public EntrySet enrichEntrySet(EntrySet entrySet, EnricherConfig config) { EntrySet enrichedSet = new EntrySet(); enrichedSet.setLevel(entrySet.getLevel()); enrichedSet.setVersion(enrichedSet.getVersion()); enrichedSet.setMinorVersion(entrySet.getMinorVersion()); for (Entry entry : entrySet.getEntries()) { Entry enrichedEntry = enrichEntry(entry, config); enrichedSet.getEntries().add(enrichedEntry); } return enrichedSet; }
public EntrySet( int level, int version, int minorVersion ) { setLevel( level ); setVersion( version ); setMinorVersion( minorVersion ); }
public static EntrySet createEntrySet(PsimiXmlVersion version, Collection<Entry> entries) { EntrySet entrySet = new EntrySet(version); entrySet.getEntries().addAll(entries); return entrySet; }
private EntrySet mergeEntriesIfNecessary(EntrySet entrySet){ if (entrySet == null){ return null; } if (entrySet.getEntries().size() > 1){ Iterator<Entry> entryIterator = entrySet.getEntries().iterator(); Entry originalEntry = entryIterator.next(); while (entryIterator.hasNext()){ Entry newEntry = entryIterator.next(); originalEntry.getExperiments().addAll(newEntry.getExperiments()); originalEntry.getInteractors().addAll(newEntry.getInteractors()); originalEntry.getInteractions().addAll(newEntry.getInteractions()); } return new EntrySet(Arrays.asList(originalEntry), entrySet.getLevel(), entrySet.getVersion(), entrySet.getMinorVersion()); } return entrySet; }
public psidev.psi.mi.xml.model.EntrySet fromJaxb( psidev.psi.mi.xml253.jaxb.EntrySet jEntrySet ) throws ConverterException { if ( jEntrySet == null ) { throw new IllegalArgumentException( "You must give a non null JAXB EntrySet." ); } psidev.psi.mi.xml.model.EntrySet mEntrySet = new psidev.psi.mi.xml.model.EntrySet(); // Initialise the model reading the Jaxb object // 1. set attributes mEntrySet.setLevel( jEntrySet.getLevel() ); mEntrySet.setVersion( jEntrySet.getVersion() ); mEntrySet.setMinorVersion( jEntrySet.getMinorVersion() ); // 2. set encapsulated objects for ( psidev.psi.mi.xml253.jaxb.EntryType jEntry : jEntrySet.getEntries() ) { mEntrySet.getEntries().add( entryConverter.fromJaxb( jEntry ) ); } return mEntrySet; }
public psidev.psi.mi.xml253.jaxb.EntrySet toJaxb( psidev.psi.mi.xml.model.EntrySet mEntrySet ) throws ConverterException { if ( mEntrySet == null ) { throw new IllegalArgumentException( "You must give a non null model EntrySet." ); } psidev.psi.mi.xml253.jaxb.EntrySet jEntrySet = new psidev.psi.mi.xml253.jaxb.EntrySet(); // Initialise the JAXB object reading the model // 1. set attributes jEntrySet.setLevel( 2 ); jEntrySet.setVersion( 5 ); jEntrySet.setMinorVersion( 3 ); // 2. set encapsulated objects for ( psidev.psi.mi.xml.model.Entry mEntry : mEntrySet.getEntries() ) { jEntrySet.getEntries().add( entryConverter.toJaxb( mEntry ) ); } return jEntrySet; } }
throw new IllegalArgumentException("convert: one or more null arguments."); if (entrySet.getLevel() != 2) { throw new IllegalArgumentException("convert: only PSI-MI Level 2.5 is supported."); for (Entry entry : entrySet.getEntries()) { entryMapper.run(entry); entrySet.getEntries().clear(); entrySet = null;
private EntrySet createEntrySet(Collection<Entry> entry) { return new EntrySet(entry, 2, 5, 3); }
for (Entry entry : entrySet.getEntries()) EntrySet entrySetToWrite = new EntrySet(Arrays.asList(entry), entrySet.getLevel(), entrySet.getVersion(), entrySet.getMinorVersion()); try
public psidev.psi.mi.xml.model.EntrySet fromJaxb( psidev.psi.mi.xml254.jaxb.EntrySet jEntrySet ) throws ConverterException { if ( jEntrySet == null ) { throw new IllegalArgumentException( "You must give a non null JAXB EntrySet." ); } psidev.psi.mi.xml.model.EntrySet mEntrySet = new psidev.psi.mi.xml.model.EntrySet(); // Initialise the model reading the Jaxb object // 1. set attributes mEntrySet.setLevel( jEntrySet.getLevel() ); mEntrySet.setVersion( jEntrySet.getVersion() ); mEntrySet.setMinorVersion( jEntrySet.getMinorVersion() ); // 2. set encapsulated objects for ( psidev.psi.mi.xml254.jaxb.Entry jEntry : jEntrySet.getEntries() ) { mEntrySet.getEntries().add( entryConverter.fromJaxb( jEntry ) ); } return mEntrySet; }
private void removeInteractorRedundancy( EntrySet mEntrySet ) { if( ConverterContext.getInstance().getConverterConfig().getXmlForm() == PsimiXmlForm.FORM_COMPACT ) { for ( Entry entry : mEntrySet.getEntries() ) { Map<Interactor, Interactor> uniqueInteractors = new HashMap<Interactor, Interactor>(); for ( Interaction interaction : entry.getInteractions() ) { for ( Participant participant : interaction.getParticipants() ) { if( participant.getInteractor() != null ) { final Interactor myInteractor = participant.getInteractor(); if( uniqueInteractors.containsKey( myInteractor ) ) { final Interactor uniq = uniqueInteractors.get( myInteractor ); participant.setInteractor( uniq ); } else { uniqueInteractors.put( myInteractor, myInteractor ); } } } // participants } // interactions // if we had a compact format, we cannot remove interactor redundancy without changing the interactions // and update the interactor xref if (!uniqueInteractors.isEmpty()){ entry.getInteractors().clear(); entry.getInteractors().addAll( uniqueInteractors.keySet() ); } } // entries } // model is compact }
EntrySet entrySet = new EntrySet(PsimiXmlVersion.VERSION_25_UNDEFINED); entry.getInteractions().addAll(interactions); entrySet.getEntries().add(entry);
public EntrySet( Collection<Entry> entries, int level, int version, int minorVersion ) { this.entries = entries; setLevel( level ); setVersion( version ); setMinorVersion( minorVersion ); }
public static void main( String[] args ) throws PsimiXmlWriterException { EntrySet entrySet = new EntrySet( 2, 5, 3 ); // Initialise your entryset, add interactions ... PsimiXmlWriter writer = new PsimiXmlWriter(); writer.write( entrySet, new File( "path/to/outputfile.xml" ) ); } }
public psidev.psi.mi.xml254.jaxb.EntrySet toJaxb( psidev.psi.mi.xml.model.EntrySet mEntrySet ) throws ConverterException { if ( mEntrySet == null ) { throw new IllegalArgumentException( "You must give a non null model EntrySet." ); } psidev.psi.mi.xml254.jaxb.EntrySet jEntrySet = new psidev.psi.mi.xml254.jaxb.EntrySet(); // Initialise the JAXB object reading the model // 1. set attributes jEntrySet.setLevel( 2 ); jEntrySet.setVersion( 5 ); jEntrySet.setMinorVersion( 4 ); // 2. set encapsulated objects for ( psidev.psi.mi.xml.model.Entry mEntry : mEntrySet.getEntries() ) { jEntrySet.getEntries().add( entryConverter.toJaxb( mEntry ) ); } return jEntrySet; } }
public EntrySet( PsimiXmlVersion version ) { setLevel( version.getLevel() ); setVersion( version.getMajor() ); setMinorVersion( version.getMinor() ); }
public void map() { final Collection<Entry> entries = es.getEntries(); for(Entry entry: entries) { mapNetworkMetaData(entry); mapNodes(entry.getInteractors()); mapEdges(entry.getInteractions()); } }
for (Entry entry : entrySet.getEntries()) {
EntrySet entrySet = pr.read( new File( "path/to/data.xml" ) ); for ( Entry entry : entrySet.getEntries() ) {
for (Entry entry : entrySet.getEntries()) { InstitutionConverter institutionConverter = new InstitutionConverter(); Institution institution;