+/*
+ * 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.datamodel.xdb.embl;
-import java.util.Iterator;
+import jalview.bin.Cache;
+import jalview.util.ArrayUtils;
+
+import java.util.Arrays;
import java.util.Vector;
-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;
+/**
+ * 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
+{
+ 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.
+ * 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 int[] { start1, end1, ... }
+ */
+ int[] getElementRanges(String accession)
+ {
+ int sepos = 0;
+ int[] se = new int[locElements.size() * 2];
+ if ("single".equalsIgnoreCase(locationType)
+ || "join".equalsIgnoreCase(locationType))
+ {
+ for (EmblFeatureLocElement loce : locElements)
+ {
+ if (accession == null || loce.accession != null
+ && accession.equals(loce.accession))
+ {
+ BasePosition bp[] = loce.getBasePositions();
+ if (bp.length == 2)
+ {
+ 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
+ {
+ System.err
+ .println("format error in EMBL CDS location, basePosition count = "
+ + bp.length);
+ }
+ }
+ }
}
- /**
- * @return the locElements
- */
- public Vector getLocElements() {
- return locElements;
+ else if (locationType != null)
+ {
+ if (Cache.log != null)
+ {
+ Cache.log
+ .error("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
+ + locationType + "'");
+ }
+ else
+ {
+ System.err
+ .println("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
+ + locationType + "'");
+ }
}
- /**
- * @param locElements the locElements to set
- */
- public void setLocElements(Vector locElements) {
- this.locElements = locElements;
+
+ if (sepos != se.length)
+ {
+ /*
+ * we failed to parse something - trim off null values
+ */
+ se = Arrays.copyOf(se, sepos);
}
- /**
- * 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, ... }
+
+ /*
+ * 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
*/
- 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;
- }
- if (locationType!=null)
- {
- jalview.bin.Cache.log.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
- }
- return null;
+ if (locationComplement)
+ {
+ ArrayUtils.reverseIntArray(se);
}
-}
\ No newline at end of file
+ return se;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff