package jalview.datamodel;
+import java.util.Vector;
+
import jalview.util.MapList;
-public class Mapping {
+public class Mapping
+{
/**
- * Contains the
- * start-end pairs mapping from
- * the associated sequence to the
- * sequence in the database
- * coordinate system
- * it also takes care of step difference between coordinate systems
+ * Contains the start-end pairs mapping from the associated sequence to the
+ * sequence in the database coordinate system it also takes care of step
+ * difference between coordinate systems
*/
- MapList map=null;
+ MapList map = null;
+
/**
* The seuqence that map maps the associated seuqence to (if any).
*/
- SequenceI to=null;
- public Mapping(MapList map) {
+ SequenceI to = null;
+
+ public Mapping(MapList map)
+ {
super();
this.map = map;
}
- public Mapping(SequenceI to, MapList map) {
+
+ public Mapping(SequenceI to, MapList map)
+ {
this(map);
this.to = to;
}
+
/**
* create a new mapping from
- * @param to the sequence being mapped
- * @param exon int[] {start,end,start,end} series on associated sequence
- * @param is int[] {start,end,...} ranges on the reference frame being mapped to
- * @param i step size on associated sequence
- * @param j step size on mapped frame
+ *
+ * @param to
+ * the sequence being mapped
+ * @param exon
+ * int[] {start,end,start,end} series on associated sequence
+ * @param is
+ * int[] {start,end,...} ranges on the reference frame being mapped
+ * to
+ * @param i
+ * step size on associated sequence
+ * @param j
+ * step size on mapped frame
*/
public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)
{
this(to, new MapList(exon, is, i, j));
}
+
/**
- * create a duplicate (and independent) mapping object with
- * the same reference to any SequenceI being mapped to.
+ * create a duplicate (and independent) mapping object with the same reference
+ * to any SequenceI being mapped to.
+ *
* @param map2
*/
public Mapping(Mapping map2)
{
- if (map2!=this && map2!=null) {
- if (map2.map!=null)
+ if (map2 != this && map2 != null)
+ {
+ if (map2.map != null)
{
- map=new MapList(map2.map);
+ map = new MapList(map2.map);
}
to = map2.to;
}
}
+
/**
* @return the map
*/
- public MapList getMap() {
+ public MapList getMap()
+ {
return map;
}
/**
- * @param map the map to set
+ * @param map
+ * the map to set
*/
- public void setMap(MapList map) {
+ public void setMap(MapList map)
+ {
this.map = map;
}
+
/**
* Equals that compares both the to references and MapList mappings.
+ *
* @param other
* @return
*/
- public boolean equals(Mapping other) {
- if (other==null)
+ public boolean equals(Mapping other)
+ {
+ if (other == null)
return false;
- if (other==this)
+ if (other == this)
return true;
- if (other.to!=to)
+ if (other.to != to)
return false;
- if ((map!=null && other.map==null) || (map==null && other.map!=null))
+ if ((map != null && other.map == null)
+ || (map == null && other.map != null))
return false;
if (map.equals(other.map))
return true;
return false;
}
+
/**
- * get the 'initial' position in the associated
- * sequence for a position in the mapped reference frame
+ * get the 'initial' position in the associated sequence for a position in the
+ * mapped reference frame
+ *
* @param mpos
* @return
*/
public int getPosition(int mpos)
{
- if (map!=null) {
+ if (map != null)
+ {
int[] mp = map.shiftTo(mpos);
- if (mp!=null)
+ if (mp != null)
{
return mp[0];
}
}
return mpos;
}
+
/**
- * gets boundary in direction of mapping
- * @param position in mapped reference frame
- * @return int{start, end} positions in associated sequence (in direction of mapped word)
+ * gets boundary in direction of mapping
+ *
+ * @param position
+ * in mapped reference frame
+ * @return int{start, end} positions in associated sequence (in direction of
+ * mapped word)
*/
- public int[] getWord(int mpos) {
- if (map!=null) {
+ public int[] getWord(int mpos)
+ {
+ if (map != null)
+ {
return map.getToWord(mpos);
}
return null;
}
+
/**
* width of mapped unit in associated sequence
- *
+ *
*/
- public int getWidth() {
- if (map!=null) {
+ public int getWidth()
+ {
+ if (map != null)
+ {
return map.getFromRatio();
}
return 1;
/**
* width of unit in mapped reference frame
+ *
* @return
*/
- public int getMappedWidth() {
- if (map!=null) {
+ public int getMappedWidth()
+ {
+ if (map != null)
+ {
return map.getToRatio();
}
return 1;
}
+
/**
- * get mapped position in the associated
- * reference frame for position pos in the
- * associated sequence.
+ * get mapped position in the associated reference frame for position pos in
+ * the associated sequence.
+ *
* @param pos
* @return
*/
- public int getMappedPosition(int pos) {
- if (map!=null) {
+ public int getMappedPosition(int pos)
+ {
+ if (map != null)
+ {
int[] mp = map.shiftFrom(pos);
- if (mp!=null)
+ if (mp != null)
{
return mp[0];
}
}
return pos;
}
- public int[] getMappedWord(int pos) {
- if (map!=null) {
+
+ public int[] getMappedWord(int pos)
+ {
+ if (map != null)
+ {
int[] mp = map.shiftFrom(pos);
- if (mp!=null)
+ if (mp != null)
{
- return new int[] { mp[0], mp[0]+mp[2]*(map.getToRatio()-1)};
+ return new int[]
+ { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
}
}
return null;
}
+
/**
- * locates the region of feature f in the associated sequence's reference frame
+ * locates the region of feature f in the associated sequence's reference
+ * frame
+ *
* @param f
* @return one or more features corresponding to f
*/
public SequenceFeature[] locateFeature(SequenceFeature f)
{
- if (true) { // f.getBegin()!=f.getEnd()) {
- if (map!=null) {
+ if (true)
+ { // f.getBegin()!=f.getEnd()) {
+ if (map != null)
+ {
int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
- SequenceFeature[] vf = new SequenceFeature[frange.length/2];
- for (int i=0,v=0;i<frange.length;i+=2,v++) {
+ SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
+ for (int i = 0, v = 0; i < frange.length; i += 2, v++)
+ {
vf[v] = new SequenceFeature(f);
vf[v].setBegin(frange[i]);
- vf[v].setEnd(frange[i+1]);
- if (frange.length>2)
- vf[v].setDescription(f.getDescription() +"\nPart "+v);
+ vf[v].setEnd(frange[i + 1]);
+ if (frange.length > 2)
+ vf[v].setDescription(f.getDescription() + "\nPart " + v);
}
return vf;
}
}
- if (false) //else
+ if (false) // else
{
int[] word = getWord(f.getBegin());
- if (word[0]<word[1])
+ if (word[0] < word[1])
{
f.setBegin(word[0]);
- } else {
+ }
+ else
+ {
f.setBegin(word[1]);
}
word = getWord(f.getEnd());
- if (word[0]>word[1])
+ if (word[0] > word[1])
{
f.setEnd(word[0]);
- } else {
+ }
+ else
+ {
f.setEnd(word[1]);
}
}
// give up and just return the feature.
- return new SequenceFeature[] { f };
+ return new SequenceFeature[]
+ { f };
}
- /**
- * return a series of contigs on the associated sequence corresponding to
- * the from,to interval on the mapped reference frame
+ /**
+ * return a series of contigs on the associated sequence corresponding to the
+ * from,to interval on the mapped reference frame
+ *
* @param from
* @param to
- * @return
+ * @return int[] { from_i, to_i for i=1 to n contiguous regions in the
+ * associated sequence}
*/
- public int[] locateRange(int from, int to) {
- //TODO
- return null;
+ public int[] locateRange(int from, int to)
+ {
+ if (map != null)
+ {
+ if (from <= to)
+ {
+ from = (map.getToLowest() < from) ? from : map.getToLowest();
+ to = (map.getToHighest() > to) ? to : map.getToHighest();
+ if (from > to)
+ return null;
+ }
+ else
+ {
+ from = (map.getToHighest() > from) ? from : map.getToHighest();
+ to = (map.getToLowest() < to) ? to : map.getToLowest();
+ if (from < to)
+ return null;
+ }
+ return map.locateInFrom(from, to);
+ }
+ return new int[]
+ { from, to };
}
+
/**
- * return a series of contigs on the mapped reference frame corresponding to
- * the from,to interval on the associated sequence
+ * return a series of mapped contigs mapped from a range on the associated
+ * sequence
+ *
* @param from
* @param to
* @return
*/
- public int[] locateMappedRange(int from, int to) {
- //TODO
- return null;
+ public int[] locateMappedRange(int from, int to)
+ {
+ if (map != null)
+ {
+
+ if (from <= to)
+ {
+ from = (map.getFromLowest() < from) ? from : map.getFromLowest();
+ to = (map.getFromHighest() > to) ? to : map.getFromHighest();
+ if (from > to)
+ return null;
+ }
+ else
+ {
+ from = (map.getFromHighest() > from) ? from : map.getFromHighest();
+ to = (map.getFromLowest() < to) ? to : map.getFromLowest();
+ if (from < to)
+ return null;
+ }
+ return map.locateInTo(from, to);
+ }
+ return new int[]
+ { from, to };
+ }
+
+ /**
+ * return a new mapping object with a maplist modifed to only map the visible
+ * regions defined by viscontigs.
+ *
+ * @param viscontigs
+ * @return
+ */
+ public Mapping intersectVisContigs(int[] viscontigs)
+ {
+ Mapping copy = new Mapping(this);
+ if (map != null)
+ {
+ int vpos = 0;
+ int apos = 0;
+ Vector toRange = new Vector();
+ Vector fromRange = new Vector();
+ for (int vc = 0; vc < viscontigs.length; vc += 2)
+ {
+ // find a mapped range in this visible region
+ int[] mpr = locateMappedRange(1+viscontigs[vc], viscontigs[vc + 1]-1);
+ if (mpr != null)
+ {
+ for (int m = 0; m < mpr.length; m += 2)
+ {
+ toRange.addElement(new int[]
+ { mpr[m], mpr[m + 1] });
+ int[] xpos = locateRange(mpr[m], mpr[m + 1]);
+ for (int x = 0; x < xpos.length; x += 2)
+ {
+ fromRange.addElement(new int[]
+ { xpos[x], xpos[x + 1] });
+ }
+ }
+ }
+ }
+ int[] from = new int[fromRange.size()*2];
+ int[] to = new int[toRange.size()*2];
+ int[] r;
+ for (int f=0,fSize=fromRange.size(); f<fSize; f++)
+ {
+ r = (int[]) fromRange.elementAt(f);
+ from[f*2] = r[0];
+ from[f*2+1] = r[1];
+ }
+ for (int f=0,fSize=toRange.size(); f<fSize; f++)
+ {
+ r = (int[]) toRange.elementAt(f);
+ to[f*2] = r[0];
+ to[f*2+1] = r[1];
+ }
+ copy.setMap(new MapList(from, to, map.getFromRatio(), map.getToRatio()));
+ }
+ return copy;
+ }
+ public static void main(String[] args)
+ {
+ /**
+ * trite test of the intersectVisContigs method
+ * for a simple DNA -> Protein exon map and a range of visContigs
+ */
+ MapList fk = new MapList(new int[] { 1,6,8,13,15,23}, new int[] { 1,7}, 3, 1);
+ Mapping m = new Mapping(fk);
+ Mapping m_1 = m.intersectVisContigs(new int[] {fk.getFromLowest(), fk.getFromHighest()});
+ Mapping m_2 = m.intersectVisContigs(new int[] {1,7,11,20});
+ System.out.println(""+m_1.map.getFromRanges());
+
+
+ }
+ /**
+ * get the sequence being mapped to - if any
+ * @return null or a dataset sequence
+ */
+ public SequenceI getTo()
+ {
+ return to;
+ }
+ /**
+ * set the dataset sequence being mapped to if any
+ * @param tto
+ */
+ public void setTo(SequenceI tto)
+ {
+ to = tto;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#finalize()
+ */
+ protected void finalize() throws Throwable
+ {
+ map = null;
+ to = null;
+ super.finalize();
}
+
}
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
{
for (Iterator i = features.iterator(); i.hasNext();)
{
- boolean nextFeature=false;
EmblFeature feature = (EmblFeature) i.next();
if (!noNa)
{
;
}
}
- if (FeatureProperties.isCodingFeature(DBRefSource.EMBL, "CDS"))
+ if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
- // extract coding region(s)
- jalview.datamodel.Mapping map = null;
- int[] exon = null;
- if (feature.locations != null && feature.locations.size() > 0)
- {
- for (Enumeration locs = feature.locations.elements(); locs
- .hasMoreElements();)
- {
- EmblFeatureLocations loc = (EmblFeatureLocations) locs
- .nextElement();
- int[] se = loc.getElementRanges(accession);
- if (exon == null)
- {
- exon = se;
- }
- else
- {
- int[] t = new int[exon.length + se.length];
- System.arraycopy(exon, 0, t, 0, exon.length);
- System.arraycopy(se, 0, t, exon.length, se.length);
- exon = t;
- }
- }
- }
- String prseq = null;
- String prname = new String();
- String prid = null;
- Hashtable vals = new Hashtable();
- int prstart = 1;
- // get qualifiers
- if (feature.getQualifiers() != null
- && feature.getQualifiers().size() > 0)
- {
- for (Iterator quals = feature.getQualifiers().iterator(); quals
- .hasNext();)
- {
- Qualifier q = (Qualifier) quals.next();
- if (q.getName().equals("translation"))
- {
- prseq = q.getValues()[0];
- }
- else if (q.getName().equals("protein_id"))
- {
- prid = q.getValues()[0];
- }
- else if (q.getName().equals("codon_start"))
- {
- prstart = Integer.parseInt(q.getValues()[0]);
- }
- else if (q.getName().equals("product"))
- {
- prname = q.getValues()[0];
- }
- else
- {
- // throw anything else into the additional properties hash
- vals.put(q.getName(), q.getValues().toString());
- }
- }
- }
- Sequence product = null;
- if (prseq != null && prname != null && prid != null)
- {
- // extract proteins.
- if (!noPeptide)
- {
- product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid
- + "|" + prname, prseq, prstart, prstart
- + prseq.length() - 1);
- product.setDescription("Protein Product from " + sourceDb);
- seqs.add(product);
- }
- // we have everything - create the mapping and perhaps the protein
- // sequence
- map = new jalview.datamodel.Mapping(product, exon, new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
- // add cds feature to dna seq - this may include the stop codon
- for (int xint = 0; xint < exon.length; xint += 2)
- {
- SequenceFeature sf = new SequenceFeature();
- sf.setBegin(exon[xint]);
- sf.setEnd(exon[xint + 1]);
- sf.setType(feature.getName());
- sf.setFeatureGroup(jalview.datamodel.DBRefSource.EMBL);
- sf.setDescription("Exon " + (1 + xint) + " for protein '"
- + prname + "' EMBLCDS:" + prid);
- sf.setValue(FeatureProperties.EXONPOS, new Integer(1+xint));
- sf.setValue(FeatureProperties.EXONPRODUCT, prname);
- if (vals != null && vals.size() > 0)
- {
- Enumeration kv = vals.elements();
- while (kv.hasMoreElements())
- {
- Object key = kv.nextElement();
- if (key != null)
- sf.setValue(key.toString(), vals.get(key));
- }
- }
- dna.addSequenceFeature(sf);
- }
- }
- // add dbRefs to sequence
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
- {
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
- {
- DBRefEntry ref = (DBRefEntry) dbr.next();
- ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
- .getSource()));
- // Hard code the kind of protein product accessions that EMBL cite
- if (ref.getSource().equals(
- jalview.datamodel.DBRefSource.UNIPROT))
- {
- ref.setMap(map);
- }
- if (product != null)
- {
- DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
- .getVersion(), ref.getAccessionId());
- pref.setMap(null); // reference is direct
- }
- dna.addDBRef(ref);
- }
- }
-
+ parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide);
}
else
{
}
}
}
- } catch (Exception e)
+ }
+ catch (Exception e)
{
System.err.println("EMBL Record Features parsing error!");
- System.err.println("Please report the following to help@jalview.org :");
- System.err.println("EMBL Record "+accession);
- System.err.println("Resulted in exception: "+e.getMessage());
+ System.err
+ .println("Please report the following to help@jalview.org :");
+ System.err.println("EMBL Record " + accession);
+ System.err.println("Resulted in exception: " + e.getMessage());
e.printStackTrace(System.err);
}
- if (!noNa && dna!=null)
+ if (!noNa && dna != null)
{
seqs.add(dna);
}
}
return sqs;
}
+
+ /**
+ * attempt to extract coding region and product from a feature and properly decorate it with annotations.
+ * @param feature coding feature
+ * @param sourceDb source database for the EMBLXML
+ * @param seqs place where sequences go
+ * @param dna parent dna sequence for this record
+ * @param noPeptide flag for generation of Peptide sequence objects
+ */
+ private void parseCodingFeature(EmblFeature feature, String sourceDb, Vector seqs, Sequence dna, boolean noPeptide)
+ {
+ boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
+ // extract coding region(s)
+ jalview.datamodel.Mapping map = null;
+ int[] exon = null;
+ if (feature.locations != null && feature.locations.size() > 0)
+ {
+ for (Enumeration locs = feature.locations.elements(); locs
+ .hasMoreElements();)
+ {
+ EmblFeatureLocations loc = (EmblFeatureLocations) locs
+ .nextElement();
+ int[] se = loc.getElementRanges(accession);
+ if (exon == null)
+ {
+ exon = se;
+ }
+ else
+ {
+ int[] t = new int[exon.length + se.length];
+ System.arraycopy(exon, 0, t, 0, exon.length);
+ System.arraycopy(se, 0, t, exon.length, se.length);
+ exon = t;
+ }
+ }
+ }
+ String prseq = null;
+ String prname = new String();
+ String prid = null;
+ Hashtable vals = new Hashtable();
+ int prstart = 1;
+ // get qualifiers
+ if (feature.getQualifiers() != null
+ && feature.getQualifiers().size() > 0)
+ {
+ for (Iterator quals = feature.getQualifiers().iterator(); quals
+ .hasNext();)
+ {
+ Qualifier q = (Qualifier) quals.next();
+ if (q.getName().equals("translation"))
+ {
+ StringBuffer prsq = new StringBuffer(q.getValues()[0]);
+ int p = prsq.indexOf(" ");
+ while (p > -1)
+ {
+ prsq.deleteCharAt(p);
+ p = prsq.indexOf(" ", p);
+ }
+ prseq = prsq.toString();
+ prsq = null;
+
+ }
+ else if (q.getName().equals("protein_id"))
+ {
+ prid = q.getValues()[0];
+ }
+ else if (q.getName().equals("codon_start"))
+ {
+ prstart = Integer.parseInt(q.getValues()[0]);
+ }
+ else if (q.getName().equals("product"))
+ {
+ prname = q.getValues()[0];
+ }
+ else
+ {
+ // throw anything else into the additional properties hash
+ vals.put(q.getName(), q.getValues().toString());
+ }
+ }
+ }
+ Sequence product = null;
+ if (prseq != null && prname != null && prid != null)
+ {
+ // extract proteins.
+ product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid
+ +((prname.length()==0) ? "" : " " + prname), prseq, prstart, prstart
+ + prseq.length() - 1);
+ product.setDescription("Protein Product from " + sourceDb);
+
+ if (!noPeptide)
+ {
+ // Protein is also added to vector of sequences returned
+ seqs.add(product);
+ }
+ // we have everything - create the mapping and perhaps the protein
+ // sequence
+ if (exon == null || exon.length == 0)
+ {
+ System.err
+ .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ + sourceDb + ":" + getAccession() + ")");
+ if (prseq.length() * 3 == dna.getSequence().length)
+ {
+ // this might occur for CDS sequences where no features are
+ // marked.
+ exon = new int[]
+ { dna.getStart(), dna.getEnd() };
+ map = new jalview.datamodel.Mapping(product, exon,
+ new int[]
+ { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ }
+ if ((prseq.length() + 1) * 3 == dna.getSequence().length)
+ {
+ exon = new int[]
+ { dna.getStart(), dna.getEnd() - 3 };
+ map = new jalview.datamodel.Mapping(product, exon,
+ new int[]
+ { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ }
+ }
+ else
+ {
+ if (isEmblCdna)
+ {
+ // TODO: Add a DbRef back to the parent EMBL sequence with the exon
+ // map
+
+ // make a new feature annotating the coding contig
+ }
+ else
+ {
+ map = new jalview.datamodel.Mapping(product, exon,
+ new int[]
+ { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ // reconstruct the EMBLCDS entry
+ DBRefEntry pcdnaref = new DBRefEntry();
+ pcdnaref.setAccessionId(prid);
+ pcdnaref.setSource(DBRefSource.EMBLCDS);
+ pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
+ jalview.util.MapList mp = new jalview.util.MapList(new int[]
+ { 1+(prstart-1)*3, 1+(prstart-1)*3 + (prseq.length()-1)*3 }, new int[] { prstart, prstart+prseq.length() - 1 }, 3, 1);
+ pcdnaref.setMap(new Mapping(mp));
+ if (product!=null)
+ product.addDBRef(pcdnaref);
+
+ }
+ }
+ // add cds feature to dna seq - this may include the stop codon
+ for (int xint = 0; exon != null && xint < exon.length; xint += 2)
+ {
+ SequenceFeature sf = new SequenceFeature();
+ sf.setBegin(exon[xint]);
+ sf.setEnd(exon[xint + 1]);
+ sf.setType(feature.getName());
+ sf.setFeatureGroup(sourceDb);
+ sf.setDescription("Exon " + (1 + xint) + " for protein '"
+ + prname + "' EMBLCDS:" + prid);
+ sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
+ sf.setValue(FeatureProperties.EXONPRODUCT, prname);
+ if (vals != null && vals.size() > 0)
+ {
+ Enumeration kv = vals.elements();
+ while (kv.hasMoreElements())
+ {
+ Object key = kv.nextElement();
+ if (key != null)
+ sf.setValue(key.toString(), vals.get(key));
+ }
+ }
+ dna.addSequenceFeature(sf);
+ }
+ }
+ // add dbRefs to sequence
+ if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ {
+ for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+ {
+ DBRefEntry ref = (DBRefEntry) dbr.next();
+ ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
+ .getSource()));
+ // Hard code the kind of protein product accessions that EMBL cite
+ if (ref.getSource().equals(
+ jalview.datamodel.DBRefSource.UNIPROT))
+ {
+ ref.setMap(map);
+ /*if (map.getTo()!=null)
+ {
+ map.getTo().setName(map.getTo().getName()+"|"+ref.getSource()+"|"+ref.getAccessionId());
+ }*/
+ }
+ if (product != null)
+ {
+ DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
+ .getVersion(), ref.getAccessionId());
+ pref.setMap(null); // reference is direct
+ product.addDBRef(pref);
+ // Add converse mapping reference
+ if (map != null)
+ {
+ Mapping pmap = new Mapping(dna, map.getMap().getInverse());
+ pref = new DBRefEntry(sourceDb, getVersion(), this
+ .getAccession());
+ pref.setMap(pmap);
+ if (map.getTo()!=null)
+ {
+ map.getTo().addDBRef(pref);
+ }
+ }
+ }
+ dna.addDBRef(ref);
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / commitdiff