X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStore.java;h=02ce1c50a5f28eb59603bab4d7b7f7d335c4cfaa;hb=5969ead0fd401f4435a3435ede9e4e87cf9c1d0b;hp=1b6277c59deafeb76512f88bc28237cd3aa95bb5;hpb=807f5945ffa954c38f07cbf9d2a4ebc22cfe5eb9;p=jalview.git
diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index 1b6277c..02ce1c5 100644
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -1,3 +1,23 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel.features;
import jalview.datamodel.ContiguousI;
@@ -33,6 +53,13 @@ public class FeatureStore
*/
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() {
@@ -45,6 +72,13 @@ public class FeatureStore
};
}
+ /**
+ * 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()
@@ -58,6 +92,13 @@ public class FeatureStore
};
}
+ /**
+ * 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 rc)
{
@@ -159,6 +200,11 @@ public class FeatureStore
*/
public boolean addFeature(SequenceFeature feature)
{
+ if (contains(feature))
+ {
+ return false;
+ }
+
/*
* keep a record of feature groups
*/
@@ -179,16 +225,13 @@ public class FeatureStore
}
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);
}
}
@@ -225,6 +268,36 @@ public class FeatureStore
}
/**
+ * 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
*
@@ -246,10 +319,10 @@ public class FeatureStore
/**
* 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
*/
@@ -259,10 +332,6 @@ public class FeatureStore
{
nonPositionalFeatures = new ArrayList();
}
- if (nonPositionalFeatures.contains(feature))
- {
- return false;
- }
nonPositionalFeatures.add(feature);
@@ -281,7 +350,7 @@ public class FeatureStore
{
if (nestedFeatures == null)
{
- nestedFeatures = new NCList(feature);
+ nestedFeatures = new NCList<>(feature);
return true;
}
return nestedFeatures.add(feature, false);
@@ -362,8 +431,8 @@ public class FeatureStore
/**
* 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
@@ -379,11 +448,6 @@ public class FeatureStore
contactFeatureEnds = new ArrayList();
}
- if (contains(contactFeatureStarts, feature))
- {
- return false;
- }
-
/*
* binary search the sorted list to find the insertion point
*/
@@ -412,7 +476,7 @@ public class FeatureStore
* @param feature
* @return
*/
- protected static boolean contains(List features,
+ protected static boolean listContains(List features,
SequenceFeature feature)
{
if (features == null || feature == null)
@@ -455,7 +519,7 @@ public class FeatureStore
*/
public List findOverlappingFeatures(long start, long end)
{
- List result = new ArrayList();
+ List result = new ArrayList<>();
findNonNestedFeatures(start, end, result);
@@ -552,28 +616,15 @@ public class FeatureStore
protected void findNonNestedFeatures(long from, long to,
List 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 result)
- {
- int i = startIndex;
+ final int startIndex1 = startIndex;
+ int i = startIndex1;
while (i < nonNestedFeatures.size())
{
SequenceFeature sf = nonNestedFeatures.get(i);
@@ -581,15 +632,12 @@ public class FeatureStore
{
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;
}
/**
@@ -633,7 +681,7 @@ public class FeatureStore
/*
* add non-nested features (may be all features for many cases)
*/
- List result = new ArrayList();
+ List result = new ArrayList<>();
result.addAll(nonNestedFeatures);
/*
@@ -667,7 +715,7 @@ public class FeatureStore
{
return Collections.emptyList();
}
- return new ArrayList(contactFeatureStarts);
+ return new ArrayList<>(contactFeatureStarts);
}
/**
@@ -682,7 +730,7 @@ public class FeatureStore
{
return Collections.emptyList();
}
- return new ArrayList(nonPositionalFeatures);
+ return new ArrayList<>(nonPositionalFeatures);
}
/**
@@ -820,27 +868,6 @@ public class FeatureStore
}
/**
- * 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
@@ -993,7 +1020,7 @@ public class FeatureStore
public List getFeaturesForGroup(boolean positional,
String group)
{
- List result = new ArrayList();
+ List result = new ArrayList<>();
/*
* if we know features don't include the target group, no need