*/
Set<String> nonPositionalFeatureGroups;
+ /*
+ * the total length of all positional features; contact features count 1 to
+ * the total and 1 to size(), consistent with an average 'feature length' of 1
+ */
+ int totalExtent;
+
+ float positionalMinScore;
+
+ float positionalMaxScore;
+
+ float nonPositionalMinScore;
+
+ float nonPositionalMaxScore;
+
/**
* Constructor
*/
{
nonNestedFeatures = new ArrayList<SequenceFeature>();
positionalFeatureGroups = new HashSet<String>();
+ nonPositionalFeatureGroups = new HashSet<String>();
+ positionalMinScore = Float.NaN;
+ positionalMaxScore = Float.NaN;
+ nonPositionalMinScore = Float.NaN;
+ nonPositionalMaxScore = Float.NaN;
// we only construct nonPositionalFeatures, contactFeatures
// or the NCList if we need to
}
}
+ if (added)
+ {
+ /*
+ * record the total extent of positional features, to make
+ * getTotalFeatureLength possible; we count the length of a
+ * contact feature as 1
+ */
+ totalExtent += getFeatureLength(feature);
+
+ /*
+ * record the minimum and maximum score for positional
+ * and non-positional features
+ */
+ float score = feature.getScore();
+ if (!Float.isNaN(score))
+ {
+ if (feature.isNonPositional())
+ {
+ nonPositionalMinScore = min(nonPositionalMinScore, score);
+ nonPositionalMaxScore = max(nonPositionalMaxScore, score);
+ }
+ else
+ {
+ positionalMinScore = min(positionalMinScore, score);
+ positionalMaxScore = max(positionalMaxScore, score);
+ }
+ }
+ }
+
return added;
}
/**
+ * Answers the 'length' of the feature, counting 0 for non-positional features
+ * and 1 for contact features
+ *
+ * @param feature
+ * @return
+ */
+ protected static int getFeatureLength(SequenceFeature feature)
+ {
+ if (feature.isNonPositional())
+ {
+ return 0;
+ }
+ if (feature.isContactFeature())
+ {
+ return 1;
+ }
+ return 1 + feature.getEnd() - feature.getBegin();
+ }
+
+ /**
* 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),
if (nonPositionalFeatures == null)
{
nonPositionalFeatures = new ArrayList<SequenceFeature>();
- nonPositionalFeatureGroups = new HashSet<String>();
}
if (nonPositionalFeatures.contains(feature))
{
if (removed)
{
- rebuildFeatureGroups(sf.getFeatureGroup(), removedNonPositional);
+ rescanAfterDelete();
}
return removed;
}
/**
- * Check whether the given feature group is still represented, in either
- * positional or non-positional features, and if not, remove it from the set
- * of feature groups
+ * Rescan all features to recompute any cached values after an entry has been
+ * deleted
+ */
+ protected synchronized void rescanAfterDelete()
+ {
+ positionalFeatureGroups.clear();
+ nonPositionalFeatureGroups.clear();
+ totalExtent = 0;
+ positionalMinScore = Float.NaN;
+ positionalMaxScore = Float.NaN;
+ nonPositionalMinScore = Float.NaN;
+ nonPositionalMaxScore = Float.NaN;
+
+ /*
+ * scan non-positional features for groups and scores
+ */
+ for (SequenceFeature sf : getNonPositionalFeatures())
+ {
+ 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())
+ {
+ positionalFeatureGroups.add(sf.getFeatureGroup());
+ float score = sf.getScore();
+ positionalMinScore = min(positionalMinScore, score);
+ positionalMaxScore = max(positionalMaxScore, score);
+ totalExtent += getFeatureLength(sf);
+ }
+ }
+
+ /**
+ * A helper method to return the minimum of two floats, where a non-NaN value
+ * is treated as 'less than' a NaN value (unlike Math.min which does the
+ * opposite)
*
- * @param featureGroup
- * @param nonPositional
+ * @param f1
+ * @param f2
*/
- protected void rebuildFeatureGroups(String featureGroup,
- boolean nonPositional)
+ protected static float min(float f1, float f2)
{
- if (nonPositional && nonPositionalFeatures != null)
+ if (Float.isNaN(f1))
{
- boolean found = false;
- for (SequenceFeature sf : nonPositionalFeatures)
- {
- String group = sf.getFeatureGroup();
- if (featureGroup == group
- || (featureGroup != null && featureGroup.equals(group)))
- {
- found = true;
- break;
- }
- }
- if (!found)
- {
- nonPositionalFeatureGroups.remove(featureGroup);
- }
+ return Float.isNaN(f2) ? f1 : f2;
+ }
+ else
+ {
+ return Float.isNaN(f2) ? f1 : Math.min(f1, f2);
+ }
+ }
+
+ /**
+ * A helper method to return the maximum of two floats, where a non-NaN value
+ * is treated as 'greater than' a NaN value (unlike Math.max which does the
+ * opposite)
+ *
+ * @param f1
+ * @param f2
+ */
+ protected static float max(float f1, float f2)
+ {
+ if (Float.isNaN(f1))
+ {
+ return Float.isNaN(f2) ? f1 : f2;
}
- else if (!findFeatureGroup(featureGroup))
+ else
{
- positionalFeatureGroups.remove(featureGroup);
+ return Float.isNaN(f2) ? f1 : Math.max(f1, f2);
}
}
return matched;
}
+
+ /**
+ * Answers the number of positional (or non-positional) features stored.
+ * Contact features count as 1.
+ *
+ * @param positional
+ * @return
+ */
+ public int getFeatureCount(boolean positional)
+ {
+ if (!positional)
+ {
+ return nonPositionalFeatures == null ? 0 : nonPositionalFeatures
+ .size();
+ }
+
+ int size = nonNestedFeatures.size();
+
+ if (contactFeatureStarts != null)
+ {
+ // note a contact feature (start/end) counts as one
+ size += contactFeatureStarts.size();
+ }
+
+ if (nestedFeatures != null)
+ {
+ size += nestedFeatures.size();
+ }
+
+ return 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
+ */
+ public int getTotalFeatureLength()
+ {
+ return totalExtent;
+ }
+
+ /**
+ * Answers the minimum score held for positional or non-positional features.
+ * This may be Float.NaN if there are no features, are none has a non-NaN
+ * score.
+ *
+ * @param positional
+ * @return
+ */
+ public float getMinimumScore(boolean positional)
+ {
+ return positional ? positionalMinScore : nonPositionalMinScore;
+ }
+
+ /**
+ * Answers the maximum score held for positional or non-positional features.
+ * This may be Float.NaN if there are no features, are none has a non-NaN
+ * score.
+ *
+ * @param positional
+ * @return
+ */
+ public float getMaximumScore(boolean positional)
+ {
+ return positional ? positionalMaxScore : nonPositionalMaxScore;
+ }
}
git://source.jalview.org / jalview.git / blobdiff