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// $Id$
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/**
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* Copyright (C) 2014 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.taxeditor.ui.section.occurrence.dna;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.molecular.Primer;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SequenceString;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
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import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
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import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
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import eu.etaxonomy.taxeditor.ui.element.NumberWithLabelElement;
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import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
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import eu.etaxonomy.taxeditor.ui.element.TimePeriodElement;
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import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
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import eu.etaxonomy.taxeditor.ui.selection.EntitySelectionElement;
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/**
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* @author pplitzner
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* @date 06.01.2014
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*
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*/
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public class SingleReadGeneralDetailElement extends AbstractCdmDetailElement<SingleRead> {
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private TimePeriodElement dateElement;
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private EntitySelectionElement<AgentBase> selectionSequencingStaff;
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private TermComboElement<DefinedTerm> comboMaterialOrMethod;
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private TextWithLabelElement textChromatogram;
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private NumberWithLabelElement textReadLength;
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private TextWithLabelElement textEditedSequence;
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private TextWithLabelElement textPrimerName;
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private TextWithLabelElement textPrimerSequence;
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private EntitySelectionElement<Reference> selectionReference;
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/**
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* @param formFactory
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* @param formElement
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*/
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public SingleReadGeneralDetailElement(CdmFormFactory formFactory, ICdmFormElement formElement) {
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super(formFactory, formElement);
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}
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/*
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* (non-Javadoc)
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*
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* @see
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* eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#createControls
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* (eu.etaxonomy.taxeditor.forms.ICdmFormElement, java.lang.Object, int)
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*/
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@Override
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protected void createControls(ICdmFormElement formElement, SingleRead entity, int style) {
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dateElement = formFactory.createTimePeriodElement(formElement, "Sequencing Date", entity.getDateSequenced(), style);
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selectionSequencingStaff = formFactory
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.createSelectionElement(AgentBase.class,
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getConversationHolder(), formElement, "Sequencing Staff",
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null,
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EntitySelectionElement.ALL, style);
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MaterialOrMethodEvent materialOrMethod = entity.getMaterialOrMethod();
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DefinedTerm definedMaterialOrMethod = null;
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if(materialOrMethod!=null){
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definedMaterialOrMethod = materialOrMethod.getDefinedMaterialOrMethod();
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}
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comboMaterialOrMethod = formFactory.createTermComboElement(DefinedTerm.class, formElement, "Mat. & Meth.", definedMaterialOrMethod, style);
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textChromatogram = formFactory.createTextWithLabelElement(formElement, "Read Chromatogram", "XXX", style);
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//TODO sequence can be null if DerivateView is opened again. Why?? When initially created it is not null
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SequenceString editedSequence = entity.getSequence();
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int readLength = 0;
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String editedSequenceString = "";
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if(editedSequence!=null){
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readLength = editedSequence.getLength();
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editedSequenceString = editedSequence.getString();
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}
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textReadLength = formFactory.createNumberTextWithLabelElement(formElement, "Read Length", readLength, style);
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textEditedSequence = formFactory.createTextWithLabelElement(formElement, "Edited Sequence 5'->3'", editedSequenceString, style);
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Primer primer = entity.getPrimer();
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String primerLabel = "";
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String primerSequence = "";
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Reference primerReference = null;
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if(primer!=null){
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primerLabel = primer.getLabel();
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primerSequence = primer.getSequence()==null?"":primer.getSequence().getSequenceString();
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primerReference = primer.getPublishedIn();
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}
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textPrimerName = formFactory.createTextWithLabelElement(formElement, "Primer Name", primerLabel, style);
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textPrimerSequence = formFactory.createTextWithLabelElement(formElement, "Primer seq. 5'->3'", primerSequence, style);
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selectionReference = formFactory
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.createSelectionElement(Reference.class,
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getConversationHolder(), formElement, "Reference",
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primerReference,
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EntitySelectionElement.ALL, style);
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}
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/*
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* (non-Javadoc)
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*
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* @see
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* eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#handleEvent(java
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* .lang.Object)
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*/
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@Override
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public void handleEvent(Object eventSource) {
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if(eventSource==dateElement){
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getEntity().setDateSequenced(dateElement.getTimePeriod());
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}
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else if(eventSource==selectionSequencingStaff){
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getEntity().setActor(selectionSequencingStaff.getSelection());
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}
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else if(eventSource==comboMaterialOrMethod){
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getEntity().getMaterialOrMethod().setDefinedMaterialOrMethod(comboMaterialOrMethod.getSelection());
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}
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else if(eventSource==textChromatogram){
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//TODO implement
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}
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else if(eventSource==textReadLength){
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getEditedSequence().setLength(textReadLength.getInteger());
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}
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else if(eventSource==textEditedSequence){
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getEditedSequence().setString(textEditedSequence.getText());
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}
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else if(eventSource==textPrimerName){
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getPrimer().setLabel(textPrimerName.getText());
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}
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else if(eventSource==textPrimerSequence){
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Sequence sequence = getPrimer().getSequence();
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if(sequence==null){
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sequence = Sequence.NewInstance("");
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}
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sequence.setSequenceString(textPrimerSequence.getText());
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}
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else if(eventSource==selectionReference){
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getPrimer().setPublishedIn(selectionReference.getSelection());
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}
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}
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/**
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* @return
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*/
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private SequenceString getEditedSequence() {
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SequenceString sequence = getEntity().getSequence();
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if(sequence==null){
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sequence = SequenceString.NewInstance();
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}
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return sequence;
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}
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private Primer getPrimer(){
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Primer primer = getEntity().getPrimer();
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if(primer==null){
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primer = Primer.NewInstance("");
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}
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return primer;
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}
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}
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