFalse(fs.addFeature(sf4)); // already stored
+ assertEquals(fs.getFeatureCount(true), 1); // positional
+ assertEquals(fs.getFeatureCount(false), 1); // non-positional
+
+ /*
+ * add contact
+ */
+ SequenceFeature sf5 = new SequenceFeature("Disulfide bond", "", 10, 20,
+ Float.NaN, null);
+ assertTrue(fs.addFeature(sf5));
+ assertEquals(fs.getFeatureCount(true), 2); // positional - add 1 for contact
+ assertEquals(fs.getFeatureCount(false), 1); // non-positional
+ SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "", 10, 20,
+ Float.NaN, null);
+ assertFalse(fs.addFeature(sf6)); // already stored
+ assertEquals(fs.getFeatureCount(true), 2); // no change
+ assertEquals(fs.getFeatureCount(false), 1); // no change
+ }
+
+ @Test(groups = "Functional")
+ public void testIsEmpty()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ assertTrue(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 0);
+
+ /*
+ * non-nested feature
+ */
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
+ Float.NaN, null);
+ fs.addFeature(sf1);
+ assertFalse(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 1);
+ fs.delete(sf1);
+ assertTrue(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 0);
+
+ /*
+ * non-positional feature
+ */
+ sf1 = new SequenceFeature("Cath", "", 0, 0, Float.NaN, null);
+ fs.addFeature(sf1);
+ assertFalse(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(false), 1); // non-positional
+ assertEquals(fs.getFeatureCount(true), 0); // positional
+ fs.delete(sf1);
+ assertTrue(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(false), 0);
+
+ /*
+ * contact feature
+ */
+ sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN, null);
+ fs.addFeature(sf1);
+ assertFalse(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 1);
+ fs.delete(sf1);
+ assertTrue(fs.isEmpty());
+ assertEquals(fs.getFeatureCount(true), 0);
+
+ /*
+ * sf2, sf3 added as nested features
+ */
+ sf1 = new SequenceFeature("Cath", "", 19, 49, Float.NaN, null);
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 20, 40,
+ Float.NaN, null);
+ SequenceFeature sf3 = new SequenceFeature("Cath", "", 25, 35,
+ Float.NaN, null);
+ fs.addFeature(sf1);
+ fs.addFeature(sf2);
+ fs.addFeature(sf3);
+ assertEquals(fs.getFeatureCount(true), 3);
+ assertTrue(fs.delete(sf1));
+ assertEquals(fs.getFeatureCount(true), 2);
+ assertEquals(fs.getFeatures().size(), 2);
+ assertFalse(fs.isEmpty());
+ assertTrue(fs.delete(sf2));
+ assertEquals(fs.getFeatureCount(true), 1);
+ assertFalse(fs.isEmpty());
+ assertTrue(fs.delete(sf3));
+ assertEquals(fs.getFeatureCount(true), 0);
+ assertTrue(fs.isEmpty()); // all gone
+ }
+
+ @Test(groups = "Functional")
+ public void testGetFeatureGroups()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ assertTrue(fs.getFeatureGroups(true).isEmpty());
+ assertTrue(fs.getFeatureGroups(false).isEmpty());
+
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+ fs.addFeature(sf1);
+ Set<String> groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("group1"));
+
+ /*
+ * add another feature of the same group, delete one, delete both
+ */
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group1");
+ fs.addFeature(sf2);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("group1"));
+ fs.delete(sf2);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("group1"));
+ fs.delete(sf1);
+ groups = fs.getFeatureGroups(true);
+ assertTrue(fs.getFeatureGroups(true).isEmpty());
+
+ SequenceFeature sf3 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group2");
+ fs.addFeature(sf3);
+ SequenceFeature sf4 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "Group2");
+ fs.addFeature(sf4);
+ SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 20, 30, 1f, null);
+ fs.addFeature(sf5);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 3);
+ assertTrue(groups.contains("group2"));
+ assertTrue(groups.contains("Group2")); // case sensitive
+ assertTrue(groups.contains(null)); // null allowed
+ assertTrue(fs.getFeatureGroups(false).isEmpty()); // non-positional
+
+ fs.delete(sf3);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 2);
+ assertFalse(groups.contains("group2"));
+ fs.delete(sf4);
+ groups = fs.getFeatureGroups(true);
+ assertEquals(groups.size(), 1);
+ assertFalse(groups.contains("Group2"));
+ fs.delete(sf5);
+ groups = fs.getFeatureGroups(true);
+ assertTrue(groups.isEmpty());
+
+ /*
+ * add non-positional feature
+ */
+ SequenceFeature sf6 = new SequenceFeature("Cath", "desc", 0, 0, 1f,
+ "CathGroup");
+ fs.addFeature(sf6);
+ groups = fs.getFeatureGroups(false);
+ assertEquals(groups.size(), 1);
+ assertTrue(groups.contains("CathGroup"));
+ assertTrue(fs.delete(sf6));
+ assertTrue(fs.getFeatureGroups(false).isEmpty());
+ }
+
+ @Test(groups = "Functional")
+ public void testGetTotalFeatureLength()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ assertEquals(fs.getTotalFeatureLength(), 0);
+
+ addFeature(fs, 10, 20); // 11
+ assertEquals(fs.getTotalFeatureLength(), 11);
+ addFeature(fs, 17, 37); // 21
+ SequenceFeature sf1 = addFeature(fs, 14, 74); // 61
+ assertEquals(fs.getTotalFeatureLength(), 93);
+
+ // non-positional features don't count
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 0, 0, 1f,
+ "group1");
+ fs.addFeature(sf2);
+ assertEquals(fs.getTotalFeatureLength(), 93);
+
+ // contact features count 1
+ SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc",
+ 15, 35, 1f, "group1");
+ fs.addFeature(sf3);
+ assertEquals(fs.getTotalFeatureLength(), 94);
+
+ assertTrue(fs.delete(sf1));
+ assertEquals(fs.getTotalFeatureLength(), 33);
+ assertFalse(fs.delete(sf1));
+ assertEquals(fs.getTotalFeatureLength(), 33);
+ assertTrue(fs.delete(sf2));
+ assertEquals(fs.getTotalFeatureLength(), 33);
+ assertTrue(fs.delete(sf3));
+ assertEquals(fs.getTotalFeatureLength(), 32);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetFeatureLength()
+ {
+ /*
+ * positional feature
+ */
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+ assertEquals(FeatureStore.getFeatureLength(sf1), 11);
+
+ /*
+ * non-positional feature
+ */
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 0, 0, 1f,
+ "CathGroup");
+ assertEquals(FeatureStore.getFeatureLength(sf2), 0);
+
+ /*
+ * contact feature counts 1
+ */
+ SequenceFeature sf3 = new SequenceFeature("Disulphide Bond", "desc",
+ 14, 28, 1f, "AGroup");
+ assertEquals(FeatureStore.getFeatureLength(sf3), 1);
+ }
+
+ @Test(groups = "Functional")
+ public void testMin()
+ {
+ assertEquals(FeatureStore.min(Float.NaN, Float.NaN), Float.NaN);
+ assertEquals(FeatureStore.min(Float.NaN, 2f), 2f);
+ assertEquals(FeatureStore.min(-2f, Float.NaN), -2f);
+ assertEquals(FeatureStore.min(2f, -3f), -3f);
+ }
+
+ @Test(groups = "Functional")
+ public void testMax()
+ {
+ assertEquals(FeatureStore.max(Float.NaN, Float.NaN), Float.NaN);
+ assertEquals(FeatureStore.max(Float.NaN, 2f), 2f);
+ assertEquals(FeatureStore.max(-2f, Float.NaN), -2f);
+ assertEquals(FeatureStore.max(2f, -3f), 2f);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetMinimumScore_getMaximumScore()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ assertEquals(fs.getMinimumScore(true), Float.NaN); // positional
+ assertEquals(fs.getMaximumScore(true), Float.NaN);
+ assertEquals(fs.getMinimumScore(false), Float.NaN); // non-positional
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+
+ // add features with no score
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 0, 0,
+ Float.NaN, "group");
+ fs.addFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("type", "desc", 10, 20,
+ Float.NaN, "group");
+ fs.addFeature(sf2);
+ assertEquals(fs.getMinimumScore(true), Float.NaN);
+ assertEquals(fs.getMaximumScore(true), Float.NaN);
+ assertEquals(fs.getMinimumScore(false), Float.NaN);
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+
+ // add positional features with score
+ SequenceFeature sf3 = new SequenceFeature("type", "desc", 10, 20, 1f,
+ "group");
+ fs.addFeature(sf3);
+ SequenceFeature sf4 = new SequenceFeature("type", "desc", 12, 16, 4f,
+ "group");
+ fs.addFeature(sf4);
+ assertEquals(fs.getMinimumScore(true), 1f);
+ assertEquals(fs.getMaximumScore(true), 4f);
+ assertEquals(fs.getMinimumScore(false), Float.NaN);
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+
+ // add non-positional features with score
+ SequenceFeature sf5 = new SequenceFeature("type", "desc", 0, 0, 11f,
+ "group");
+ fs.addFeature(sf5);
+ SequenceFeature sf6 = new SequenceFeature("type", "desc", 0, 0, -7f,
+ "group");
+ fs.addFeature(sf6);
+ assertEquals(fs.getMinimumScore(true), 1f);
+ assertEquals(fs.getMaximumScore(true), 4f);
+ assertEquals(fs.getMinimumScore(false), -7f);
+ assertEquals(fs.getMaximumScore(false), 11f);
+
+ // delete one positional and one non-positional
+ // min-max should be recomputed
+ assertTrue(fs.delete(sf6));
+ assertTrue(fs.delete(sf3));
+ assertEquals(fs.getMinimumScore(true), 4f);
+ assertEquals(fs.getMaximumScore(true), 4f);
+ assertEquals(fs.getMinimumScore(false), 11f);
+ assertEquals(fs.getMaximumScore(false), 11f);
+
+ // delete remaining features with score
+ assertTrue(fs.delete(sf4));
+ assertTrue(fs.delete(sf5));
+ assertEquals(fs.getMinimumScore(true), Float.NaN);
+ assertEquals(fs.getMaximumScore(true), Float.NaN);
+ assertEquals(fs.getMinimumScore(false), Float.NaN);
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+
+ // delete all features
+ assertTrue(fs.delete(sf1));
+ assertTrue(fs.delete(sf2));
+ assertTrue(fs.isEmpty());
+ assertEquals(fs.getMinimumScore(true), Float.NaN);
+ assertEquals(fs.getMaximumScore(true), Float.NaN);
+ assertEquals(fs.getMinimumScore(false), Float.NaN);
+ assertEquals(fs.getMaximumScore(false), Float.NaN);
+ }
+
+ @Test(groups = "Functional")
+ public void testListContains()
+ {
+ assertFalse(FeatureStore.listContains(null, null));
+ List<SequenceFeature> features = new ArrayList<>();
+ assertFalse(FeatureStore.listContains(features, null));
+
+ SequenceFeature sf1 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
+ "group1");
+ assertFalse(FeatureStore.listContains(null, sf1));
+ assertFalse(FeatureStore.listContains(features, sf1));
+
+ features.add(sf1);
+ SequenceFeature sf2 = new SequenceFeature("type1", "desc1", 20, 30, 3f,
+ "group1");
+ SequenceFeature sf3 = new SequenceFeature("type1", "desc1", 20, 40, 3f,
+ "group1");
+
+ // sf2.equals(sf1) so contains should return true
+ assertTrue(FeatureStore.listContains(features, sf2));
+ assertFalse(FeatureStore.listContains(features, sf3));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetFeaturesForGroup()
+ {
+ FeatureStoreI fs = newFeatureStore();
+
+ /*
+ * with no features
+ */
+ assertTrue(fs.getFeaturesForGroup(true, null).isEmpty());
+ assertTrue(fs.getFeaturesForGroup(false, null).isEmpty());
+ assertTrue(fs.getFeaturesForGroup(true, "uniprot").isEmpty());
+ assertTrue(fs.getFeaturesForGroup(false, "uniprot").isEmpty());
+
+ /*
+ * sf1: positional feature in the null group
+ */
+ SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
+ null);
+ fs.addFeature(sf1);
+ assertTrue(fs.getFeaturesForGroup(true, "uniprot").isEmpty());
+ assertTrue(fs.getFeaturesForGroup(false, "uniprot").isEmpty());
+ assertTrue(fs.getFeaturesForGroup(false, null).isEmpty());
+ List<SequenceFeature> features = fs.getFeaturesForGroup(true, null);
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf1));
+
+ /*
+ * sf2: non-positional feature in the null group
+ * sf3: positional feature in a non-null group
+ * sf4: non-positional feature in a non-null group
+ */
+ SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
+ null);
+ SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
+ "Uniprot");
+ SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
+ "Rfam");
+ fs.addFeature(sf2);
+ fs.addFeature(sf3);
+ fs.addFeature(sf4);
+
+ features = fs.getFeaturesForGroup(true, null);
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf1));
+
+ features = fs.getFeaturesForGroup(false, null);
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf2));
+
+ features = fs.getFeaturesForGroup(true, "Uniprot");
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf3));
+
+ features = fs.getFeaturesForGroup(false, "Rfam");
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf4));
+ }
+
+ @Test(groups = "Functional")
+ public void testShiftFeatures()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ assertFalse(fs.shiftFeatures(0, 1)); // nothing to do
+
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
+ fs.addFeature(sf1);
+ // nested feature:
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 8, 14, 0f, null);
+ fs.addFeature(sf2);
+ // contact feature:
+ SequenceFeature sf3 = new SequenceFeature("Disulfide bond", "", 23, 32,
+ 0f, null);
+ fs.addFeature(sf3);
+ // non-positional feature:
+ SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, 0f, null);
+ fs.addFeature(sf4);
+
+ /*
+ * shift all features right by 5
+ */
+ assertTrue(fs.shiftFeatures(0, 5));
+
+ // non-positional features untouched:
+ List<SequenceFeature> nonPos = fs.getNonPositionalFeatures();
+ assertEquals(nonPos.size(), 1);
+ assertTrue(nonPos.contains(sf4));
+
+ // positional features are replaced
+ List<SequenceFeature> pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 3);
+ assertFalse(pos.contains(sf1));
+ assertFalse(pos.contains(sf2));
+ assertFalse(pos.contains(sf3));
+ SequenceFeatures.sortFeatures(pos, true); // ascending start pos
+ assertEquals(pos.get(0).getBegin(), 7);
+ assertEquals(pos.get(0).getEnd(), 10);
+ assertEquals(pos.get(1).getBegin(), 13);
+ assertEquals(pos.get(1).getEnd(), 19);
+ assertEquals(pos.get(2).getBegin(), 28);
+ assertEquals(pos.get(2).getEnd(), 37);
+
+ /*
+ * now shift left by 15
+ * feature at [7-10] should be removed
+ * feature at [13-19] should become [1-4]
+ */
+ assertTrue(fs.shiftFeatures(0, -15));
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertEquals(pos.get(0).getBegin(), 1);
+ assertEquals(pos.get(0).getEnd(), 4);
+ assertEquals(pos.get(1).getBegin(), 13);
+ assertEquals(pos.get(1).getEnd(), 22);
+
+ /*
+ * shift right by 4 from position 2 onwards
+ * feature at [1-4] unchanged, feature at [13-22] shifts
+ */
+ assertTrue(fs.shiftFeatures(2, 4));
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertEquals(pos.get(0).getBegin(), 1);
+ assertEquals(pos.get(0).getEnd(), 4);
+ assertEquals(pos.get(1).getBegin(), 17);
+ assertEquals(pos.get(1).getEnd(), 26);
+
+ /*
+ * shift right by 4 from position 18 onwards
+ * should be no change
+ */
+ SequenceFeature f1 = pos.get(0);
+ SequenceFeature f2 = pos.get(1);
+ assertFalse(fs.shiftFeatures(18, 4)); // no update
+ pos = fs.getPositionalFeatures();
+ assertEquals(pos.size(), 2);
+ SequenceFeatures.sortFeatures(pos, true);
+ assertSame(pos.get(0), f1);
+ assertSame(pos.get(1), f2);
+ }
+
+ @Test(groups = "Functional")
+ public void testDelete_readd()
+ {
+ /*
+ * add a feature and a nested feature
+ */
+ FeatureStoreI store = newFeatureStore();
+ SequenceFeature sf1 = addFeature(store, 10, 20);
+ // sf2 is nested in sf1 so will be stored in nestedFeatures
+ SequenceFeature sf2 = addFeature(store, 12, 14);
+ List<SequenceFeature> features = store.getPositionalFeatures();
+ assertEquals(features.size(), 2);
+ assertTrue(features.contains(sf1));
+ assertTrue(features.contains(sf2));
+ assertTrue(store.getFeatures().contains(sf1));
+ assertTrue(store.getFeatures().contains(sf2));
+
+ /*
+ * delete the first feature
+ */
+ assertTrue(store.delete(sf1));
+ features = store.getPositionalFeatures();
+ assertFalse(features.contains(sf1));
+ assertTrue(features.contains(sf2));
+
+ /*
+ * re-add the 'nested' feature; is it now duplicated?
+ */
+ store.addFeature(sf2);
+ features = store.getPositionalFeatures();
+ assertEquals(features.size(), 1);
+ assertTrue(features.contains(sf2));
+ }
+
+ @Test(groups = "Functional")
+ public void testContains()
+ {
+ FeatureStoreI fs = newFeatureStore();
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
+ Float.NaN, "group1");
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
+ Float.NaN, "group2");
+ SequenceFeature sf3 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
+ "group1");
+ SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, 0f,
+ "group1");
+ SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "", 5, 15,
+ Float.NaN, "group1");
+ SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "", 5, 15,
+ Float.NaN, "group2");
+
+ fs.addFeature(sf1);
+ fs.addFeature(sf3);
+ fs.addFeature(sf5);
+ assertTrue(fs.contains(sf1)); // positional feature
+ assertTrue(fs.contains(new SequenceFeature(sf1))); // identical feature
+ assertFalse(fs.contains(sf2)); // different group
+ assertTrue(fs.contains(sf3)); // non-positional
+ assertTrue(fs.contains(new SequenceFeature(sf3)));
+ assertFalse(fs.contains(sf4)); // different score
+ assertTrue(fs.contains(sf5)); // contact feature
+ assertTrue(fs.contains(new SequenceFeature(sf5)));
+ assertFalse(fs.contains(sf6)); // different group
+
+ /*
+ * add a nested feature
+ */
+ SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16,
+ Float.NaN, "group1");
+ fs.addFeature(sf7);
+ assertTrue(fs.contains(sf7));
+ assertTrue(fs.contains(new SequenceFeature(sf7)));
+
+ /*
+ * delete the outer (enclosing, non-nested) feature
+ */
+ fs.delete(sf1);
+ assertFalse(fs.contains(sf1));
+ assertTrue(fs.contains(sf7));
+ }
+}
@Test(groups = "Functional")
public void testFindFeatures_nonNested()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN,
null));
// same range different description
assertEquals(overlaps.get(0).getEnd(), 35);
}
+ private FeatureStoreI newFeatureStore()
+ {
+ // return new FeatureStoreJS();
+ return new FeatureStoreImpl();
+ }
+
@Test(groups = "Functional")
public void testFindFeatures_nested()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
SequenceFeature sf1 = addFeature(fs, 10, 50);
SequenceFeature sf2 = addFeature(fs, 10, 40);
SequenceFeature sf3 = addFeature(fs, 20, 30);
@Test(groups = "Functional")
public void testFindFeatures_mixed()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
SequenceFeature sf1 = addFeature(fs, 10, 50);
SequenceFeature sf2 = addFeature(fs, 1, 15);
SequenceFeature sf3 = addFeature(fs, 20, 30);
* @param to
* @return
*/
- SequenceFeature addFeature(FeatureStore fs, int from, int to)
+ SequenceFeature addFeature(FeatureStoreI fs, int from, int to)
{
SequenceFeature sf1 = new SequenceFeature("", "", from, to, Float.NaN,
null);
@Test(groups = "Functional")
public void testFindFeatures_contactFeatures()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
SequenceFeature sf = new SequenceFeature("disulphide bond", "bond", 10,
20, Float.NaN, null);
@Test(groups = "Functional")
public void testGetPositionalFeatures()
{
- FeatureStore store = new FeatureStore();
+ FeatureStoreI store = newFeatureStore();
SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
Float.NaN, null);
store.addFeature(sf1);
@Test(groups = "Functional")
public void testDelete()
{
- FeatureStore store = new FeatureStore();
+ FeatureStoreI store = newFeatureStore();
SequenceFeature sf1 = addFeature(store, 10, 20);
assertTrue(store.getPositionalFeatures().contains(sf1));
@Test(groups = "Functional")
public void testAddFeature()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
Float.NaN, null);
@Test(groups = "Functional")
public void testIsEmpty()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
assertTrue(fs.isEmpty());
assertEquals(fs.getFeatureCount(true), 0);
assertEquals(fs.getFeatureCount(true), 3);
assertTrue(fs.delete(sf1));
assertEquals(fs.getFeatureCount(true), 2);
- assertEquals(fs.features.size(), 2);
+ assertEquals(fs.getFeatures().size(), 2);
assertFalse(fs.isEmpty());
assertTrue(fs.delete(sf2));
assertEquals(fs.getFeatureCount(true), 1);
@Test(groups = "Functional")
public void testGetFeatureGroups()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
assertTrue(fs.getFeatureGroups(true).isEmpty());
assertTrue(fs.getFeatureGroups(false).isEmpty());
@Test(groups = "Functional")
public void testGetTotalFeatureLength()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
assertEquals(fs.getTotalFeatureLength(), 0);
addFeature(fs, 10, 20); // 11
@Test(groups = "Functional")
public void testGetMinimumScore_getMaximumScore()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
assertEquals(fs.getMinimumScore(true), Float.NaN); // positional
assertEquals(fs.getMaximumScore(true), Float.NaN);
assertEquals(fs.getMinimumScore(false), Float.NaN); // non-positional
@Test(groups = "Functional")
public void testGetFeaturesForGroup()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
/*
* with no features
@Test(groups = "Functional")
public void testShiftFeatures()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
assertFalse(fs.shiftFeatures(0, 1)); // nothing to do
SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
/*
* add a feature and a nested feature
*/
- FeatureStore store = new FeatureStore();
+ FeatureStoreI store = newFeatureStore();
SequenceFeature sf1 = addFeature(store, 10, 20);
// sf2 is nested in sf1 so will be stored in nestedFeatures
SequenceFeature sf2 = addFeature(store, 12, 14);
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf2));
- assertTrue(store.features.contains(sf1));
- assertTrue(store.features.contains(sf2));
+ assertTrue(store.getFeatures().contains(sf1));
+ assertTrue(store.getFeatures().contains(sf2));
/*
* delete the first feature
@Test(groups = "Functional")
public void testContains()
{
- FeatureStore fs = new FeatureStore();
+ FeatureStoreI fs = newFeatureStore();
SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
Float.NaN, "group1");
SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
* no type specified - get all types stored
* they are returned in keyset (alphabetical) order
*/
- Map<String, FeatureStore> featureStores = (Map<String, FeatureStore>) PA
+ Map<String, FeatureStoreI> featureStores = (Map<String, FeatureStoreI>) PA
.getValue(sf, "featureStore");
- Iterable<FeatureStore> types = sf.varargToTypes();
- Iterator<FeatureStore> iterator = types.iterator();
+ Iterable<FeatureStoreI> types = sf.varargToTypes();
+ Iterator<FeatureStoreI> iterator = types.iterator();
assertTrue(iterator.hasNext());
assertSame(iterator.next(), featureStores.get("Cath"));
assertTrue(iterator.hasNext());
git://source.jalview.org / jalview.git / commitdiff