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

   1 // $Id$
   2 /**
   3 * Copyright (C) 2013 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 java.net.URI;
  13 import java.net.URISyntaxException;
  14
  15 import org.eclipse.swt.widgets.Text;
  16
  17 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  18 import eu.etaxonomy.cdm.model.common.TermType;
  19 import eu.etaxonomy.cdm.model.molecular.Sequence;
  20 import eu.etaxonomy.cdm.model.molecular.SequenceString;
  21 import eu.etaxonomy.taxeditor.preference.Resources;
  22 import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
  23 import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
  24 import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
  25 import eu.etaxonomy.taxeditor.ui.element.NumberWithLabelElement;
  26 import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
  27 import eu.etaxonomy.taxeditor.ui.element.UriWithLabelElement;
  28 import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
  29
  30 /**
  31  * @author pplitzner
  32  * @date 19.12.2013
  33  *
  34  */
  35 public class SequenceGeneralDetailElement extends AbstractCdmDetailElement<Sequence> {
  36
  37     private TermComboElement<DefinedTerm> comboMarker;
  38     private TextWithLabelElement textConsensusSequence;
  39     private NumberWithLabelElement textConsensusSequenceLength;
  40     private TextWithLabelElement textBarcodeSequence;
  41     private TextWithLabelElement textGeneticAccessNo;
  42     private UriWithLabelElement textNCBIUri;
  43     private UriWithLabelElement textENAUri;
  44     private UriWithLabelElement textDDBJUri;
  45     private TextWithLabelElement textBoldProcessID;
  46     private UriWithLabelElement textBoldUri;
  47
  48     /**
  49      * @param formFactory
  50      * @param formElement
  51      */
  52     public SequenceGeneralDetailElement(CdmFormFactory formFactory, ICdmFormElement formElement) {
  53         super(formFactory, formElement);
  54     }
  55
  56     /*
  57      * (non-Javadoc)
  58      *
  59      * @see
  60      * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#createControls
  61      * (eu.etaxonomy.taxeditor.forms.ICdmFormElement, java.lang.Object, int)
  62      */
  63     @Override
  64     protected void createControls(ICdmFormElement formElement, Sequence entity, int style) {
  65         comboMarker = formFactory.createDefinedTermComboElement(TermType.DnaMarker, formElement, "DNA Marker", entity.getDnaMarker(), style);
  66 //        textConsensusSequence = formFactory.createTextWithLabelElement(formElement, "Consensus Sequence 5'->3'", entity.getConsensusSequence().getString(), style);
  67 //        textConsensusSequenceLength = formFactory.createNumberTextWithLabelElement(formElement, "Consensus Seq. Length", entity.getConsensusSequence().getLength(), style);
  68 //        ((Text) textConsensusSequenceLength.getMainControl()).setEditable(false);
  69         textBarcodeSequence = formFactory.createTextWithLabelElement(formElement, "Barcode Sequence 5'->3'", entity.getBarcodeSequencePart()==null?"":entity.getBarcodeSequencePart().getString(), style);
  70
  71         URI genBankUri = null;
  72         URI emblUri = null;
  73         URI ddbjUri = null;
  74         URI boldUri = null;
  75         try{
  76             genBankUri = entity.getGenBankUri();
  77             emblUri = entity.getEmblUri();
  78             ddbjUri = entity.getDdbjUri();
  79             boldUri = entity.getBoldUri();
  80         }
  81         catch(URISyntaxException e){
  82
  83         }
  84         textGeneticAccessNo = formFactory.createTextWithLabelElement(formElement, "Genetic Acc. No.", entity.getGeneticAccessionNumber(), style);
  85         textNCBIUri = formFactory.createUriWithLabelElement(formElement, "NCBI URI", genBankUri, style);
  86         ((Text) textNCBIUri.getMainControl()).setEditable(false);
  87         textENAUri = formFactory.createUriWithLabelElement(formElement, "ENA URI", emblUri, style);
  88         ((Text) textENAUri.getMainControl()).setEditable(false);
  89         textDDBJUri = formFactory.createUriWithLabelElement(formElement, "DDBJ URI", ddbjUri, style);
  90         ((Text) textDDBJUri.getMainControl()).setEditable(false);
  91         textBoldProcessID = formFactory.createTextWithLabelElement(formElement, "BOLD Process ID", entity.getBoldProcessId(), style);
  92         textBoldUri = formFactory.createUriWithLabelElement(formElement, "BOLD URI", boldUri, style);
  93         ((Text) textBoldUri.getMainControl()).setEditable(false);
  94         ((Text) textBoldUri.getMainControl()).setToolTipText("Query BOLD");
  95     }
  96
  97     /*
  98      * (non-Javadoc)
  99      *
 100      * @see
 101      * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#handleEvent(java
 102      * .lang.Object)
 103      */
 104     @Override
 105     public void handleEvent(Object eventSource) {
 106         if(eventSource==comboMarker){
 107             getEntity().setDnaMarker(comboMarker.getSelection());
 108         }
 109         else if(eventSource==textConsensusSequence){
 110             SequenceString consensusSequence = getEntity().getConsensusSequence();
 111             if(consensusSequence==null){
 112                 consensusSequence = SequenceString.NewInstance();
 113             }
 114             consensusSequence.setString(textConsensusSequence.getText());
 115             getEntity().setConsensusSequence(consensusSequence);
 116             textConsensusSequenceLength.setNumber(consensusSequence.getLength());
 117         }
 118         else if(eventSource==textBarcodeSequence){
 119             SequenceString barcodeSequencePart = getEntity().getBarcodeSequencePart();
 120             if(barcodeSequencePart==null){
 121                 barcodeSequencePart = SequenceString.NewInstance();
 122             }
 123             barcodeSequencePart.setString(textBarcodeSequence.getText());
 124             getEntity().setBarcodeSequencePart(barcodeSequencePart);
 125         }
 126         else if(eventSource==textGeneticAccessNo){
 127             textGeneticAccessNo.setBackground(getPersistentBackground());
 128             getEntity().setGeneticAccessionNumber(textGeneticAccessNo.getText());
 129             if(textGeneticAccessNo.getText()!=null && !textGeneticAccessNo.getText().isEmpty()){
 130                 try {
 131                     textNCBIUri.setUri(getEntity().getGenBankUri());
 132                     textENAUri.setUri(getEntity().getEmblUri());
 133                     textDDBJUri.setUri(getEntity().getDdbjUri());
 134                 } catch (URISyntaxException e) {
 135                     textGeneticAccessNo.setBackground(getColor(Resources.COLOR_PARSE_ERROR));
 136                 }
 137             }
 138             else{
 139                 textNCBIUri.setText("");
 140                 textENAUri.setText("");
 141                 textDDBJUri.setText("");
 142             }
 143         }
 144         else if(eventSource==textBoldProcessID){
 145             textBoldProcessID.setBackground(getPersistentBackground());
 146             getEntity().setBoldProcessId(textBoldProcessID.getText());
 147             if(textBoldProcessID.getText()!=null && !textBoldProcessID.getText().isEmpty()){
 148                 try {
 149                     textBoldUri.setUri(getEntity().getBoldUri());
 150                 } catch (URISyntaxException e) {
 151                     textBoldProcessID.setBackground(getColor(Resources.COLOR_PARSE_ERROR));
 152                 }
 153             }
 154             else{
 155                 textBoldUri.setText("");
 156             }
 157         }
 158     }
 159
 160 }