*/
package jalview.datamodel;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.features.SequenceFeatures;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.MapList;
-import jalview.util.StringUtils;
-
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.StringUtils;
/**
*
getStart(), getEnd());
datasetSequence = dsseq;
+ updateDatasetFrom(dsseq, this);
+ }
+ return datasetSequence;
+ }
- dsseq.setDescription(description);
- // move features and database references onto dataset sequence
- dsseq.sequenceFeatureStore = sequenceFeatureStore;
- sequenceFeatureStore = null;
- dsseq.dbrefs = dbrefs;
- dbrefs = null;
- // TODO: search and replace any references to this sequence with
- // references to the dataset sequence in Mappings on dbref
- dsseq.pdbIds = pdbIds;
- pdbIds = null;
- datasetSequence.updatePDBIds();
- if (annotation != null)
+ /**
+ * used by createDatasetSequence - transfers dataset-only properties to dsseq
+ * from sequence2
+ *
+ * @param dsseq
+ * - newly created dataset sequenceI for sequence
+ * @param sequence2
+ * - sequence object that needs a dataset
+ */
+ protected void updateDatasetFrom(Sequence dsseq, Sequence sequence2)
+ {
+ dsseq.setDescription(description);
+ // move features and database references onto dataset sequence
+ dsseq.sequenceFeatureStore = sequenceFeatureStore;
+ sequenceFeatureStore = null;
+ dsseq.dbrefs = dbrefs;
+ dbrefs = null;
+ // TODO: search and replace any references to this sequence with
+ // references to the dataset sequence in Mappings on dbref
+ dsseq.pdbIds = pdbIds;
+ pdbIds = null;
+ datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ // annotation is cloned rather than moved, to preserve what's currently
+ // on the alignment
+ for (AlignmentAnnotation aa : annotation)
{
- // annotation is cloned rather than moved, to preserve what's currently
- // on the alignment
- for (AlignmentAnnotation aa : annotation)
- {
- AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
- _aa.sequenceRef = datasetSequence;
- _aa.adjustForAlignment(); // uses annotation's own record of
- // sequence-column mapping
- datasetSequence.addAlignmentAnnotation(_aa);
- }
+ AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+ _aa.sequenceRef = datasetSequence;
+ _aa.adjustForAlignment(); // uses annotation's own record of
+ // sequence-column mapping
+ datasetSequence.addAlignmentAnnotation(_aa);
}
}
- return datasetSequence;
}
/*
*/
package jalview.datamodel;
+import org.apache.logging.log4j.util.Strings;
+
public class SequenceDummy extends Sequence
{
public SequenceDummy(String sequenceId)
// required for correct behaviour of SequenceIdMatcher
return super.getDisplayId(false);
}
+
+ @Override
+ public int getStart()
+ {
+ return super.getStart();
+ }
+
+ @Override
+ public int getEnd()
+ {
+ if (datasetSequence == null && dummy && getFeatures() != null
+ && getFeatures().hasFeatures())
+ {
+ return getFeatures().getFeatureExtent().get(1);
+ }
+ return super.getEnd();
+ }
+
+ @Override
+ public char[] getSequence()
+ {
+ checkSeqData();
+ return super.getSequence();
+ }
+
+ @Override
+ public String getSequenceAsString(int start, int end)
+ {
+ checkSeqData();
+ return super.getSequenceAsString(start, end);
+ }
+
+ private void checkSeqData()
+ {
+ // materialise a dummy sequence of the correct length
+ if (datasetSequence == null && dummy && getFeatures() != null
+ && getFeatures().hasFeatures())
+ {
+ int endS = getEnd();
+ char[] sq = super.getSequence();
+ if (endS > sq.length)
+ {
+ setSequence(
+ String.valueOf(sq) + Strings.repeat("X", endS - sq.length));
+ }
+ }
+ }
+
+ @Override
+ public String getSequenceAsString()
+ {
+ checkSeqData();
+ return super.getSequenceAsString();
+ }
+
+ @Override
+ public SequenceI createDatasetSequence()
+ {
+ if (dummy && datasetSequence == null)
+ {
+ checkSeqData();
+ datasetSequence = new SequenceDummy(this.getName());
+ super.updateDatasetFrom((Sequence) datasetSequence, this);
+ super.setEnd(datasetSequence.getEnd());
+ }
+ return super.createDatasetSequence();
+ }
}
*/
int totalExtent;
+ /*
+ * range covered by positional features
+ */
+ int minExtent, maxExtent;
+
float positionalMinScore;
float positionalMaxScore;
positionalMaxScore = Float.NaN;
nonPositionalMinScore = Float.NaN;
nonPositionalMaxScore = Float.NaN;
+ minExtent = 0;
+ maxExtent = 0;
// we only construct nonPositionalFeatures, contactFeatures if we need to
}
if (!feature.isNonPositional())
{
positionalFeatureGroups.add(feature.getFeatureGroup());
+ if (minExtent == 0)
+ {
+ minExtent = feature.begin;
+ maxExtent = feature.end;
+ }
+ else
+ {
+ minExtent = Math.min(feature.begin, minExtent);
+ maxExtent = Math.max(feature.end, maxExtent);
+ }
}
if (feature.isContactFeature())
float score = sf.getScore();
positionalMinScore = min(positionalMinScore, score);
positionalMaxScore = max(positionalMaxScore, score);
+ if (totalExtent == 0)
+ {
+ minExtent = sf.begin;
+ maxExtent = sf.begin;
+ }
+ else
+ {
+ minExtent = Math.min(sf.begin, minExtent);
+ maxExtent = Math.max(sf.end, maxExtent);
+ }
totalExtent += getFeatureLength(sf);
}
}
}
return modified;
}
+
+ public int getBegin()
+ {
+ return minExtent;
+ }
+
+ public int getEnd()
+ {
+ return maxExtent;
+ }
}
package jalview.datamodel.features;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
* {@inheritDoc}
*/
@Override
+ public List<Integer> getFeatureExtent(String... type)
+ {
+ Integer from = 0, to = 0;
+
+ for (FeatureStore featureSet : varargToTypes(type))
+ {
+ if (from == 0)
+ {
+ from = featureSet.getBegin();
+ to = featureSet.getEnd();
+ }
+ else
+ {
+ from = Math.min(from, featureSet.getBegin());
+ to = Math.max(to, featureSet.getEnd());
+ }
+ }
+ return Arrays.asList(from, to);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
public List<SequenceFeature> getPositionalFeatures(String... type)
{
List<SequenceFeature> result = new ArrayList<>();
*/
package jalview.datamodel.features;
-import jalview.datamodel.SequenceFeature;
-
import java.util.List;
import java.util.Set;
+import jalview.datamodel.SequenceFeature;
+
public interface SequenceFeaturesI
{
* Deletes all positional and non-positional features
*/
void deleteAll();
+
+ /**
+ * @return lowest and highest positions for positional features in this store
+ */
+ List<Integer> getFeatureExtent(String... type);
}
git://source.jalview.org / jalview.git / commitdiff