3 * Copyright (C) 2013 EDIT
4 * European Distributed Institute of Taxonomy
5 * http://www.e-taxonomy.eu
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.
10 package eu
.etaxonomy
.taxeditor
.ui
.section
.occurrence
.dna
;
13 import java
.net
.URISyntaxException
;
15 import org
.eclipse
.swt
.widgets
.Text
;
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
;
35 public class SequenceGeneralDetailElement
extends AbstractCdmDetailElement
<Sequence
> {
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
;
52 public SequenceGeneralDetailElement(CdmFormFactory formFactory
, ICdmFormElement formElement
) {
53 super(formFactory
, formElement
);
60 * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#createControls
61 * (eu.etaxonomy.taxeditor.forms.ICdmFormElement, java.lang.Object, int)
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
);
71 URI genBankUri
= null;
76 genBankUri
= entity
.getGenBankUri();
77 emblUri
= entity
.getEmblUri();
78 ddbjUri
= entity
.getDdbjUri();
79 boldUri
= entity
.getBoldUri();
81 catch(URISyntaxException e
){
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");
101 * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#handleEvent(java
105 public void handleEvent(Object eventSource
) {
106 if(eventSource
==comboMarker
){
107 getEntity().setDnaMarker(comboMarker
.getSelection());
109 else if(eventSource
==textConsensusSequence
){
110 SequenceString consensusSequence
= getEntity().getConsensusSequence();
111 if(consensusSequence
==null){
112 consensusSequence
= SequenceString
.NewInstance();
114 consensusSequence
.setString(textConsensusSequence
.getText());
115 getEntity().setConsensusSequence(consensusSequence
);
116 textConsensusSequenceLength
.setNumber(consensusSequence
.getLength());
118 else if(eventSource
==textBarcodeSequence
){
119 SequenceString barcodeSequencePart
= getEntity().getBarcodeSequencePart();
120 if(barcodeSequencePart
==null){
121 barcodeSequencePart
= SequenceString
.NewInstance();
123 barcodeSequencePart
.setString(textBarcodeSequence
.getText());
124 getEntity().setBarcodeSequencePart(barcodeSequencePart
);
126 else if(eventSource
==textGeneticAccessNo
){
127 textGeneticAccessNo
.setBackground(getPersistentBackground());
128 getEntity().setGeneticAccessionNumber(textGeneticAccessNo
.getText());
129 if(textGeneticAccessNo
.getText()!=null && !textGeneticAccessNo
.getText().isEmpty()){
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
));
139 textNCBIUri
.setText("");
140 textENAUri
.setText("");
141 textDDBJUri
.setText("");
144 else if(eventSource
==textBoldProcessID
){
145 textBoldProcessID
.setBackground(getPersistentBackground());
146 getEntity().setBoldProcessId(textBoldProcessID
.getText());
147 if(textBoldProcessID
.getText()!=null && !textBoldProcessID
.getText().isEmpty()){
149 textBoldUri
.setUri(getEntity().getBoldUri());
150 } catch (URISyntaxException e
) {
151 textBoldProcessID
.setBackground(getColor(Resources
.COLOR_PARSE_ERROR
));
155 textBoldUri
.setText("");