/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.Enumeration;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
+
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-
+/**
+ * Data model for one entry returned from an EMBL query, as marshalled by a
+ * Castor binding file
+ *
+ * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+ *
+ * @see embl_mapping.xml
+ */
public class EmblEntry
{
String accession;
String lastUpdated;
- Vector keywords;
-
- Vector refs;
+ Vector<String> keywords;
- Vector dbRefs;
+ Vector<DBRefEntry> dbRefs;
- Vector features;
+ Vector<EmblFeature> features;
EmblSequence sequence;
/**
* @return the dbRefs
*/
- public Vector getDbRefs()
+ public Vector<DBRefEntry> getDbRefs()
{
return dbRefs;
}
* @param dbRefs
* the dbRefs to set
*/
- public void setDbRefs(Vector dbRefs)
+ public void setDbRefs(Vector<DBRefEntry> dbRefs)
{
this.dbRefs = dbRefs;
}
/**
* @return the features
*/
- public Vector getFeatures()
+ public Vector<EmblFeature> getFeatures()
{
return features;
}
* @param features
* the features to set
*/
- public void setFeatures(Vector features)
+ public void setFeatures(Vector<EmblFeature> features)
{
this.features = features;
}
/**
* @return the keywords
*/
- public Vector getKeywords()
+ public Vector<String> getKeywords()
{
return keywords;
}
* @param keywords
* the keywords to set
*/
- public void setKeywords(Vector keywords)
+ public void setKeywords(Vector<String> keywords)
{
this.keywords = keywords;
}
}
/**
- * @return the refs
- */
- public Vector getRefs()
- {
- return refs;
- }
-
- /**
- * @param refs
- * the refs to set
- */
- public void setRefs(Vector refs)
- {
- this.refs = refs;
- }
-
- /**
* @return the releaseCreated
*/
public String getRCreated()
* @param releaseCreated
* the releaseCreated to set
*/
- public void setRcreated(String releaseCreated)
+ public void setRCreated(String releaseCreated)
{
this.rCreated = releaseCreated;
}
{ 1, dna.getLength() }, 1, 1));
// TODO: transform EMBL Database refs to canonical form
if (dbRefs != null)
+ {
for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
.addDBRef((DBRefEntry) i.next()))
+ {
;
+ }
+ }
}
try
{
{
for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
.addDBRef((DBRefEntry) dbr.next()))
+ {
;
+ }
}
}
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
.addDBRef((DBRefEntry) dbr.next()))
+ {
;
+ }
}
}
}
}
}
Sequence product = null;
+ DBRefEntry protEMBLCDS = null;
exon = adjustForPrStart(prstart, exon);
+ boolean noProteinDbref=true;
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
product = new Sequence(prid, prseq, 1, prseq.length());
- product
- .setDescription(((prname.length() == 0) ? "Protein Product from "
- + sourceDb
- : prname));
+ product.setDescription(((prname.length() == 0) ? "Protein Product from "
+ + sourceDb
+ : prname));
if (!noPeptide)
{
// Protein is also added to vector of sequences returned
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 == (1-prstart + dna.getSequence().length))
+ if (prseq.length() * 3 == (1 - prstart + dna.getSequence().length))
{
System.err
.println("Not allowing for additional stop codon at end of cDNA fragment... !");
map = new jalview.datamodel.Mapping(product, exon, new int[]
{ 1, prseq.length() }, 3, 1);
}
- if ((prseq.length() + 1) * 3 == (1-prstart + dna.getSequence().length))
+ if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
{
System.err
.println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
}
else
{
- // Trim the exon mapping if necessary - the given product may only be a fragment of a larger protein. (EMBL:AY043181 is an example)
-
-
+ // Trim the exon mapping if necessary - the given product may only be a
+ // fragment of a larger protein. (EMBL:AY043181 is an example)
+
if (isEmblCdna)
{
// TODO: Add a DbRef back to the parent EMBL sequence with the exon
else
{
// final product length trunctation check
-
- map = new jalview.datamodel.Mapping(product, adjustForProteinLength(prseq.length(),exon), new int[]
- { 1, prseq.length() }, 3, 1);
+
+ map = new jalview.datamodel.Mapping(product,
+ adjustForProteinLength(prseq.length(), exon), new int[]
+ { 1, prseq.length() }, 3, 1);
// reconstruct the EMBLCDS entry
- // TODO: this is only necessary when there codon annotation is complete (I think JBPNote)
+ // TODO: this is only necessary when there codon annotation is
+ // complete (I think JBPNote)
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, prseq.length() },
- new int[]
- { 1 + (prstart - 1),
- (prstart - 1) + 3 * prseq.length() }, 1, 3);
+ { 1, prseq.length() }, new int[]
+ { 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
// { 1 + (prstart - 1) * 3,
// 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
// { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
pcdnaref.setMap(new Mapping(mp));
if (product != null)
+ {
product.addDBRef(pcdnaref);
-
+ protEMBLCDS = new DBRefEntry(pcdnaref);
+ protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+ product.addDBRef(protEMBLCDS);
+
+ }
+
}
}
// add cds feature to dna seq - this may include the stop codon
sf.setEnd(exon[xint + 1]);
sf.setType(feature.getName());
sf.setFeatureGroup(sourceDb);
- sf.setDescription("Exon " + (1 + (int) (xint / 2))
+ sf.setDescription("Exon " + (1 + xint / 2)
+ " 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();
+ Enumeration kv = vals.keys();
while (kv.hasMoreElements())
{
Object key = kv.nextElement();
if (key != null)
+ {
sf.setValue(key.toString(), vals.get(key));
+ }
}
}
dna.addSequenceFeature(sf);
+ ref.getAccessionId());
}
}
+ noProteinDbref = false;
}
if (product != null)
{
- DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
- .getVersion(), ref.getAccessionId());
+ 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 = new DBRefEntry(sourceDb, getVersion(),
+ this.getAccession());
pref.setMap(pmap);
if (map.getTo() != null)
{
}
dna.addDBRef(ref);
}
+ if (noProteinDbref && product != null)
+ {
+ // add protein coding reference to dna sequence so xref matches
+ if (protEMBLCDS == null)
+ {
+ protEMBLCDS = new DBRefEntry();
+ protEMBLCDS.setAccessionId(prid);
+ protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+ protEMBLCDS.setVersion(getVersion());
+ protEMBLCDS
+ .setMap(new Mapping(product, map.getMap().getInverse()));
+ }
+ product.addDBRef(protEMBLCDS);
+
+ // Add converse mapping reference
+ if (map != null)
+ {
+ Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
+ .getInverse());
+ DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
+ ncMap.setMap(pmap);
+ if (map.getTo() != null)
+ {
+ dna.addDBRef(ncMap);
+ }
+ }
+ }
}
}
}
return exon;
}
+
/**
- * truncate the last exon interval to the prlength'th codon
+ * truncate the last exon interval to the prlength'th codon
+ *
* @param prlength
* @param exon
* @return new exon
private int[] adjustForProteinLength(int prlength, int[] exon)
{
- int origxon[], sxpos = -1,endxon=0,cdslength=prlength*3;
+ int origxon[], sxpos = -1, endxon = 0, cdslength = prlength * 3;
int sxstart, sxstop; // unnecessary variables used for debugging
// first adjust range for codon start attribute
- if (prlength >= 1 && exon!=null)
+ if (prlength >= 1 && exon != null)
{
origxon = new int[exon.length];
System.arraycopy(exon, 0, origxon, 0, exon.length);
int cdspos = 0;
- for (int x = 0; x < exon.length && sxpos==-1; x += 2)
+ for (int x = 0; x < exon.length && sxpos == -1; x += 2)
{
cdspos += exon[x + 1] - exon[x] + 1;
if (cdslength <= cdspos)
sxpos = x;
sxstart = exon[x];
sxstop = exon[x + 1];
- if (cdslength!=cdspos) {
- System.err.println("Truncating final exon interval on region by "+(cdspos-cdslength));
+ if (cdslength != cdspos)
+ {
+ System.err
+ .println("Truncating final exon interval on region by "
+ + (cdspos - cdslength));
}
// locate the new end boundary of final exon as endxon
- endxon = exon[x+1] - cdspos + cdslength;
+ endxon = exon[x + 1] - cdspos + cdslength;
break;
}
}
- if (sxpos !=-1)
+ if (sxpos != -1)
{
// and trim the exon interval set if necessary
- int[] nxon = new int[sxpos+2];
- System.arraycopy(exon, 0, nxon, 0, sxpos+2);
- nxon[sxpos+1] = endxon; // update the end boundary for the new exon set
+ int[] nxon = new int[sxpos + 2];
+ System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+ nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+ // set
exon = nxon;
}
}
git://source.jalview.org / jalview.git / blobdiff