+/*
+ * 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.ContiguousI;
import jalview.datamodel.SequenceFeature;
import java.util.ArrayList;
*/
abstract boolean compare(SequenceFeature entry);
+ /**
+ * serves a search condition for finding the first feature whose start
+ * position follows a given target location
+ *
+ * @param target
+ * @return
+ */
static SearchCriterion byStart(final long target)
{
return new SearchCriterion() {
};
}
+ /**
+ * serves a search condition for finding the first feature whose end
+ * position is at or follows a given target location
+ *
+ * @param target
+ * @return
+ */
static SearchCriterion byEnd(final long target)
{
return new SearchCriterion()
};
}
+ /**
+ * serves a search condition for finding the first feature which follows the
+ * given range as determined by a supplied comparator
+ *
+ * @param target
+ * @return
+ */
static SearchCriterion byFeature(final ContiguousI to,
final Comparator<ContiguousI> rc)
{
*/
public boolean addFeature(SequenceFeature feature)
{
+ if (contains(feature))
+ {
+ return false;
+ }
+
/*
* keep a record of feature groups
*/
}
else
{
- if (!contains(nonNestedFeatures, feature))
+ added = addNonNestedFeature(feature);
+ if (!added)
{
- added = addNonNestedFeature(feature);
- if (!added)
- {
- /*
- * detected a nested feature - put it in the NCList structure
- */
- added = addNestedFeature(feature);
- }
+ /*
+ * detected a nested feature - put it in the NCList structure
+ */
+ added = addNestedFeature(feature);
}
}
}
/**
+ * Answers true if this store contains the given feature (testing by
+ * SequenceFeature.equals), else false
+ *
+ * @param feature
+ * @return
+ */
+ public boolean contains(SequenceFeature feature)
+ {
+ if (feature.isNonPositional())
+ {
+ return nonPositionalFeatures == null ? false : nonPositionalFeatures
+ .contains(feature);
+ }
+
+ if (feature.isContactFeature())
+ {
+ return contactFeatureStarts == null ? false : listContains(
+ contactFeatureStarts, feature);
+ }
+
+ if (listContains(nonNestedFeatures, feature))
+ {
+ return true;
+ }
+
+ return nestedFeatures == null ? false : nestedFeatures
+ .contains(feature);
+ }
+
+ /**
* Answers the 'length' of the feature, counting 0 for non-positional features
* and 1 for contact features
*
/**
* Adds the feature to the list of non-positional features (with lazy
- * instantiation of the list if it is null), and returns true. If the
- * non-positional features already include the new feature (by equality test),
- * then it is not added, and this method returns false. The feature group is
- * added to the set of distinct feature groups for non-positional features.
+ * instantiation of the list if it is null), and returns true. The feature
+ * group is added to the set of distinct feature groups for non-positional
+ * features. This method allows duplicate features, so test before calling to
+ * prevent this.
*
* @param feature
*/
{
nonPositionalFeatures = new ArrayList<SequenceFeature>();
}
- if (nonPositionalFeatures.contains(feature))
- {
- return false;
- }
nonPositionalFeatures.add(feature);
{
if (nestedFeatures == null)
{
- nestedFeatures = new NCList<SequenceFeature>(feature);
+ nestedFeatures = new NCList<>(feature);
return true;
}
return nestedFeatures.add(feature, false);
/**
* 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
- * ordered, and returns true. If the contact feature lists already contain the
- * given feature (by test for equality), does not add it and returns false.
+ * ordered, and returns true. This method allows duplicate features to be
+ * added, so test before calling to avoid this.
*
* @param feature
* @return
contactFeatureEnds = new ArrayList<SequenceFeature>();
}
- if (contains(contactFeatureStarts, feature))
- {
- return false;
- }
-
/*
* binary search the sorted list to find the insertion point
*/
* @param feature
* @return
*/
- protected static boolean contains(List<SequenceFeature> features,
+ protected static boolean listContains(List<SequenceFeature> features,
SequenceFeature feature)
{
if (features == null || feature == null)
*/
public List<SequenceFeature> findOverlappingFeatures(long start, long end)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
findNonNestedFeatures(start, end, result);
protected void findNonNestedFeatures(long from, long to,
List<SequenceFeature> result)
{
+ /*
+ * find the first feature whose end position is
+ * after the target range start
+ */
int startIndex = binarySearch(nonNestedFeatures,
SearchCriterion.byEnd(from));
- findNonNestedFeatures(startIndex, from, to, result);
- }
-
- /**
- * Scans the list of non-nested features, starting from startIndex, to find
- * those that overlap the from-to range, and adds them to the result list.
- * Returns the index of the first feature whose start position is after the
- * target range (or the length of the whole list if none such feature exists).
- *
- * @param startIndex
- * @param from
- * @param to
- * @param result
- * @return
- */
- protected int findNonNestedFeatures(final int startIndex, long from,
- long to, List<SequenceFeature> result)
- {
- int i = startIndex;
+ final int startIndex1 = startIndex;
+ int i = startIndex1;
while (i < nonNestedFeatures.size())
{
SequenceFeature sf = nonNestedFeatures.get(i);
{
break;
}
- int start = sf.getBegin();
- int end = sf.getEnd();
- if (start <= to && end >= from)
+ if (sf.getBegin() <= to && sf.getEnd() >= from)
{
result.add(sf);
}
i++;
}
- return i;
}
/**
/*
* add non-nested features (may be all features for many cases)
*/
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
result.addAll(nonNestedFeatures);
/*
{
return Collections.emptyList();
}
- return new ArrayList<SequenceFeature>(contactFeatureStarts);
+ return new ArrayList<>(contactFeatureStarts);
}
/**
{
return Collections.emptyList();
}
- return new ArrayList<SequenceFeature>(nonPositionalFeatures);
+ return new ArrayList<>(nonPositionalFeatures);
}
/**
}
/**
- * Scans all positional features to check whether the given feature group is
- * found, and returns true if found, else false
- *
- * @param featureGroup
- * @return
- */
- protected boolean findFeatureGroup(String featureGroup)
- {
- for (SequenceFeature sf : getPositionalFeatures())
- {
- String group = sf.getFeatureGroup();
- if (group == featureGroup
- || (group != null && group.equals(featureGroup)))
- {
- return true;
- }
- }
- return false;
- }
-
- /**
* Answers true if this store has no features, else false
*
* @return
public List<SequenceFeature> getFeaturesForGroup(boolean positional,
String group)
{
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+ List<SequenceFeature> result = new ArrayList<>();
/*
* if we know features don't include the target group, no need
}
/**
- * 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());
- 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;
}
git://source.jalview.org / jalview.git / blobdiff