|
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
|
}
|