|
1
|
/**
|
|
2
|
* Copyright (C) 2016 EDIT
|
|
3
|
* European Distributed Institute of Taxonomy
|
|
4
|
* http://www.e-taxonomy.eu
|
|
5
|
*
|
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
|
8
|
*/
|
|
9
|
package eu.etaxonomy.taxeditor.molecular.io.wizard;
|
|
10
|
|
|
11
|
|
|
12
|
import info.bioinfweb.commons.bio.SequenceUtils;
|
|
13
|
import info.bioinfweb.jphyloio.events.type.EventContentType;
|
|
14
|
import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;
|
|
15
|
import info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo;
|
|
16
|
|
|
17
|
import java.util.ArrayList;
|
|
18
|
import java.util.Collections;
|
|
19
|
import java.util.List;
|
|
20
|
|
|
21
|
import org.eclipse.core.databinding.observable.value.IObservableValue;
|
|
22
|
import org.eclipse.core.databinding.observable.value.WritableValue;
|
|
23
|
|
|
24
|
|
|
25
|
|
|
26
|
/**
|
|
27
|
* The data model for a wizard to export single read alignments to different file formats using <i>JPhyloIO</i>.
|
|
28
|
*
|
|
29
|
* @author Ben Stöver
|
|
30
|
* @date 16.11.2016
|
|
31
|
*/
|
|
32
|
public class ExportSingleReadAlignmentWizardModel {
|
|
33
|
protected static final JPhyloIOReaderWriterFactory READER_WRITER_FACTORY = new JPhyloIOReaderWriterFactory();
|
|
34
|
protected static final List<JPhyloIOFormatInfo> FORMATS = createFormatInfoList();
|
|
35
|
|
|
36
|
|
|
37
|
private IObservableValue formatInfo = new WritableValue(0, Integer.class);
|
|
38
|
private IObservableValue fileName = new WritableValue(null, String.class);
|
|
39
|
private IObservableValue exportSingleReads = new WritableValue(true, Boolean.class);
|
|
40
|
private IObservableValue exportConsensusSequence = new WritableValue(true, Boolean.class);
|
|
41
|
private IObservableValue consensusSequenceLabel = new WritableValue("Consensus", String.class);
|
|
42
|
private IObservableValue elongateSequences = new WritableValue(false, Boolean.class);
|
|
43
|
private IObservableValue useGapToken = new WritableValue(true, Boolean.class);
|
|
44
|
|
|
45
|
|
|
46
|
private static List<JPhyloIOFormatInfo> createFormatInfoList() {
|
|
47
|
List<JPhyloIOFormatInfo> result = new ArrayList<JPhyloIOFormatInfo>();
|
|
48
|
for (String formatID : READER_WRITER_FACTORY.getFormatIDsSet()) {
|
|
49
|
JPhyloIOFormatInfo info = READER_WRITER_FACTORY.getFormatInfo(formatID);
|
|
50
|
if (info.isElementModeled(EventContentType.ALIGNMENT, false)) { // Check if the current format allows to write alignments.
|
|
51
|
result.add(info);
|
|
52
|
}
|
|
53
|
}
|
|
54
|
return Collections.unmodifiableList(result);
|
|
55
|
}
|
|
56
|
|
|
57
|
|
|
58
|
protected IObservableValue getFormatInfoObservable() {
|
|
59
|
return formatInfo;
|
|
60
|
}
|
|
61
|
|
|
62
|
|
|
63
|
/**
|
|
64
|
* Returns the <i>JPhyloIO</i> format info object to be used for exporting.
|
|
65
|
*
|
|
66
|
* @return the format info
|
|
67
|
*/
|
|
68
|
public JPhyloIOFormatInfo getFormatInfo() {
|
|
69
|
return FORMATS.get((Integer)formatInfo.getValue());
|
|
70
|
}
|
|
71
|
|
|
72
|
|
|
73
|
public String getFileName() {
|
|
74
|
return (String)fileName.getValue();
|
|
75
|
}
|
|
76
|
|
|
77
|
|
|
78
|
protected IObservableValue getFileNameObservable() {
|
|
79
|
return fileName;
|
|
80
|
}
|
|
81
|
|
|
82
|
|
|
83
|
public boolean isExportSingleReads() {
|
|
84
|
return (Boolean)exportSingleReads.getValue();
|
|
85
|
}
|
|
86
|
|
|
87
|
|
|
88
|
protected IObservableValue getExportSingleReadsObservable() {
|
|
89
|
return exportSingleReads;
|
|
90
|
}
|
|
91
|
|
|
92
|
|
|
93
|
public boolean isExportConsensusSequence() {
|
|
94
|
return (Boolean)exportConsensusSequence.getValue();
|
|
95
|
}
|
|
96
|
|
|
97
|
|
|
98
|
protected IObservableValue getExportConsensusSequenceObservable() {
|
|
99
|
return exportConsensusSequence;
|
|
100
|
}
|
|
101
|
|
|
102
|
|
|
103
|
public String getConsensusSequenceLabel() {
|
|
104
|
return (String)consensusSequenceLabel.getValue();
|
|
105
|
}
|
|
106
|
|
|
107
|
|
|
108
|
protected IObservableValue getConsensusSequenceLabelObservable() {
|
|
109
|
return consensusSequenceLabel;
|
|
110
|
}
|
|
111
|
|
|
112
|
|
|
113
|
public String getElongationToken() {
|
|
114
|
if ((Boolean)elongateSequences.getValue()) {
|
|
115
|
if ((Boolean)useGapToken.getValue()) {
|
|
116
|
return Character.toString(SequenceUtils.GAP_CHAR);
|
|
117
|
}
|
|
118
|
else {
|
|
119
|
return Character.toString(SequenceUtils.MISSING_DATA_CHAR);
|
|
120
|
}
|
|
121
|
}
|
|
122
|
else {
|
|
123
|
return null;
|
|
124
|
}
|
|
125
|
}
|
|
126
|
|
|
127
|
|
|
128
|
protected IObservableValue getElongateSequencesObservable() {
|
|
129
|
return elongateSequences;
|
|
130
|
}
|
|
131
|
|
|
132
|
|
|
133
|
protected IObservableValue getUseGapTokenObservable() {
|
|
134
|
return useGapToken;
|
|
135
|
}
|
|
136
|
}
|