replace hashedmap, was a typo
@@ -18,7 +18,6 @@ package org.opencb.cellbase.lib.builders;
import com.fasterxml.jackson.databind.ObjectMapper;
import htsjdk.tribble.readers.TabixReader;
-import org.apache.commons.collections.map.HashedMap;
import org.opencb.biodata.formats.feature.gff.Gff2;
import org.opencb.biodata.formats.feature.gtf.Gtf;
import org.opencb.biodata.formats.feature.gtf.io.GtfReader;
@@ -573,7 +572,7 @@ public class GeneBuilder extends CellBaseBuilder {
}
private Map<String, Map<String, Map<String, Object>>> loadGTFMap(GtfReader gtfReader) throws FileFormatException {
- Map<String, Map<String, Map<String, Object>>> gtfMap = new HashedMap();
+ Map<String, Map<String, Map<String, Object>>> gtfMap = new HashMap();
Gtf gtf;
while ((gtf = gtfReader.read()) != null) {
if (gtf.getFeature().equals("gene") || gtf.getFeature().equals("transcript")
@@ -588,7 +587,7 @@ public class GeneBuilder extends CellBaseBuilder {
if (gtfMap.containsKey(geneId)) {
gtfMapGeneEntry = gtfMap.get(geneId);
} else {
- gtfMapGeneEntry = new HashedMap();
+ gtfMapGeneEntry = new HashMap();
gtfMap.put(geneId, gtfMapGeneEntry);
}
@@ -598,7 +597,7 @@ public class GeneBuilder extends CellBaseBuilder {
if (gtfMapGeneEntry.containsKey(transcriptId)) {
gtfMapTranscriptEntry = gtfMapGeneEntry.get(transcriptId);
} else {
- gtfMapTranscriptEntry = new HashedMap();
+ gtfMapTranscriptEntry = new HashMap();
gtfMapGeneEntry.put(transcriptId, gtfMapTranscriptEntry);
}
