import java.util.Iterator;
import java.util.Vector;
-public class EmblEntry {
+public class EmblEntry
+{
String accession;
+
String version;
+
String taxDivision;
+
String desc;
+
String rCreated;
+
String rLastUpdated;
+
String lastUpdated;
+
Vector keywords;
+
Vector refs;
+
Vector dbRefs;
+
Vector features;
+
EmblSequence sequence;
+
/**
* @return the accession
*/
- public String getAccession() {
+ public String getAccession()
+ {
return accession;
}
+
/**
- * @param accession the accession to set
+ * @param accession
+ * the accession to set
*/
- public void setAccession(String accession) {
+ public void setAccession(String accession)
+ {
this.accession = accession;
}
+
/**
* @return the dbRefs
*/
- public Vector getDbRefs() {
+ public Vector getDbRefs()
+ {
return dbRefs;
}
+
/**
- * @param dbRefs the dbRefs to set
+ * @param dbRefs
+ * the dbRefs to set
*/
- public void setDbRefs(Vector dbRefs) {
+ public void setDbRefs(Vector dbRefs)
+ {
this.dbRefs = dbRefs;
}
+
/**
* @return the desc
*/
- public String getDesc() {
+ public String getDesc()
+ {
return desc;
}
+
/**
- * @param desc the desc to set
+ * @param desc
+ * the desc to set
*/
- public void setDesc(String desc) {
+ public void setDesc(String desc)
+ {
this.desc = desc;
}
+
/**
* @return the features
*/
- public Vector getFeatures() {
+ public Vector getFeatures()
+ {
return features;
}
+
/**
- * @param features the features to set
+ * @param features
+ * the features to set
*/
- public void setFeatures(Vector features) {
+ public void setFeatures(Vector features)
+ {
this.features = features;
}
+
/**
* @return the keywords
*/
- public Vector getKeywords() {
+ public Vector getKeywords()
+ {
return keywords;
}
+
/**
- * @param keywords the keywords to set
+ * @param keywords
+ * the keywords to set
*/
- public void setKeywords(Vector keywords) {
+ public void setKeywords(Vector keywords)
+ {
this.keywords = keywords;
}
+
/**
* @return the lastUpdated
*/
- public String getLastUpdated() {
+ public String getLastUpdated()
+ {
return lastUpdated;
}
+
/**
- * @param lastUpdated the lastUpdated to set
+ * @param lastUpdated
+ * the lastUpdated to set
*/
- public void setLastUpdated(String lastUpdated) {
+ public void setLastUpdated(String lastUpdated)
+ {
this.lastUpdated = lastUpdated;
}
+
/**
* @return the refs
*/
- public Vector getRefs() {
+ public Vector getRefs()
+ {
return refs;
}
+
/**
- * @param refs the refs to set
+ * @param refs
+ * the refs to set
*/
- public void setRefs(Vector refs) {
+ public void setRefs(Vector refs)
+ {
this.refs = refs;
}
+
/**
* @return the releaseCreated
*/
- public String getRCreated() {
+ public String getRCreated()
+ {
return rCreated;
}
+
/**
- * @param releaseCreated the releaseCreated to set
+ * @param releaseCreated
+ * the releaseCreated to set
*/
- public void setRcreated(String releaseCreated) {
+ public void setRcreated(String releaseCreated)
+ {
this.rCreated = releaseCreated;
}
+
/**
* @return the releaseLastUpdated
*/
- public String getRLastUpdated() {
+ public String getRLastUpdated()
+ {
return rLastUpdated;
}
+
/**
- * @param releaseLastUpdated the releaseLastUpdated to set
+ * @param releaseLastUpdated
+ * the releaseLastUpdated to set
*/
- public void setRLastUpdated(String releaseLastUpdated) {
+ public void setRLastUpdated(String releaseLastUpdated)
+ {
this.rLastUpdated = releaseLastUpdated;
}
+
/**
* @return the sequence
*/
- public EmblSequence getSequence() {
+ public EmblSequence getSequence()
+ {
return sequence;
}
+
/**
- * @param sequence the sequence to set
+ * @param sequence
+ * the sequence to set
*/
- public void setSequence(EmblSequence sequence) {
+ public void setSequence(EmblSequence sequence)
+ {
this.sequence = sequence;
}
+
/**
* @return the taxDivision
*/
- public String getTaxDivision() {
+ public String getTaxDivision()
+ {
return taxDivision;
}
+
/**
- * @param taxDivision the taxDivision to set
+ * @param taxDivision
+ * the taxDivision to set
*/
- public void setTaxDivision(String taxDivision) {
+ public void setTaxDivision(String taxDivision)
+ {
this.taxDivision = taxDivision;
}
+
/**
* @return the version
*/
- public String getVersion() {
+ public String getVersion()
+ {
return version;
}
+
/**
- * @param version the version to set
+ * @param version
+ * the version to set
*/
- public void setVersion(String version) {
+ public void setVersion(String version)
+ {
this.version = version;
}
-/*
- * EMBL Feature support is limited. The text below is included for the benefit of
- * any developer working on improving EMBL feature import in Jalview.
- * Extract from EMBL feature specification
- * see http://www.embl-ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
-3.5 Location
-3.5.1 Purpose
-
-The location indicates the region of the presented sequence which corresponds
-to a feature.
-
-3.5.2 Format and conventions
-The location contains at least one sequence location descriptor and may
-contain one or more operators with one or more sequence location descriptors.
-Base numbers refer to the numbering in the entry. This numbering designates
-the first base (5' end) of the presented sequence as base 1.
-Base locations beyond the range of the presented sequence may not be used in
-location descriptors, the only exception being location in a remote entry (see
-3.5.2.1, e).
-
-Location operators and descriptors are discussed in more detail below.
-
-3.5.2.1 Location descriptors
-
-The location descriptor can be one of the following:
-(a) a single base number
-(b) a site between two indicated adjoining bases
-(c) a single base chosen from within a specified range of bases (not allowed for new
- entries)
-(d) the base numbers delimiting a sequence span
-(e) a remote entry identifier followed by a local location descriptor
- (i.e., a-d)
-
-A site between two adjoining nucleotides, such as endonucleolytic cleavage
-site, is indicated by listing the two points separated by a carat (^). The
-permitted formats for this descriptor are n^n+1 (for example 55^56), or, for
-circular molecules, n^1, where "n" is the full length of the molecule, ie
-1000^1 for circular molecule with length 1000.
-
-A single base chosen from a range of bases is indicated by the first base
-number and the last base number of the range separated by a single period
-(e.g., '12.21' indicates a single base taken from between the indicated
-points). From October 2006 the usage of this descriptor is restricted :
-it is illegal to use "a single base from a range" (c) either on its own or
-in combination with the "sequence span" (d) descriptor for newly created entries.
-The existing entries where such descriptors exist are going to be retrofitted.
-
-Sequence spans are indicated by the starting base number and the ending base
-number separated by two periods (e.g., '34..456'). The '<' and '>' symbols may
-be used with the starting and ending base numbers to indicate that an end
-point is beyond the specified base number. The starting and ending base
-positions can be represented as distinct base numbers ('34..456') or a site
-between two indicated adjoining bases.
-
-A location in a remote entry (not the entry to which the feature table
-belongs) can be specified by giving the accession-number and sequence version
-of the remote entry, followed by a colon ":", followed by a location
-descriptor which applies to that entry's sequence (i.e. J12345.1:1..15, see
-also examples below)
-
-3.5.2.2 Operators
-
-The location operator is a prefix that specifies what must be done to the
-indicated sequence to find or construct the location corresponding to the
-feature. A list of operators is given below with their definitions and most
-common format.
-
-complement(location)
-Find the complement of the presented sequence in the span specified by "
-location" (i.e., read the complement of the presented strand in its 5'-to-3'
-direction)
-
-join(location,location, ... location)
-The indicated elements should be joined (placed end-to-end) to form one
-contiguous sequence
-
-order(location,location, ... location)
-The elements can be found in the
-specified order (5' to 3' direction), but nothing is implied about the
-reasonableness about joining them
-
-Note : location operator "complement" can be used in combination with either "
-join" or "order" within the same location; combinations of "join" and "order"
-within the same location (nested operators) are illegal.
-
-
-
-3.5.3 Location examples
-
-The following is a list of common location descriptors with their meanings:
-
-Location Description
-
-467 Points to a single base in the presented sequence
-
-340..565 Points to a continuous range of bases bounded by and
- including the starting and ending bases
-
-<345..500 Indicates that the exact lower boundary point of a feature
- is unknown. The location begins at some base previous to
- the first base specified (which need not be contained in
- the presented sequence) and continues to and includes the
- ending base
-
-<1..888 The feature starts before the first sequenced base and
- continues to and includes base 888
-
-1..>888 The feature starts at the first sequenced base and
- continues beyond base 888
-
-102.110 Indicates that the exact location is unknown but that it is
- one of the bases between bases 102 and 110, inclusive
-
-123^124 Points to a site between bases 123 and 124
-
-join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to form
- one contiguous sequence
-
-
-complement(34..126) Start at the base complementary to 126 and finish at the
- base complementary to base 34 (the feature is on the strand
- complementary to the presented strand)
-
-
-complement(join(2691..4571,4918..5163))
- Joins regions 2691 to 4571 and 4918 to 5163, then
- complements the joined segments (the feature is on the
- strand complementary to the presented strand)
-join(complement(4918..5163),complement(2691..4571))
- Complements regions 4918 to 5163 and 2691 to 4571, then
- joins the complemented segments (the feature is on the
- strand complementary to the presented strand)
-
-J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
- this database) with primary accession number 'J00194'
-
-join(1..100,J00194.1:100..202)
- Joins region 1..100 of the existing entry with the region
- 100..202 of remote entry J00194
-
- */
+ /*
+ * EMBL Feature support is limited. The text below is included for the benefit
+ * of any developer working on improving EMBL feature import in Jalview.
+ * Extract from EMBL feature specification see
+ * http://www.embl-ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
+ * 3.5 Location 3.5.1 Purpose
+ *
+ * The location indicates the region of the presented sequence which
+ * corresponds to a feature.
+ *
+ * 3.5.2 Format and conventions The location contains at least one sequence
+ * location descriptor and may contain one or more operators with one or more
+ * sequence location descriptors. Base numbers refer to the numbering in the
+ * entry. This numbering designates the first base (5' end) of the presented
+ * sequence as base 1. Base locations beyond the range of the presented
+ * sequence may not be used in location descriptors, the only exception being
+ * location in a remote entry (see 3.5.2.1, e).
+ *
+ * Location operators and descriptors are discussed in more detail below.
+ *
+ * 3.5.2.1 Location descriptors
+ *
+ * The location descriptor can be one of the following: (a) a single base
+ * number (b) a site between two indicated adjoining bases (c) a single base
+ * chosen from within a specified range of bases (not allowed for new entries)
+ * (d) the base numbers delimiting a sequence span (e) a remote entry
+ * identifier followed by a local location descriptor (i.e., a-d)
+ *
+ * A site between two adjoining nucleotides, such as endonucleolytic cleavage
+ * site, is indicated by listing the two points separated by a carat (^). The
+ * permitted formats for this descriptor are n^n+1 (for example 55^56), or,
+ * for circular molecules, n^1, where "n" is the full length of the molecule,
+ * ie 1000^1 for circular molecule with length 1000.
+ *
+ * A single base chosen from a range of bases is indicated by the first base
+ * number and the last base number of the range separated by a single period
+ * (e.g., '12.21' indicates a single base taken from between the indicated
+ * points). From October 2006 the usage of this descriptor is restricted : it
+ * is illegal to use "a single base from a range" (c) either on its own or in
+ * combination with the "sequence span" (d) descriptor for newly created
+ * entries. The existing entries where such descriptors exist are going to be
+ * retrofitted.
+ *
+ * Sequence spans are indicated by the starting base number and the ending
+ * base number separated by two periods (e.g., '34..456'). The '<' and '>'
+ * symbols may be used with the starting and ending base numbers to indicate
+ * that an end point is beyond the specified base number. The starting and
+ * ending base positions can be represented as distinct base numbers
+ * ('34..456') or a site between two indicated adjoining bases.
+ *
+ * A location in a remote entry (not the entry to which the feature table
+ * belongs) can be specified by giving the accession-number and sequence
+ * version of the remote entry, followed by a colon ":", followed by a
+ * location descriptor which applies to that entry's sequence (i.e.
+ * J12345.1:1..15, see also examples below)
+ *
+ * 3.5.2.2 Operators
+ *
+ * The location operator is a prefix that specifies what must be done to the
+ * indicated sequence to find or construct the location corresponding to the
+ * feature. A list of operators is given below with their definitions and most
+ * common format.
+ *
+ * complement(location) Find the complement of the presented sequence in the
+ * span specified by " location" (i.e., read the complement of the presented
+ * strand in its 5'-to-3' direction)
+ *
+ * join(location,location, ... location) The indicated elements should be
+ * joined (placed end-to-end) to form one contiguous sequence
+ *
+ * order(location,location, ... location) The elements can be found in the
+ * specified order (5' to 3' direction), but nothing is implied about the
+ * reasonableness about joining them
+ *
+ * Note : location operator "complement" can be used in combination with
+ * either " join" or "order" within the same location; combinations of "join"
+ * and "order" within the same location (nested operators) are illegal.
+ *
+ *
+ *
+ * 3.5.3 Location examples
+ *
+ * The following is a list of common location descriptors with their meanings:
+ *
+ * Location Description
+ *
+ * 467 Points to a single base in the presented sequence
+ *
+ * 340..565 Points to a continuous range of bases bounded by and including the
+ * starting and ending bases
+ *
+ * <345..500 Indicates that the exact lower boundary point of a feature is
+ * unknown. The location begins at some base previous to the first base
+ * specified (which need not be contained in the presented sequence) and
+ * continues to and includes the ending base
+ *
+ * <1..888 The feature starts before the first sequenced base and continues to
+ * and includes base 888
+ *
+ * 1..>888 The feature starts at the first sequenced base and continues beyond
+ * base 888
+ *
+ * 102.110 Indicates that the exact location is unknown but that it is one of
+ * the bases between bases 102 and 110, inclusive
+ *
+ * 123^124 Points to a site between bases 123 and 124
+ *
+ * join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to
+ * form one contiguous sequence
+ *
+ *
+ * complement(34..126) Start at the base complementary to 126 and finish at
+ * the base complementary to base 34 (the feature is on the strand
+ * complementary to the presented strand)
+ *
+ *
+ * complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918
+ * to 5163, then complements the joined segments (the feature is on the strand
+ * complementary to the presented strand)
+ *
+ * join(complement(4918..5163),complement(2691..4571)) Complements regions
+ * 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the
+ * feature is on the strand complementary to the presented strand)
+ *
+ * J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
+ * this database) with primary accession number 'J00194'
+ *
+ * join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
+ * with the region 100..202 of remote entry J00194
+ *
+ */
/**
* Recover annotated sequences from EMBL file
- * @param noNa don't return nucleic acid sequences
- * @param sourceDb TODO
- * @param noProtein don't return any translated protein sequences marked in features
+ *
+ * @param noNa
+ * don't return nucleic acid sequences
+ * @param sourceDb
+ * TODO
+ * @param noProtein
+ * don't return any translated protein sequences marked in features
* @return dataset sequences with DBRefs and features - DNA always comes first
*/
- public jalview.datamodel.SequenceI[] getSequences(boolean noNa, boolean noPeptide, String sourceDb) {
- Vector seqs=new Vector();
- Sequence dna=null;
- if (!noNa) {
- dna = new Sequence(sourceDb+"|"+accession, sequence.getSequence());
+ public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
+ boolean noPeptide, String sourceDb)
+ {
+ Vector seqs = new Vector();
+ Sequence dna = null;
+ if (!noNa)
+ {
+ dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
dna.setDescription(desc);
dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
// TODO: add mapping for parentAccession attribute
// TODO: transform EMBL Database refs to canonical form
- if (dbRefs!=null)
- for (Iterator i=dbRefs.iterator(); i.hasNext(); dna.addDBRef((DBRefEntry)i.next()));
+ if (dbRefs != null)
+ for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
+ .addDBRef((DBRefEntry) i.next()))
+ ;
}
- for (Iterator i=features.iterator(); i.hasNext(); ) {
- EmblFeature feature = (EmblFeature) i.next();
- if (!noNa) {
- if (feature.dbRefs!=null && feature.dbRefs.size()>0) {
- for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); dna.addDBRef((DBRefEntry)dbr.next()) )
- ;
+ try
+ {
+ for (Iterator i = features.iterator(); i.hasNext();)
+ {
+ boolean nextFeature=false;
+ EmblFeature feature = (EmblFeature) i.next();
+ if (!noNa)
+ {
+ if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ {
+ for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
+ .addDBRef((DBRefEntry) dbr.next()))
+ ;
+ }
}
- }
- if (feature.getName().equalsIgnoreCase("CDS")) {
- // extract coding region(s)
- jalview.datamodel.Mapping map = null;
- int[] exon=null;
- if (feature.locations!=null && feature.locations.size()>0) {
- for (Iterator locs=feature.locations.iterator();
- locs.hasNext(); ) {
- EmblFeatureLocations loc = (EmblFeatureLocations) locs.next();
- int[] se = loc.getElementRanges();
- 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;
+ if (feature.getName().equalsIgnoreCase("CDS"))
+ {
+ // 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"))
+ 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();)
{
- prseq=q.getValues()[0];
- }
- else
- if (q.getName().equals("protein_id"))
+ 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"))
{
- prid=q.getValues()[0];
+ prstart = Integer.parseInt(q.getValues()[0]);
+ }
+ else if (q.getName().equals("product"))
+ {
+ prname = q.getValues()[0];
}
else
- if (q.getName().equals("codon_start"))
+ {
+ // 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);
+ if (vals != null && vals.size() > 0)
+ {
+ Enumeration kv = vals.elements();
+ while (kv.hasMoreElements())
{
- 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());
+ Object key = kv.nextElement();
+ if (key != null)
+ sf.setValue(key.toString(), vals.get(key));
}
+ }
+ dna.addSequenceFeature(sf);
+ }
}
- }
- 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);
- 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));
+ // 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()));
+ 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);
}
- dna.addSequenceFeature(sf);
}
+
}
- // add dbRefs to sequence
- if (feature.dbRefs!=null && feature.dbRefs.size()>0)
+ else
{
- for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); )
+ // General feature type.
+ if (!noNa)
{
- DBRefEntry ref = (DBRefEntry)dbr.next();
- ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref.getSource()));
- if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
+ if (feature.dbRefs != null && feature.dbRefs.size() > 0)
{
- ref.setMap(map);
- }
- if (product!=null) {
- DBRefEntry pref = new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId());
- pref.setMap(null); // reference is direct
+ for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
+ .addDBRef((DBRefEntry) dbr.next()))
+ ;
}
- dna.addDBRef(ref);
- }
- }
-
- } else {
- // General feature type.
- if (!noNa) {
- if (feature.dbRefs!=null && feature.dbRefs.size()>0) {
- for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); dna.addDBRef((DBRefEntry)dbr.next()) )
- ;
}
}
}
-
+ } 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());
+ e.printStackTrace(System.err);
}
- if (!noNa) {
+ if (!noNa && dna!=null)
+ {
seqs.add(dna);
}
SequenceI[] sqs = new SequenceI[seqs.size()];
- for (int i=0,j=seqs.size();i<j; i++) {
+ for (int i = 0, j = seqs.size(); i < j; i++)
+ {
sqs[i] = (SequenceI) seqs.elementAt(i);
seqs.set(i, null);
}
git://source.jalview.org / jalview.git / commitdiff