-public class EmblFeatureLocations {
- Vector locElements;
- String locationType;
- boolean locationComplement;
- /**
- * @return the locationComplement
- */
- public boolean isLocationComplement() {
- return locationComplement;
- }
- /**
- * @param locationComplement the locationComplement to set
- */
- public void setLocationComplement(boolean locationComplement) {
- this.locationComplement = locationComplement;
- }
- /**
- * @return the locationType
- */
- public String getLocationType() {
- return locationType;
- }
- /**
- * @param locationType the locationType to set
- */
- public void setLocationType(String locationType) {
- this.locationType = locationType;
- }
- /**
- * @return the locElements
- */
- public Vector getLocElements() {
- return locElements;
- }
- /**
- * @param locElements the locElements to set
- */
- public void setLocElements(Vector locElements) {
- this.locElements = locElements;
- }
- /**
- * Return all location elements as start-end pairs on referenced sequence
- * TODO: pass back complement and 'less than or more than' range information
- * @return int[] { start1, end1, ... }
- */
- public int[] getElementRanges() {
- if (locationType.equalsIgnoreCase("single")) {
- int[] se = new int[locElements.size()*2];
- int sepos=0;
- for (Iterator le=locElements.iterator();le.hasNext();) {
- EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();
- BasePosition bp[] = loce.getBasePositions();
- if (bp.length==2) {
- se[sepos++] = Integer.parseInt(bp[0].getPos());
- se[sepos++] = Integer.parseInt(bp[1].getPos());
- }
- }
- return se;
- }
- if (locationType.equalsIgnoreCase("join")) {
- int[] se = new int[locElements.size()*2];
- int sepos=0;
- for (Iterator le=locElements.iterator();le.hasNext();) {
- EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();
- BasePosition bp[] = loce.getBasePositions();
- if (bp.length==2) {
- se[sepos++] = Integer.parseInt(bp[0].getPos());
- se[sepos++] = Integer.parseInt(bp[1].getPos());
- }
- }
- return se;
+/**
+ * Data model for a <loctaion> child element of a <feature> read
+ * from an EMBL query reply
+ *
+ * @see embl_mapping.xml
+ */
+public class EmblFeatureLocations
+{
+ Vector<EmblFeatureLocElement> locElements;
+
+ String locationType;
+
+ boolean locationComplement;
+
+ /**
+ * @return the locationComplement
+ */
+ public boolean isLocationComplement()
+ {
+ return locationComplement;
+ }
+
+ /**
+ * @param locationComplement
+ * the locationComplement to set
+ */
+ public void setLocationComplement(boolean locationComplement)
+ {
+ this.locationComplement = locationComplement;
+ }
+
+ /**
+ * @return the locationType
+ */
+ public String getLocationType()
+ {
+ return locationType;
+ }
+
+ /**
+ * @param locationType
+ * the locationType to set
+ */
+ public void setLocationType(String locationType)
+ {
+ this.locationType = locationType;
+ }
+
+ /**
+ * @return the locElements
+ */
+ public Vector<EmblFeatureLocElement> getLocElements()
+ {
+ return locElements;
+ }
+
+ /**
+ * @param locElements
+ * the locElements to set
+ */
+ public void setLocElements(Vector<EmblFeatureLocElement> locElements)
+ {
+ this.locElements = locElements;
+ }
+
+ /**
+ * Return all location elements as start-end pairs (without accessions) TODO:
+ * pass back complement and 'less than or more than' range information Note:
+ * do not use this since it throws away any accessionIds associated with each
+ * location!
+ *
+ * @return int[] { start1, end1, ... }
+ */
+ public int[] getElementRanges()
+ {
+ return getElementRanges(null);
+ }
+
+ /**
+ * 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
+ *
+ * @param accession
+ * the accession string for which locations are requested, or null
+ * for all locations
+ * @return null or int[] { start1, end1, ... }
+ */
+
+ public int[] getElementRanges(String accession)
+ {
+ int sepos = 0;
+ int[] se = new int[locElements.size() * 2];
+ if (locationType.equalsIgnoreCase("single")) // TODO: or "simple" ?
+ {
+ for (EmblFeatureLocElement loce : locElements)
+ {
+ if (accession == null || loce.accession != null
+ && accession.equals(loce.accession))
+ {
+ BasePosition bp[] = loce.getBasePositions();
+ if (bp.length == 2)
+ {
+ se[sepos++] = Integer.parseInt(bp[0].getPos());
+ se[sepos++] = Integer.parseInt(bp[1].getPos());
+ }