eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateContentProvider.java

   1 package eu.etaxonomy.taxeditor.editor.view.derivate;
   2
   3 import java.util.ArrayList;
   4 import java.util.Collections;
   5 import java.util.List;
   6 import java.util.Set;
   7
   8 import org.eclipse.jface.viewers.ITreeContentProvider;
   9 import org.eclipse.jface.viewers.Viewer;
  10
  11 import eu.etaxonomy.cdm.model.molecular.Amplification;
  12 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  13 import eu.etaxonomy.cdm.model.molecular.Sequence;
  14 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  15 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  16 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  17 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  18 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  19 import eu.etaxonomy.taxeditor.editor.EditorUtil;
  20 import eu.etaxonomy.taxeditor.model.AbstractUtility;
  21
  22 public class DerivateContentProvider implements ITreeContentProvider {
  23
  24         @Override
  25         public void dispose() {
  26                 // TODO Auto-generated method stub
  27
  28         }
  29
  30         @Override
  31         public void inputChanged(Viewer viewer, Object oldInput, Object newInput) {
  32         }
  33
  34         @Override
  35         public Object[] getElements(Object inputElement) {
  36             SpecimenOrObservationBase<?> specimen = null;
  37             if(inputElement instanceof DerivateViewEditorInput){
  38                 inputElement = ((DerivateViewEditorInput) inputElement).getDerivate();
  39             }
  40
  41             // return the parent FieldUnit if element is a DerivedUnit
  42             if(inputElement instanceof DerivedUnit){
  43                 specimen = EditorUtil.getFieldUnit((DerivedUnit)inputElement);
  44             }
  45             else if(inputElement instanceof FieldUnit){
  46                 specimen = (FieldUnit) inputElement;
  47             }
  48             else{
  49                 AbstractUtility.error(DerivateContentProvider.class, "Invalid input of type " + inputElement.getClass(), new UnsupportedOperationException());
  50             }
  51             if(specimen!=null){
  52                 return Collections.singleton(specimen).toArray();
  53             }
  54             else {
  55                 return Collections.EMPTY_LIST.toArray();
  56             }
  57         }
  58
  59         @Override
  60         public Object[] getChildren(Object parentElement) {
  61         if(parentElement instanceof DerivateViewEditorInput){
  62             parentElement = ((DerivateViewEditorInput) parentElement).getDerivate();
  63             }
  64         if(parentElement instanceof DnaSample){
  65             DnaSample dnaSample = (DnaSample)parentElement;
  66             List<Object> children = new ArrayList<Object>();
  67             //order is important: users want to see Sequences first
  68             children.addAll(dnaSample.getSequences());
  69             children.addAll(dnaSample.getAmplifications());
  70             return children.toArray();
  71         }
  72         else if(parentElement instanceof Amplification){
  73          return ((Amplification) parentElement).getSingleReads().toArray();
  74         }
  75         else if(parentElement instanceof Sequence){
  76             return ((Sequence) parentElement).getSingleReads().toArray();
  77         }
  78         else if(parentElement instanceof SpecimenOrObservationBase){
  79                 return getDerivates((SpecimenOrObservationBase) parentElement).toArray();
  80             }
  81         else if(parentElement instanceof SingleRead){
  82             List<Object> children = new ArrayList<Object>();
  83             children.add(((SingleRead) parentElement).getAmplification());
  84             //TODO getConsensusSequence??
  85             return children.toArray();
  86         }
  87             return null;
  88         }
  89
  90         @Override
  91         public Object getParent(Object element) {
  92         if(element instanceof DerivateViewEditorInput){
  93             element = ((DerivateViewEditorInput) element).getDerivate();
  94             }
  95
  96         if(element instanceof FieldUnit){
  97             return element;
  98         }
  99         else if(element instanceof DerivedUnit){
 100                 DerivedUnit derivedUnit = (DerivedUnit)element;
 101                 return derivedUnit.getOriginalUnit();
 102             }
 103         else if(element instanceof Amplification){
 104             ((Amplification) element).getDnaSample();
 105         }
 106         else if(element instanceof Sequence){
 107             ((Sequence) element).getDnaSample();
 108         }
 109         else if(element instanceof SingleRead){
 110             // TODO there are multiple possible parents
 111             // does returning null help?
 112             return null;
 113         }
 114                 return null;
 115         }
 116
 117         @Override
 118         public boolean hasChildren(Object element) {
 119         if(element instanceof DerivateViewEditorInput){
 120             element = ((DerivateViewEditorInput) element).getDerivate();
 121             }
 122
 123         if(element instanceof DnaSample){
 124             DnaSample dnaSample = (DnaSample)element;
 125             if(!dnaSample.getSequences().isEmpty() || !dnaSample.getAmplifications().isEmpty()){
 126                 return true;
 127             }
 128         }
 129         else if(element instanceof Amplification){
 130             Amplification amplification = (Amplification)element;
 131             return !amplification.getSingleReads().isEmpty();
 132         }
 133         else if(element instanceof Sequence){
 134             Sequence sequence = (Sequence)element;
 135             return !sequence.getSingleReads().isEmpty();
 136         }
 137         else if(element instanceof SpecimenOrObservationBase){
 138                 SpecimenOrObservationBase specimenOrObservation = (SpecimenOrObservationBase)element;
 139                 for(DerivationEvent event:(Set<DerivationEvent>)specimenOrObservation.getDerivationEvents()){
 140                     if(!event.getDerivatives().isEmpty()){
 141                         return true;
 142                     }
 143                 }
 144             }
 145                 return false;
 146         }
 147
 148         private List<DerivedUnit> getDerivates(SpecimenOrObservationBase specimenOrObservation){
 149             List<DerivedUnit> derivates = new ArrayList<DerivedUnit>();
 150             for(DerivationEvent derivationEvent:(Set<DerivationEvent>)specimenOrObservation.getDerivationEvents()){
 151                 derivates.addAll(derivationEvent.getDerivatives());
 152             }
 153             return derivates;
 154         }
 155
 156 }