--- /dev/null
+<?xml version="1.0"?>\r
+<mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
+ xsi:schemaLocation="http://castor.exolab.org/ castor-mapping.xsd">\r
+ <!-- -->\r
+ <class name="jalview.datamodel.xdb.embl.EmblFile">\r
+ <map-to xml="EMBL_Services"/>\r
+ <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">\r
+ <bind-xml name="entry"/>\r
+ </field>\r
+ \r
+ <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">\r
+ <bind-xml name="Error"/>\r
+ </field>\r
+ </class>\r
+ <class name="jalview.datamodel.xdb.embl.EmblEntry">\r
+ <map-to xml="entry"/>\r
+ <field name="accession" type="string">
+ <bind-xml location="accession" node="attribute"/>
+ </field>\r
+ <field name="lastUpdated" type="string">\r
+ <bind-xml location="last-updated" node="attribute"/>\r
+ </field>\r
+ <field name="version" type="string">\r
+ <bind-xml location="version" node="attribute"/>\r
+ </field>\r
+ \r
+ <field name="rCreated" type="string">\r
+ <bind-xml location="releaseCreated" node="attribute"/>\r
+ </field>\r
+ <field name="rLastUpdated" type="string">\r
+ <bind-xml location="releaseLastUpdated" node="attribute"/>\r
+ </field>\r
+ <field name="desc" type="string">
+ <bind-xml name="description" node="element"/>
+ </field>\r
+ <field name="Keywords" type="string" collection="vector">\r
+ <bind-xml name="keyword" node="element"/>\r
+ </field>\r
+ <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">\r
+ <bind-xml location="sequence" node="element"/>\r
+ </field>\r
+ <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">\r
+ <bind-xml name="feature"/>
+ </field>\r
+ <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
+ <bind-xml name="dbreference" />\r
+ </field>\r
+ </class>\r
+ <class name="jalview.datamodel.xdb.embl.EmblSequence">
+ <map-to xml="sequence"/>\r
+ <field name="type" type="string">\r
+ <bind-xml name="type" node="attribute" location="type"/>\r
+ </field>\r
+ <field name="version" type="string">\r
+ <bind-xml name="version" node="attribute" location="version"/>\r
+ </field>\r
+ <field name="sequence" type="string">\r
+ <bind-xml node="text"/>\r
+ </field>
+ </class>\r
+ <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">\r
+ <map-to xml="feature"/>\r
+ <field name="name" type="string">
+ <bind-xml name="name" node="attribute"/>
+ </field>\r
+ <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
+ <bind-xml name="dbreference" node="element"/>
+ </field>\r
+ <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">\r
+ <bind-xml name="qualifier"/>\r
+ </field> \r
+ <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">\r
+ <bind-xml name="location"/>\r
+ </field>\r
+ </class>\r
+ <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">\r
+ <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->\r
+ <bind-xml name="primary" node="attribute"/>\r
+ </field>\r
+ <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->\r
+ <bind-xml name="db" node="attribute"/>\r
+ </field>\r
+ <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->\r
+ <bind-xml name="secondary" node="attribute"/>\r
+ </field>\r
+ </class>\r
+ <class name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
+ <map-to xml="Qualifier"/>\r
+ <field name="name">\r
+ <bind-xml name="name" node="attribute"/>\r
+ </field>\r
+ <field name="value">
+ <bind-xml node="text"/>
+ </field>\r
+ </class>\r
+ <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">\r
+ <map-to xml="location"/>\r
+ <field name="locationType" type="string">\r
+ <bind-xml name="type" node="attribute"/>\r
+ </field>\r
+ <field name="locationComplement" type="boolean">\r
+ <bind-xml name="complement" node="attribute"/>\r
+ </field>\r
+ <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">\r
+ <bind-xml name="locationElement"/>\r
+ </field>\r
+ </class>\r
+ <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">\r
+ <map-to xml="locationElement"/>\r
+ <field name="type" type="string">\r
+ <bind-xml name="type" node="attribute"/>\r
+ </field>\r
+ <field name="accession" type="string">\r
+ <bind-xml name="accession" node="attribute"/> \r
+ </field>\r
+ <field name="version" type="string">\r
+ <bind-xml name="version" node="attribute"/>\r
+ </field>\r
+ <field name="complement" type="boolean">\r
+ <bind-xml name="complement"/>\r
+ </field>\r
+ <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">\r
+ <bind-xml name="basePosition" node="element"/>\r
+ </field>\r
+ </class>\r
+ <class name="jalview.datamodel.xdb.embl.BasePosition">
+ <map-to xml="basePosition"/>\r
+ <field name="type">
+ <bind-xml name="type" node="attribute"/>
+ </field>\r
+ <field name="pos">
+ <bind-xml node="text"/>\r
+ </field>\r
+ </class>\r
+</mapping>\r
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+\r
+public class BasePosition {\r
+ String type;\r
+ String pos;\r
+ /**\r
+ * @return the pos\r
+ */\r
+ public String getPos() {\r
+ return pos;\r
+ }\r
+ /**\r
+ * @param pos the pos to set\r
+ */\r
+ public void setPos(String pos) {\r
+ this.pos = pos;\r
+ }\r
+ /**\r
+ * @return the type\r
+ */\r
+ public String getType() {\r
+ return type;\r
+ }\r
+ /**\r
+ * @param type the type to set\r
+ */\r
+ public void setType(String type) {\r
+ this.type = type;\r
+ }\r
+}\r
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+\r
+import jalview.datamodel.DBRefEntry;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceFeature;\r
+import jalview.datamodel.SequenceI;\r
+\r
+import java.util.Iterator;\r
+import java.util.Vector;\r
+\r
+public class EmblEntry {\r
+ String accession;\r
+ String version;\r
+ String taxDivision;\r
+ String desc;\r
+ String rCreated;\r
+ String rLastUpdated;\r
+ String lastUpdated;\r
+ Vector keywords;\r
+ Vector refs;\r
+ Vector dbRefs;\r
+ Vector features;\r
+ EmblSequence sequence;\r
+ /**\r
+ * @return the accession\r
+ */\r
+ public String getAccession() {\r
+ return accession;\r
+ }\r
+ /**\r
+ * @param accession the accession to set\r
+ */\r
+ public void setAccession(String accession) {\r
+ this.accession = accession;\r
+ }\r
+ /**\r
+ * @return the dbRefs\r
+ */\r
+ public Vector getDbRefs() {\r
+ return dbRefs;\r
+ }\r
+ /**\r
+ * @param dbRefs the dbRefs to set\r
+ */\r
+ public void setDbRefs(Vector dbRefs) {\r
+ this.dbRefs = dbRefs;\r
+ }\r
+ /**\r
+ * @return the desc\r
+ */\r
+ public String getDesc() {\r
+ return desc;\r
+ }\r
+ /**\r
+ * @param desc the desc to set\r
+ */\r
+ public void setDesc(String desc) {\r
+ this.desc = desc;\r
+ }\r
+ /**\r
+ * @return the features\r
+ */\r
+ public Vector getFeatures() {\r
+ return features;\r
+ }\r
+ /**\r
+ * @param features the features to set\r
+ */\r
+ public void setFeatures(Vector features) {\r
+ this.features = features;\r
+ }\r
+ /**\r
+ * @return the keywords\r
+ */\r
+ public Vector getKeywords() {\r
+ return keywords;\r
+ }\r
+ /**\r
+ * @param keywords the keywords to set\r
+ */\r
+ public void setKeywords(Vector keywords) {\r
+ this.keywords = keywords;\r
+ }\r
+ /**\r
+ * @return the lastUpdated\r
+ */\r
+ public String getLastUpdated() {\r
+ return lastUpdated;\r
+ }\r
+ /**\r
+ * @param lastUpdated the lastUpdated to set\r
+ */\r
+ public void setLastUpdated(String lastUpdated) {\r
+ this.lastUpdated = lastUpdated;\r
+ }\r
+ /**\r
+ * @return the refs\r
+ */\r
+ public Vector getRefs() {\r
+ return refs;\r
+ }\r
+ /**\r
+ * @param refs the refs to set\r
+ */\r
+ public void setRefs(Vector refs) {\r
+ this.refs = refs;\r
+ }\r
+ /**\r
+ * @return the releaseCreated\r
+ */\r
+ public String getRCreated() {\r
+ return rCreated;\r
+ }\r
+ /**\r
+ * @param releaseCreated the releaseCreated to set\r
+ */\r
+ public void setRcreated(String releaseCreated) {\r
+ this.rCreated = releaseCreated;\r
+ }\r
+ /**\r
+ * @return the releaseLastUpdated\r
+ */\r
+ public String getRLastUpdated() {\r
+ return rLastUpdated;\r
+ }\r
+ /**\r
+ * @param releaseLastUpdated the releaseLastUpdated to set\r
+ */\r
+ public void setRLastUpdated(String releaseLastUpdated) {\r
+ this.rLastUpdated = releaseLastUpdated;\r
+ }\r
+ /**\r
+ * @return the sequence\r
+ */\r
+ public EmblSequence getSequence() {\r
+ return sequence;\r
+ }\r
+ /**\r
+ * @param sequence the sequence to set\r
+ */\r
+ public void setSequence(EmblSequence sequence) {\r
+ this.sequence = sequence;\r
+ }\r
+ /**\r
+ * @return the taxDivision\r
+ */\r
+ public String getTaxDivision() {\r
+ return taxDivision;\r
+ }\r
+ /**\r
+ * @param taxDivision the taxDivision to set\r
+ */\r
+ public void setTaxDivision(String taxDivision) {\r
+ this.taxDivision = taxDivision;\r
+ }\r
+ /**\r
+ * @return the version\r
+ */\r
+ public String getVersion() {\r
+ return version;\r
+ }\r
+ /**\r
+ * @param version the version to set\r
+ */\r
+ public void setVersion(String version) {\r
+ this.version = version;\r
+ }\r
+\r
+ /**\r
+ * Recover annotated sequences from EMBL file\r
+ * @param noNa don't return nucleic acid sequences \r
+ * @param sourceDb TODO\r
+ * @param noProtein don't return any translated protein sequences marked in features\r
+ * @return dataset sequences with DBRefs and features - DNA always comes first\r
+ */\r
+ public jalview.datamodel.SequenceI[] getSequences(boolean noNa, boolean noPeptide, String sourceDb) {\r
+ Vector seqs=new Vector();\r
+ Sequence dna=null;\r
+ if (!noNa) {\r
+ dna = new Sequence(sourceDb+"|"+accession, sequence.getSequence());\r
+ dna.setDescription(desc);\r
+ dna.addDBRef(new DBRefEntry(sourceDb, version, accession));\r
+ // TODO: add mapping for parentAccession attribute\r
+ // TODO: transform EMBL Database refs to canonical form\r
+ if (dbRefs!=null)\r
+ for (Iterator i=dbRefs.iterator(); i.hasNext(); dna.addDBRef((DBRefEntry)i.next()));\r
+ }\r
+ for (Iterator i=features.iterator(); i.hasNext(); ) {\r
+ EmblFeature feature = (EmblFeature) i.next();\r
+ if (!noNa) {\r
+ if (feature.dbRefs!=null && feature.dbRefs.size()>0) {\r
+ for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); dna.addDBRef((DBRefEntry)dbr.next()) )\r
+ ;\r
+ }\r
+ }\r
+ if (feature.getName().equalsIgnoreCase("CDS")) {\r
+ // extract coding region(s)\r
+ jalview.datamodel.Mapping map = null;\r
+ int[] exon=null;\r
+ if (feature.locations!=null && feature.locations.size()>0) {\r
+ for (Iterator locs=feature.locations.iterator();\r
+ locs.hasNext(); ) {\r
+ EmblFeatureLocations loc = (EmblFeatureLocations) locs.next();\r
+ int[] se = loc.getElementRanges();\r
+ if (exon==null) {\r
+ exon=se;\r
+ } else {\r
+ int[] t=new int[exon.length+se.length];\r
+ System.arraycopy(exon, 0, t, 0, exon.length);\r
+ System.arraycopy(se, 0, t, exon.length,se.length);\r
+ exon=t;\r
+ }\r
+ }\r
+ }\r
+ String prseq=null;\r
+ String prname=null;\r
+ String prid=null;\r
+ int prstart=1;\r
+ // get qualifiers\r
+ if (feature.getQualifiers()!=null && feature.getQualifiers().size()>0) {\r
+ for (Iterator quals=feature.getQualifiers().iterator(); quals.hasNext(); ) {\r
+ Qualifier q = (Qualifier) quals.next();\r
+ if (q.getName().equals("translation")) \r
+ {\r
+ prseq=q.getValue();\r
+ } \r
+ else\r
+ if (q.getName().equals("protein_id")) \r
+ {\r
+ prid=q.getValue();\r
+ }\r
+ else\r
+ if (q.getName().equals("codon_start"))\r
+ {\r
+ prstart = Integer.parseInt(q.getValue());\r
+ }\r
+ else\r
+ if (q.getName().equals("product")) {\r
+ prname = q.getValue();\r
+ }\r
+ }\r
+ }\r
+ Sequence product=null;\r
+ if (prseq!=null && prname!=null && prid!=null) {\r
+ // extract proteins.\r
+ if (!noPeptide) {\r
+ product = new Sequence(sourceDb+"|"+"EMBLCDS|"+prid+"|"+prname, prseq, prstart, prstart+prseq.length()-1);\r
+ product.setDescription("Protein Product from "+sourceDb);\r
+ seqs.add(product);\r
+ }\r
+ // we have everything - create the mapping and perhaps the protein sequence\r
+ map = new jalview.datamodel.Mapping(product, exon, new int[] { prstart, prstart+prseq.length()-1}, 3, 1);\r
+ // add cds feature to dna seq - this may include the stop codon\r
+ for (int xint=0;xint<exon.length; xint+=2) {\r
+ SequenceFeature sf = new SequenceFeature();\r
+ sf.setBegin(exon[xint]);\r
+ sf.setEnd(exon[xint+1]);\r
+ sf.setType(feature.getName());\r
+ sf.setFeatureGroup(jalview.datamodel.DBRefSource.EMBL);\r
+ sf.setDescription("Exon "+(1+xint)+" for protein '"+prname+"' EMBLCDS:"+prid);\r
+ dna.addSequenceFeature(sf);\r
+ }\r
+ }\r
+ // add dbRefs to sequence\r
+ if (feature.dbRefs!=null && feature.dbRefs.size()>0) \r
+ {\r
+ for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); ) \r
+ {\r
+ DBRefEntry ref = (DBRefEntry)dbr.next();\r
+ ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref.getSource()));\r
+ if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT)) \r
+ {\r
+ ref.setMap(map);\r
+ }\r
+ if (product!=null) {\r
+ DBRefEntry pref = new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId());\r
+ pref.setMap(null); // reference is direct\r
+ }\r
+ dna.addDBRef(ref);\r
+ }\r
+ }\r
+ \r
+ } else {\r
+ // General feature type.\r
+ if (!noNa) {\r
+ if (feature.dbRefs!=null && feature.dbRefs.size()>0) {\r
+ for (Iterator dbr=feature.dbRefs.iterator(); dbr.hasNext(); dna.addDBRef((DBRefEntry)dbr.next()) )\r
+ ;\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ if (!noNa) {\r
+ seqs.add(dna);\r
+ }\r
+ SequenceI[] sqs = new SequenceI[seqs.size()];\r
+ for (int i=0,j=seqs.size();i<j; i++) {\r
+ sqs[i] = (SequenceI) seqs.elementAt(i);\r
+ seqs.set(i, null);\r
+ }\r
+ return sqs;\r
+ }\r
+}\r
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+\r
+public class EmblError {\r
+ String accession;\r
+\r
+ /**\r
+ * @return the accession\r
+ */\r
+ public String getAccession() {\r
+ return accession;\r
+ }\r
+\r
+ /**\r
+ * @param accession the accession to set\r
+ */\r
+ public void setAccession(String accession) {\r
+ this.accession = accession;\r
+ }\r
+}\r
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
+public class EmblFeature {\r
+ String name;\r
+ Vector dbRefs;\r
+ Vector qualifiers;\r
+ Vector locations;\r
+ \r
+ /**\r
+ * @return the dbRefs\r
+ */\r
+ public Vector getDbRefs() {\r
+ return dbRefs;\r
+ }\r
+ /**\r
+ * @param dbRefs the dbRefs to set\r
+ */\r
+ public void setDbRefs(Vector dbRefs) {\r
+ this.dbRefs = dbRefs;\r
+ }\r
+ /**\r
+ * @return the locations\r
+ */\r
+ public Vector getLocations() {\r
+ return locations;\r
+ }\r
+ /**\r
+ * @param locations the locations to set\r
+ */\r
+ public void setLocations(Vector locations) {\r
+ this.locations = locations;\r
+ }\r
+ /**\r
+ * @return the name\r
+ */\r
+ public String getName() {\r
+ return name;\r
+ }\r
+ /**\r
+ * @param name the name to set\r
+ */\r
+ public void setName(String name) {\r
+ this.name = name;\r
+ }\r
+ /**\r
+ * @return the qualifiers\r
+ */\r
+ public Vector getQualifiers() {\r
+ return qualifiers;\r
+ }\r
+ /**\r
+ * @param qualifiers the qualifiers to set\r
+ */\r
+ public void setQualifiers(Vector qualifiers) {\r
+ this.qualifiers = qualifiers;\r
+ }\r
+}\r
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+\r
+public class EmblFeatureLocElement {\r
+ String type;\r
+ String accession;\r
+ String version;\r
+ boolean complement;\r
+ BasePosition basePositions[]; \r
+ /**\r
+ * @return the accession\r
+ */\r
+ public String getAccession() {\r
+ return accession;\r
+ }\r
+ /**\r
+ * @param accession the accession to set\r
+ */\r
+ public void setAccession(String accession) {\r
+ this.accession = accession;\r
+ }\r
+ /**\r
+ * @return the basePositions\r
+ */\r
+ public BasePosition[] getBasePositions() {\r
+ return basePositions;\r
+ }\r
+ /**\r
+ * @param basePositions the basePositions to set\r
+ */\r
+ public void setBasePositions(BasePosition[] basePositions) {\r
+ this.basePositions = basePositions;\r
+ }\r
+ /**\r
+ * @return the complement\r
+ */\r
+ public boolean isComplement() {\r
+ return complement;\r
+ }\r
+ /**\r
+ * @param complement the complement to set\r
+ */\r
+ public void setComplement(boolean complement) {\r
+ this.complement = complement;\r
+ }\r
+ /**\r
+ * @return the type\r
+ */\r
+ public String getType() {\r
+ return type;\r
+ }\r
+ /**\r
+ * @param type the type to set\r
+ */\r
+ public void setType(String type) {\r
+ this.type = type;\r
+ }\r
+ /**\r
+ * @return the version\r
+ */\r
+ public String getVersion() {\r
+ return version;\r
+ }\r
+ /**\r
+ * @param version the version to set\r
+ */\r
+ public void setVersion(String version) {\r
+ this.version = version;\r
+ }\r
+ }\r
+ \r
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+\r
+import java.util.Iterator;\r
+import java.util.Vector;\r
+\r
+public class EmblFeatureLocations {\r
+ Vector locElements;\r
+ String locationType;\r
+ boolean locationComplement;\r
+ /**\r
+ * @return the locationComplement\r
+ */\r
+ public boolean isLocationComplement() {\r
+ return locationComplement;\r
+ }\r
+ /**\r
+ * @param locationComplement the locationComplement to set\r
+ */\r
+ public void setLocationComplement(boolean locationComplement) {\r
+ this.locationComplement = locationComplement;\r
+ }\r
+ /**\r
+ * @return the locationType\r
+ */\r
+ public String getLocationType() {\r
+ return locationType;\r
+ }\r
+ /**\r
+ * @param locationType the locationType to set\r
+ */\r
+ public void setLocationType(String locationType) {\r
+ this.locationType = locationType;\r
+ }\r
+ /**\r
+ * @return the locElements\r
+ */\r
+ public Vector getLocElements() {\r
+ return locElements;\r
+ }\r
+ /**\r
+ * @param locElements the locElements to set\r
+ */\r
+ public void setLocElements(Vector locElements) {\r
+ this.locElements = locElements;\r
+ }\r
+ /**\r
+ * Return all location elements as start-end pairs on referenced sequence \r
+ * @return int[] { start1, end1, ... }\r
+ */\r
+ public int[] getElementRanges() {\r
+ if (locationType.equalsIgnoreCase("single")) {\r
+ int[] se = new int[locElements.size()*2]; \r
+ int sepos=0;\r
+ for (Iterator le=locElements.iterator();le.hasNext();) {\r
+ EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();\r
+ BasePosition bp[] = loce.getBasePositions();\r
+ if (bp.length==2) {\r
+ se[sepos++] = Integer.parseInt(bp[0].getPos());\r
+ se[sepos++] = Integer.parseInt(bp[1].getPos());\r
+ }\r
+ }\r
+ return se;\r
+ }\r
+ return null;\r
+ }\r
+}
\ No newline at end of file
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+\r
+\r
+import java.io.File;\r
+import java.io.FileReader;\r
+import java.io.Reader;\r
+import java.util.Vector;\r
+\r
+import org.exolab.castor.mapping.Mapping;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+public class EmblFile {\r
+ Vector entries;\r
+ Vector errors;\r
+ /**\r
+ * @return the entries\r
+ */\r
+ public Vector getEntries() {\r
+ return entries;\r
+ }\r
+ /**\r
+ * @param entries the entries to set\r
+ */\r
+ public void setEntries(Vector entries) {\r
+ this.entries = entries;\r
+ }\r
+ /**\r
+ * @return the errors\r
+ */\r
+ public Vector getErrors() {\r
+ return errors;\r
+ }\r
+ /**\r
+ * @param errors the errors to set\r
+ */\r
+ public void setErrors(Vector errors) {\r
+ this.errors = errors;\r
+ }\r
+ /**\r
+ * Parse an EmblXML file into an EmblFile object\r
+ * @param file\r
+ * @return parsed EmblXML or null if exceptions were raised\r
+ */\r
+ public static EmblFile getEmblFile(File file)\r
+ {\r
+ if (file==null)\r
+ return null;\r
+ try {\r
+ return EmblFile.getEmblFile(new FileReader(file));\r
+ }\r
+ catch (Exception e) {\r
+ System.err.println("Exception whilst reading EMBLfile from "+file);\r
+ e.printStackTrace(System.err);\r
+ }\r
+ return null;\r
+ }\r
+ public static EmblFile getEmblFile(Reader file) {\r
+ EmblFile record = new EmblFile();\r
+ try\r
+ {\r
+ // 1. Load the mapping information from the file\r
+ Mapping map = new Mapping(record.getClass().getClassLoader());\r
+ java.net.URL url = record.getClass().getResource("/embl_mapping.xml");\r
+ map.loadMapping(url);\r
+\r
+ // 2. Unmarshal the data\r
+ Unmarshaller unmar = new Unmarshaller(record);\r
+ try {\r
+ // uncomment to DEBUG EMBLFile reading unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());\r
+ } catch (Exception e) {};\r
+ unmar.setIgnoreExtraElements(true);\r
+ unmar.setMapping(map);\r
+\r
+ record = (EmblFile) unmar.unmarshal(file);\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace(System.err);\r
+ record=null;\r
+ }\r
+\r
+\r
+ return record;\r
+ }\r
+ public static void main(String args[]) {\r
+ EmblFile myfile = EmblFile.getEmblFile(new File("C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecord.xml"));\r
+ if (myfile!=null && myfile.entries!=null && myfile.entries.size()>0)\r
+ System.out.println(myfile.entries.size()+" Records read.");\r
+ }\r
+}\r
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+\r
+public class EmblSequence {\r
+ String version;\r
+ String sequence;\r
+ String type;\r
+ /**\r
+ * @return the sequence\r
+ */\r
+ public String getSequence() {\r
+ return sequence;\r
+ }\r
+ /**\r
+ * @param sequence the sequence to set\r
+ */\r
+ public void setSequence(String sequence) {\r
+ this.sequence = sequence;\r
+ }\r
+ /**\r
+ * @return the type\r
+ */\r
+ public String getType() {\r
+ return type;\r
+ }\r
+ /**\r
+ * @param type the type to set\r
+ */\r
+ public void setType(String type) {\r
+ this.type = type;\r
+ }\r
+ /**\r
+ * @return the version\r
+ */\r
+ public String getVersion() {\r
+ return version;\r
+ }\r
+ /**\r
+ * @param version the version to set\r
+ */\r
+ public void setVersion(String version) {\r
+ this.version = version;\r
+ }\r
+}\r
--- /dev/null
+package jalview.datamodel.xdb.embl;\r
+\r
+public class Qualifier {\r
+ String name;\r
+ String value;\r
+ /**\r
+ * @return the name\r
+ */\r
+ public String getName() {\r
+ return name;\r
+ }\r
+ /**\r
+ * @param name the name to set\r
+ */\r
+ public void setName(String name) {\r
+ this.name = name;\r
+ }\r
+ /**\r
+ * @return the value\r
+ */\r
+ public String getValue() {\r
+ return value;\r
+ }\r
+ /**\r
+ * @param value the value to set\r
+ */\r
+ public void setValue(String value) {\r
+ this.value = value;\r
+ }\r
+ \r
+}\r
git://source.jalview.org / jalview.git / commitdiff