Package org.broadinstitute.gatk.engine.datasources.providers

Examples of org.broadinstitute.gatk.engine.datasources.providers.ReadReferenceView$Provider

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    private Iterator<MapData> makeDataIterator(final ReadShardDataProvider dataProvider) {
        return new Iterator<MapData> ()  {
            final ReadView reads = new ReadView(dataProvider);
            final ReadReferenceView reference = new ReadReferenceView(dataProvider);
            final ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
            final Iterator<SAMRecord> readIterator = reads.iterator();

            @Override public boolean hasNext() { return ! engine.exceedsRuntimeLimit() && readIterator.hasNext(); }

            @Override
            public MapData next() {
                final SAMRecord read = readIterator.next();
                final ReferenceContext refContext = ! read.getReadUnmappedFlag()
                        ? reference.getReferenceContext(read)
                        : null;

                // if the read is mapped, create a metadata tracker
                final RefMetaDataTracker tracker = read.getReferenceIndex() >= 0
                        ? rodView.getReferenceOrderedDataForRead(read)
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                else if (listener instanceof JmsListener) {
                    final Bus bus = model.getBus(listener.getBusidref()) ;
                    if (!(bus instanceof JmsBus))
                        continue ;
                   
                    final Provider provider = model.getProvider(bus) ;
                    if (provider instanceof JmsJcaProvider) {
                        // Jms JCA provider defaults to true
                        final JmsJcaProvider jmsJcaProvider = (JmsJcaProvider)provider ;
                        if (!jmsJcaProvider.isSetTransacted() || jmsJcaProvider.getTransacted())
                            return true ;
                    } else if (provider instanceof JmsProviderType) {
                        JmsMessageFilter filter = ((JmsListener)listener).getJmsMessageFilter() ;
                        if (filter == null)
                            filter = ((JmsBus)bus).getJmsMessageFilter() ;
                        if ((filter != null) && filter.getTransacted())
                            return true ;
                    }
                } else if (listener instanceof SqlListener) {
                    final Bus bus = model.getBus(listener.getBusidref()) ;
                    if (!(bus instanceof SqlBus))
                        continue ;
                   
                    final Provider provider = model.getProvider(bus) ;
                    if ((provider instanceof SqlProvider) && ((SqlProvider)provider).getTransacted())
                        return true ;
                }
            }
        }
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    }
    Bus bus = model.getBus(listener.getBusidref());
    if(bus.getClass() != BusImpl.class) {
      throw new ConfigurationException("The base Listener config [" + listener.getName() + "] must reference a base Bus config type (<bus>).");
    }
    Provider provider = model.getProvider(bus);
    if(provider.getClass().isAssignableFrom(BusProviderImpl.class)) {
      throw new ConfigurationException("A base Bus config type (<bus>) must be contained within a base Provider type (<bus-provider>).");
    }
  }
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    JmsListenerDocument.JmsListener jmsListener = (JmsListener) listeners.get(0);
    assertEquals ( false, jmsListener.getIsGateway() );
   
    JmsBusDocument.JmsBus jmsBus = (JmsBusDocument.JmsBus) model.getBus( jmsListener.getBusidref() );
    assertNotNull( "JmsBus element should exist", jmsBus );
    Provider provider = model.getProvider( jmsBus );
    assertTrue( provider instanceof JmsJcaProvider );
    return (JmsJcaProvider) provider;
  }
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    }
    Bus bus = model.getBus(listener.getBusidref());
    if(bus.getClass() != BusImpl.class) {
      throw new ConfigurationException("The base Listener config [" + listener.getName() + "] must reference a base Bus config type (<bus>).");
    }
    Provider provider = model.getProvider(bus);
    if(provider.getClass().isAssignableFrom(BusProviderImpl.class)) {
      throw new ConfigurationException("A base Bus config type (<bus>) must be contained within a base Provider type (<bus-provider>).");
    }
  }
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                else if (listener instanceof JmsListener) {
                    final Bus bus = model.getBus(listener.getBusidref()) ;
                    if (!(bus instanceof JmsBus))
                        continue ;
                   
                    final Provider provider = model.getProvider(bus) ;
                    if (provider instanceof JmsJcaProvider) {
                        // Jms JCA provider defaults to true
                        final JmsJcaProvider jmsJcaProvider = (JmsJcaProvider)provider ;
                        if (!jmsJcaProvider.isSetTransacted() || jmsJcaProvider.getTransacted())
                            return true ;
                    } else if (provider instanceof JmsProviderType) {
                        JmsMessageFilter filter = ((JmsListener)listener).getJmsMessageFilter() ;
                        if (filter == null)
                            filter = ((JmsBus)bus).getJmsMessageFilter() ;
                        if ((filter != null) && filter.getTransacted())
                            return true ;
                    }
                } else if (listener instanceof SqlListener) {
                    final Bus bus = model.getBus(listener.getBusidref()) ;
                    if (!(bus instanceof SqlBus))
                        continue ;
                   
                    final Provider provider = model.getProvider(bus) ;
                    if ((provider instanceof SqlProvider) && ((SqlProvider)provider).getTransacted())
                        return true ;
                }
            }
        }
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    JmsListenerDocument.JmsListener jmsListener = (JmsListener) listeners.get(0);
    assertEquals ( false, jmsListener.getIsGateway() );
   
    JmsBusDocument.JmsBus jmsBus = (JmsBusDocument.JmsBus) model.getBus( jmsListener.getBusidref() );
    assertNotNull( "JmsBus element should exist", jmsBus );
    Provider provider = model.getProvider( jmsBus );
    assertTrue( provider instanceof JmsJcaProvider );
    return (JmsJcaProvider) provider;
  }
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    }
    Bus bus = model.getBus(listener.getBusidref());
    if(bus.getClass() != BusImpl.class) {
      throw new ConfigurationException("The base Listener config [" + listener.getName() + "] must reference a base Bus config type (<bus>).");
    }
    Provider provider = model.getProvider(bus);
    if(provider.getClass().isAssignableFrom(BusProviderImpl.class)) {
      throw new ConfigurationException("A base Bus config type (<bus>) must be contained within a base Provider type (<bus-provider>).");
    }
  }
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                else if (listener instanceof JmsListener) {
                    final Bus bus = model.getBus(listener.getBusidref()) ;
                    if (!(bus instanceof JmsBus))
                        continue ;

                    final Provider provider = model.getProvider(bus) ;
                    if (provider instanceof JmsJcaProvider) {
                        // Jms JCA provider defaults to true
                        final JmsJcaProvider jmsJcaProvider = (JmsJcaProvider)provider ;
                        if (!jmsJcaProvider.isSetTransacted() || jmsJcaProvider.getTransacted())
                            return true ;
                    } else if (provider instanceof JmsProviderType) {
                        JmsMessageFilter filter = ((JmsListener)listener).getJmsMessageFilter() ;
                        if (filter == null)
                            filter = ((JmsBus)bus).getJmsMessageFilter() ;
                        if ((filter != null) && filter.getTransacted())
                            return true ;
                    }
                } else if (listener instanceof SqlListener) {
                    final Bus bus = model.getBus(listener.getBusidref()) ;
                    if (!(bus instanceof SqlBus))
                        continue ;

                    final Provider provider = model.getProvider(bus) ;
                    if ((provider instanceof SqlProvider) && ((SqlProvider)provider).getTransacted())
                        return true ;
                }
            }
        }
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    JmsListenerDocument.JmsListener jmsListener = (JmsListener) listeners.get(0);
    assertEquals ( false, jmsListener.getIsGateway() );
   
    JmsBusDocument.JmsBus jmsBus = (JmsBusDocument.JmsBus) model.getBus( jmsListener.getBusidref() );
    assertNotNull( "JmsBus element should exist", jmsBus );
    Provider provider = model.getProvider( jmsBus );
    assertTrue( provider instanceof JmsJcaProvider );
    return (JmsJcaProvider) provider;
  }
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