From 0f3ec4858fa41dcc8b815402ba971fb2184ae27b Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 17 Apr 2007 11:32:26 +0000 Subject: [PATCH] ascii type --- src/jalview/datamodel/xdb/embl/BasePosition.java | 60 +- src/jalview/datamodel/xdb/embl/EmblEntry.java | 918 ++++++++++---------- src/jalview/datamodel/xdb/embl/EmblError.java | 38 +- src/jalview/datamodel/xdb/embl/EmblFeature.java | 116 +-- .../datamodel/xdb/embl/EmblFeatureLocElement.java | 140 +-- .../datamodel/xdb/embl/EmblFeatureLocations.java | 166 ++-- src/jalview/datamodel/xdb/embl/EmblFile.java | 180 ++-- src/jalview/datamodel/xdb/embl/EmblSequence.java | 86 +- src/jalview/datamodel/xdb/embl/Qualifier.java | 62 +- 9 files changed, 883 insertions(+), 883 deletions(-) diff --git a/src/jalview/datamodel/xdb/embl/BasePosition.java b/src/jalview/datamodel/xdb/embl/BasePosition.java index 0b2dcbe..e0fe833 100644 --- a/src/jalview/datamodel/xdb/embl/BasePosition.java +++ b/src/jalview/datamodel/xdb/embl/BasePosition.java @@ -1,30 +1,30 @@ -package jalview.datamodel.xdb.embl; - -public class BasePosition { - String type; - String pos; - /** - * @return the pos - */ - public String getPos() { - return pos; - } - /** - * @param pos the pos to set - */ - public void setPos(String pos) { - this.pos = pos; - } - /** - * @return the type - */ - public String getType() { - return type; - } - /** - * @param type the type to set - */ - public void setType(String type) { - this.type = type; - } -} +package jalview.datamodel.xdb.embl; + +public class BasePosition { + String type; + String pos; + /** + * @return the pos + */ + public String getPos() { + return pos; + } + /** + * @param pos the pos to set + */ + public void setPos(String pos) { + this.pos = pos; + } + /** + * @return the type + */ + public String getType() { + return type; + } + /** + * @param type the type to set + */ + public void setType(String type) { + this.type = type; + } +} diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index 6a1146d..0f4fc24 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -1,459 +1,459 @@ -package jalview.datamodel.xdb.embl; - -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; - -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Iterator; -import java.util.Vector; - -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() { - return accession; - } - /** - * @param accession the accession to set - */ - public void setAccession(String accession) { - this.accession = accession; - } - /** - * @return the dbRefs - */ - public Vector getDbRefs() { - return dbRefs; - } - /** - * @param dbRefs the dbRefs to set - */ - public void setDbRefs(Vector dbRefs) { - this.dbRefs = dbRefs; - } - /** - * @return the desc - */ - public String getDesc() { - return desc; - } - /** - * @param desc the desc to set - */ - public void setDesc(String desc) { - this.desc = desc; - } - /** - * @return the features - */ - public Vector getFeatures() { - return features; - } - /** - * @param features the features to set - */ - public void setFeatures(Vector features) { - this.features = features; - } - /** - * @return the keywords - */ - public Vector getKeywords() { - return keywords; - } - /** - * @param keywords the keywords to set - */ - public void setKeywords(Vector keywords) { - this.keywords = keywords; - } - /** - * @return the lastUpdated - */ - public String getLastUpdated() { - return lastUpdated; - } - /** - * @param lastUpdated the lastUpdated to set - */ - public void setLastUpdated(String lastUpdated) { - this.lastUpdated = lastUpdated; - } - /** - * @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() { - return rCreated; - } - /** - * @param releaseCreated the releaseCreated to set - */ - public void setRcreated(String releaseCreated) { - this.rCreated = releaseCreated; - } - /** - * @return the releaseLastUpdated - */ - public String getRLastUpdated() { - return rLastUpdated; - } - /** - * @param releaseLastUpdated the releaseLastUpdated to set - */ - public void setRLastUpdated(String releaseLastUpdated) { - this.rLastUpdated = releaseLastUpdated; - } - /** - * @return the sequence - */ - public EmblSequence getSequence() { - return sequence; - } - /** - * @param sequence the sequence to set - */ - public void setSequence(EmblSequence sequence) { - this.sequence = sequence; - } - /** - * @return the taxDivision - */ - public String getTaxDivision() { - return taxDivision; - } - /** - * @param taxDivision the taxDivision to set - */ - public void setTaxDivision(String taxDivision) { - this.taxDivision = taxDivision; - } - /** - * @return the version - */ - public String getVersion() { - return version; - } - /** - * @param version the version to set - */ - 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 - - */ - /** - * 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 - * @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()); - 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())); - } - 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()) ) - ; - } - } - 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; - } - } - } - 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.getValue(); - } - else - if (q.getName().equals("protein_id")) - { - prid=q.getValue(); - } - else - if (q.getName().equals("codon_start")) - { - prstart = Integer.parseInt(q.getValue()); - } - else - if (q.getName().equals("product")){ - prname = q.getValue(); - } else { - // throw anything else into the additional properties hash - vals.put(q.getName(), q.getValue()); - } - } - } - 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;xint0) { - 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())); - 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); - } - } - - } 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()) ) - ; - } - } - } - - } - if (!noNa) { - seqs.add(dna); - } - SequenceI[] sqs = new SequenceI[seqs.size()]; - for (int i=0,j=seqs.size();i' 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 + * @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()); + 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())); + } + 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()) ) + ; + } + } + 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; + } + } + } + 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.getValue(); + } + else + if (q.getName().equals("protein_id")) + { + prid=q.getValue(); + } + else + if (q.getName().equals("codon_start")) + { + prstart = Integer.parseInt(q.getValue()); + } + else + if (q.getName().equals("product")){ + prname = q.getValue(); + } else { + // throw anything else into the additional properties hash + vals.put(q.getName(), q.getValue()); + } + } + } + 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;xint0) { + 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())); + 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); + } + } + + } 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()) ) + ; + } + } + } + + } + if (!noNa) { + seqs.add(dna); + } + SequenceI[] sqs = new SequenceI[seqs.size()]; + for (int i=0,j=seqs.size();i0) - System.out.println(myfile.entries.size()+" Records read."); - } -} +package jalview.datamodel.xdb.embl; + + +import java.io.File; +import java.io.FileReader; +import java.io.Reader; +import java.util.Vector; + +import org.exolab.castor.mapping.Mapping; +import org.exolab.castor.xml.Unmarshaller; + +public class EmblFile { + Vector entries; + Vector errors; + /** + * @return the entries + */ + public Vector getEntries() { + return entries; + } + /** + * @param entries the entries to set + */ + public void setEntries(Vector entries) { + this.entries = entries; + } + /** + * @return the errors + */ + public Vector getErrors() { + return errors; + } + /** + * @param errors the errors to set + */ + public void setErrors(Vector errors) { + this.errors = errors; + } + /** + * Parse an EmblXML file into an EmblFile object + * @param file + * @return parsed EmblXML or null if exceptions were raised + */ + public static EmblFile getEmblFile(File file) + { + if (file==null) + return null; + try { + return EmblFile.getEmblFile(new FileReader(file)); + } + catch (Exception e) { + System.err.println("Exception whilst reading EMBLfile from "+file); + e.printStackTrace(System.err); + } + return null; + } + public static EmblFile getEmblFile(Reader file) { + EmblFile record = new EmblFile(); + try + { + // 1. Load the mapping information from the file + Mapping map = new Mapping(record.getClass().getClassLoader()); + java.net.URL url = record.getClass().getResource("/embl_mapping.xml"); + map.loadMapping(url); + + // 2. Unmarshal the data + Unmarshaller unmar = new Unmarshaller(record); + try { + // uncomment to DEBUG EMBLFile reading unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled()); + } catch (Exception e) {}; + unmar.setIgnoreExtraElements(true); + unmar.setMapping(map); + + record = (EmblFile) unmar.unmarshal(file); + } + catch (Exception e) + { + e.printStackTrace(System.err); + record=null; + } + + + return record; + } + public static void main(String args[]) { + EmblFile myfile = EmblFile.getEmblFile(new File("C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecord.xml")); + if (myfile!=null && myfile.entries!=null && myfile.entries.size()>0) + System.out.println(myfile.entries.size()+" Records read."); + } +} diff --git a/src/jalview/datamodel/xdb/embl/EmblSequence.java b/src/jalview/datamodel/xdb/embl/EmblSequence.java index ac0bfef..c68bcc5 100644 --- a/src/jalview/datamodel/xdb/embl/EmblSequence.java +++ b/src/jalview/datamodel/xdb/embl/EmblSequence.java @@ -1,43 +1,43 @@ -package jalview.datamodel.xdb.embl; - -public class EmblSequence { - String version; - String sequence; - String type; - /** - * @return the sequence - */ - public String getSequence() { - return sequence; - } - /** - * @param sequence the sequence to set - */ - public void setSequence(String sequence) { - this.sequence = sequence; - } - /** - * @return the type - */ - public String getType() { - return type; - } - /** - * @param type the type to set - */ - public void setType(String type) { - this.type = type; - } - /** - * @return the version - */ - public String getVersion() { - return version; - } - /** - * @param version the version to set - */ - public void setVersion(String version) { - this.version = version; - } -} +package jalview.datamodel.xdb.embl; + +public class EmblSequence { + String version; + String sequence; + String type; + /** + * @return the sequence + */ + public String getSequence() { + return sequence; + } + /** + * @param sequence the sequence to set + */ + public void setSequence(String sequence) { + this.sequence = sequence; + } + /** + * @return the type + */ + public String getType() { + return type; + } + /** + * @param type the type to set + */ + public void setType(String type) { + this.type = type; + } + /** + * @return the version + */ + public String getVersion() { + return version; + } + /** + * @param version the version to set + */ + public void setVersion(String version) { + this.version = version; + } +} diff --git a/src/jalview/datamodel/xdb/embl/Qualifier.java b/src/jalview/datamodel/xdb/embl/Qualifier.java index 1c2d66e..8fae059 100644 --- a/src/jalview/datamodel/xdb/embl/Qualifier.java +++ b/src/jalview/datamodel/xdb/embl/Qualifier.java @@ -1,31 +1,31 @@ -package jalview.datamodel.xdb.embl; - -public class Qualifier { - String name; - String value; - /** - * @return the name - */ - public String getName() { - return name; - } - /** - * @param name the name to set - */ - public void setName(String name) { - this.name = name; - } - /** - * @return the value - */ - public String getValue() { - return value; - } - /** - * @param value the value to set - */ - public void setValue(String value) { - this.value = value; - } - -} +package jalview.datamodel.xdb.embl; + +public class Qualifier { + String name; + String value; + /** + * @return the name + */ + public String getName() { + return name; + } + /** + * @param name the name to set + */ + public void setName(String name) { + this.name = name; + } + /** + * @return the value + */ + public String getValue() { + return value; + } + /** + * @param value the value to set + */ + public void setValue(String value) { + this.value = value; + } + +} -- 1.7.10.2