eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SingleReadGeneralDetailElement.java

   1 // $Id$
   2 /**
   3  * Copyright (C) 2014 EDIT
   4  * European Distributed Institute of Taxonomy
   5  * http://www.e-taxonomy.eu
   6  *
   7  * The contents of this file are subject to the Mozilla Public License Version 1.1
   8  * See LICENSE.TXT at the top of this package for the full license terms.
   9  */
  10 package eu.etaxonomy.taxeditor.ui.section.occurrence.dna;
  11
  12 import eu.etaxonomy.cdm.model.agent.AgentBase;
  13 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  14 import eu.etaxonomy.cdm.model.molecular.Primer;
  15 import eu.etaxonomy.cdm.model.molecular.Sequence;
  16 import eu.etaxonomy.cdm.model.molecular.SequenceString;
  17 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  18 import eu.etaxonomy.cdm.model.reference.Reference;
  19 import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
  20 import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
  21 import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
  22 import eu.etaxonomy.taxeditor.ui.element.NumberWithLabelElement;
  23 import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
  24 import eu.etaxonomy.taxeditor.ui.element.TimePeriodElement;
  25 import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
  26 import eu.etaxonomy.taxeditor.ui.selection.EntitySelectionElement;
  27
  28 /**
  29  * @author pplitzner
  30  * @date 06.01.2014
  31  *
  32  */
  33 public class SingleReadGeneralDetailElement extends AbstractCdmDetailElement<SingleRead> {
  34
  35
  36     private TimePeriodElement dateElement;
  37     private EntitySelectionElement<AgentBase> selectionSequencingStaff;
  38     private TermComboElement<DefinedTerm> comboMaterialOrMethod;
  39     private NumberWithLabelElement numberReadLength;
  40     private TextWithLabelElement textEditedSequence;
  41     private TextWithLabelElement textPrimerName;
  42     private TextWithLabelElement textPrimerSequence;
  43     private EntitySelectionElement<Reference> selectionReference;
  44
  45     /**
  46      * @param formFactory
  47      * @param formElement
  48      */
  49     public SingleReadGeneralDetailElement(CdmFormFactory formFactory, ICdmFormElement formElement) {
  50         super(formFactory, formElement);
  51     }
  52
  53     /*
  54      * (non-Javadoc)
  55      *
  56      * @see
  57      * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#createControls
  58      * (eu.etaxonomy.taxeditor.forms.ICdmFormElement, java.lang.Object, int)
  59      */
  60     @Override
  61     protected void createControls(ICdmFormElement formElement, SingleRead entity, int style) {
  62
  63 //        dateElement = formFactory.createTimePeriodElement(formElement, "Sequencing Date", entity.getDateSequenced(), style);
  64 //        selectionSequencingStaff = formFactory
  65 //                .createSelectionElement(AgentBase.class,
  66 //                        getConversationHolder(), formElement, "Sequencing Staff",
  67 //                        null,
  68 //                        EntitySelectionElement.ALL, style);
  69 //        MaterialOrMethodEvent materialOrMethod = entity.getMaterialOrMethod();
  70 //        DefinedTerm definedMaterialOrMethod = null;
  71 //        if(materialOrMethod!=null){
  72 //            definedMaterialOrMethod = materialOrMethod.getDefinedMaterialOrMethod();
  73 //        }
  74 //        comboMaterialOrMethod = formFactory.createTermComboElement(DefinedTerm.class, formElement, "Mat. & Meth.", definedMaterialOrMethod, style);
  75 //
  76 //        //TODO sequence can be null if DerivateView is opened again. Why?? When initially created it is not null
  77 //        SequenceString editedSequence = entity.getSequence();
  78 //        Integer readLength = 0;
  79 //        String editedSequenceString = "";
  80 //        if(editedSequence!=null){
  81 //            Integer length = editedSequence.getLength();
  82 //            if(length!=null){
  83 //                readLength = length;
  84 //            }
  85 //            editedSequenceString = editedSequence.getString();
  86 //        }
  87 //        textReadLength = formFactory.createNumberTextWithLabelElement(formElement, "Read Length", readLength, style);
  88 //        textEditedSequence = formFactory.createTextWithLabelElement(formElement, "Edited Sequence 5'->3'", editedSequenceString, style);
  89
  90         Primer primer = entity.getPrimer();
  91         String primerLabel = "";
  92         String primerSequence = "";
  93         Reference primerReference = null;
  94         if(primer!=null){
  95            primerLabel = primer.getLabel();
  96            primerSequence = primer.getSequence()==null?"":primer.getSequence().getSequenceString();
  97            primerReference = primer.getPublishedIn();
  98         }
  99         textPrimerName = formFactory.createTextWithLabelElement(formElement, "Primer Name", primerLabel, style);
 100         textPrimerSequence = formFactory.createTextWithLabelElement(formElement, "Primer seq. 5'->3'", primerSequence, style);
 101
 102         selectionReference = formFactory
 103                 .createSelectionElement(Reference.class,
 104                         getConversationHolder(), formElement, "Reference",
 105                         primerReference,
 106                         EntitySelectionElement.ALL, style);
 107     }
 108
 109     /*
 110      * (non-Javadoc)
 111      *
 112      * @see
 113      * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#handleEvent(java
 114      * .lang.Object)
 115      */
 116     @Override
 117     public void handleEvent(Object eventSource) {
 118         if(eventSource==dateElement){
 119             getEntity().setDateSequenced(dateElement.getTimePeriod());
 120         }
 121         else if(eventSource==selectionSequencingStaff){
 122             getEntity().setActor(selectionSequencingStaff.getSelection());
 123         }
 124         else if(eventSource==comboMaterialOrMethod){
 125             getEntity().getMaterialOrMethod().setDefinedMaterialOrMethod(comboMaterialOrMethod.getSelection());
 126         }
 127         else if(eventSource==numberReadLength){
 128             getEditedSequence().setLength(numberReadLength.getInteger());
 129         }
 130         else if(eventSource==textEditedSequence){
 131             getEditedSequence().setString(textEditedSequence.getText());
 132         }
 133         else if(eventSource==textPrimerName){
 134             getPrimer().setLabel(textPrimerName.getText());
 135         }
 136         else if(eventSource==textPrimerSequence){
 137             Sequence sequence = getPrimer().getSequence();
 138             if(sequence==null){
 139                 sequence = Sequence.NewInstance("");
 140             }
 141             sequence.setSequenceString(textPrimerSequence.getText());
 142         }
 143         else if(eventSource==selectionReference){
 144             getPrimer().setPublishedIn(selectionReference.getSelection());
 145         }
 146     }
 147
 148     /**
 149      * @return
 150      */
 151     private SequenceString getEditedSequence() {
 152         SequenceString sequence = getEntity().getSequence();
 153         if(sequence==null){
 154             sequence = SequenceString.NewInstance();
 155         }
 156         return sequence;
 157     }
 158
 159     private Primer getPrimer(){
 160         Primer primer = getEntity().getPrimer();
 161         if(primer==null){
 162             primer = Primer.NewInstance("");
 163         }
 164         return primer;
 165     }
 166
 167 }