+/*
+ * 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.ext.ensembl;
import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntologyFactory;
+import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyI;
+import java.util.ArrayList;
+import java.util.List;
+
import com.stevesoft.pat.Regex;
/**
}
/**
- * Answers true if the sequence feature type is 'exon' (or a subtype of exon
- * in the Sequence Ontology), and the Parent of the feature is the transcript
- * we are retrieving
+ * Answers a list of sequence features (if any) whose type is 'exon' (or a
+ * subtype of exon in the Sequence Ontology), and whose Parent is the
+ * transcript we are retrieving
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
- SequenceOntologyI.EXON))
+ List<SequenceFeature> result = new ArrayList<>();
+ List<SequenceFeature> sfs = seq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.EXON);
+ for (SequenceFeature sf : sfs)
{
String parentFeature = (String) sf.getValue(PARENT);
- if (("transcript:" + accId).equals(parentFeature))
+ if (accId.equals(parentFeature))
{
- return true;
+ result.add(sf);
}
}
- return false;
+
+ return result;
+ }
+
+ /**
+ * Parameter object_type=Transcaript added to ensure cdna and not peptide is
+ * returned (JAL-2529)
+ */
+ @Override
+ protected String getObjectType()
+ {
+ return OBJECT_TYPE_TRANSCRIPT;
}
}