*/
package jalview.datamodel.xdb.embl;
+import jalview.bin.Cache;
+import jalview.util.ArrayUtils;
+
+import java.util.Arrays;
import java.util.Vector;
/**
- * Data model for a <loctaion> child element of a <feature> read
+ * Data model for a <location> child element of a <feature> read
* from an EMBL query reply
*
* @see embl_mapping.xml
+ * @see http://www.insdc.org/files/feature_table.html#3.4.2
*/
public class EmblFeatureLocations
{
}
/**
- * Return all location elements concerning given accession as start-end pairs
- * TODO: pass back complement and 'less than or more than' range information
- * TODO: deal with multiple accessions
+ * Return all location elements concerning given accession as start-end pairs.
+ * If the CDS feature is on the forward strand, then start <= end, if on the
+ * reverse strand then start > end.
*
* @param accession
* the accession string for which locations are requested, or null
* for all locations
- * @return null or int[] { start1, end1, ... }
+ * @return int[] { start1, end1, ... }
*/
-
- public int[] getElementRanges(String accession)
+ int[] getElementRanges(String accession)
{
int sepos = 0;
int[] se = new int[locElements.size() * 2];
- if (locationType.equalsIgnoreCase("single")) // TODO: or "simple" ?
+ if ("single".equalsIgnoreCase(locationType)
+ || "join".equalsIgnoreCase(locationType))
{
for (EmblFeatureLocElement loce : locElements)
{
BasePosition bp[] = loce.getBasePositions();
if (bp.length == 2)
{
- se[sepos++] = Integer.parseInt(bp[0].getPos());
- se[sepos++] = Integer.parseInt(bp[1].getPos());
+ try
+ {
+ int start = Integer.parseInt(bp[0].getPos());
+ int end = Integer.parseInt(bp[1].getPos());
+ se[sepos++] = start;
+ se[sepos++] = end;
+ } catch (NumberFormatException e)
+ {
+ System.err
+ .println("format error in EMBL CDS location basePosition: "
+ + e.getMessage());
+ }
}
- }
- }
- }
- else if (locationType.equalsIgnoreCase("join"))
- {
- for (EmblFeatureLocElement loce : locElements)
- {
- if (accession == null || loce.accession != null
- && accession.equals(loce.accession))
- {
- BasePosition bp[] = loce.getBasePositions();
- if (bp.length == 2)
+ else
{
- se[sepos++] = Integer.parseInt(bp[0].getPos());
- se[sepos++] = Integer.parseInt(bp[1].getPos());
+ System.err
+ .println("format error in EMBL CDS location, basePosition count = "
+ + bp.length);
}
}
}
- return se;
}
else if (locationType != null)
{
- if (jalview.bin.Cache.log != null)
+ if (Cache.log != null)
{
- jalview.bin.Cache.log
- .error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+ Cache.log
+ .error("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
+ locationType + "'");
}
else
{
System.err
- .println("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+ .println("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
+ locationType + "'");
}
}
- // trim range if necessary.
- if (se != null && sepos != se.length)
+
+ if (sepos != se.length)
+ {
+ /*
+ * we failed to parse something - trim off null values
+ */
+ se = Arrays.copyOf(se, sepos);
+ }
+
+ /*
+ * If on the complement, reverse the ranges to [end, start, ...end1, start1].
+ * For an example of a joined complement, see (tRNA feature) CAGL0B00165r on
+ * http://www.ebi.ac.uk/ena/data/view/CR380948&display=xml
+ * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/CR380948/emblxml
+ */
+ if (locationComplement)
{
- int[] trimmed = new int[sepos];
- System.arraycopy(se, 0, trimmed, 0, sepos);
- se = trimmed;
+ ArrayUtils.reverseIntArray(se);
}
return se;
}