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.editor.molecular;
|
11
|
|
12
|
|
13
|
import java.io.File;
|
14
|
|
15
|
import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment;
|
16
|
import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;
|
17
|
import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;
|
18
|
import info.bioinfweb.libralign.AlignmentArea;
|
19
|
import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
|
20
|
import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
|
21
|
import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
|
22
|
import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider;
|
23
|
import info.bioinfweb.libralign.pherogram.PherogramProvider;
|
24
|
import info.bioinfweb.libralign.pherogram.ReverseComplementPherogramProvider;
|
25
|
import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
|
26
|
import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
|
27
|
|
28
|
import org.biojava.bio.chromatogram.ChromatogramFactory;
|
29
|
import org.biojava3.core.sequence.DNASequence;
|
30
|
import org.biojava3.core.sequence.compound.NucleotideCompound;
|
31
|
import org.eclipse.core.runtime.IProgressMonitor;
|
32
|
import org.eclipse.swt.SWT;
|
33
|
import org.eclipse.swt.widgets.Composite;
|
34
|
import org.eclipse.ui.IEditorInput;
|
35
|
import org.eclipse.ui.IEditorSite;
|
36
|
import org.eclipse.ui.PartInitException;
|
37
|
import org.eclipse.ui.part.EditorPart;
|
38
|
|
39
|
|
40
|
|
41
|
/**
|
42
|
* Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
|
43
|
* a consensus sequence.
|
44
|
* <p>
|
45
|
* The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
|
46
|
*
|
47
|
* @author pplitzner
|
48
|
* @author Ben Stöver
|
49
|
* @date 04.08.2014
|
50
|
*/
|
51
|
public class AlignmentEditor extends EditorPart {
|
52
|
public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
|
53
|
|
54
|
private AlignmentArea alignmentArea;
|
55
|
|
56
|
|
57
|
private AlignmentArea createAlignmentArea() {
|
58
|
try {
|
59
|
//ResourcesPlugin.getWorkspace().getRoot().getFile("/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf");
|
60
|
//System.out.println(AlignmentEditor.class.getResource("/"));
|
61
|
//System.out.println(AlignmentEditor.class.getResource("/../resources/TestPherogram_qualityScore.scf"));
|
62
|
// BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
|
63
|
// new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf")));
|
64
|
//TODO Replace this absolute path with a path working with every workspace location.
|
65
|
|
66
|
Alignment<DNASequence, NucleotideCompound> alignment =
|
67
|
new SimpleAlignment<DNASequence, NucleotideCompound>();
|
68
|
alignment.add("Read 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCA-CCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
|
69
|
alignment.add("Read 2", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
|
70
|
//alignment.add("Consensus edit 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
|
71
|
|
72
|
// StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength());
|
73
|
// for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) {
|
74
|
// seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase());
|
75
|
// }
|
76
|
// alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) +
|
77
|
// seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49))); // One A is deleted for shift change specified below.
|
78
|
|
79
|
BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
|
80
|
new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
|
81
|
new BioJavaTokenSet<NucleotideCompound>(
|
82
|
AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
|
83
|
alignment);
|
84
|
|
85
|
AlignmentArea result = new AlignmentArea();
|
86
|
result.getContentArea().setSequenceProvider(sequenceProvider, false);
|
87
|
SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result.getContentArea());
|
88
|
//sequenceIndexArea.setFirstIndex(5);
|
89
|
//sequenceIndexArea.setHeight(25);
|
90
|
result.getContentArea().getDataAreas().getTopAreas().add(sequenceIndexArea);
|
91
|
|
92
|
// PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider);
|
93
|
// pherogramArea.setFirstSeqPos(34 + 5);
|
94
|
// pherogramArea.setLeftCutPosition(34);
|
95
|
// pherogramArea.setRightCutPosition(820);
|
96
|
// pherogramArea.getAlignmentModel().setShiftChange(38, -1);
|
97
|
// pherogramArea.getAlignmentModel().setShiftChange(49, 2);
|
98
|
// result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea);
|
99
|
|
100
|
PherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
|
101
|
new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\AlignmentTestData\\JR430_JR-P01.ab1")));
|
102
|
PherogramArea pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);
|
103
|
pherogramArea.setFirstSeqPos(1);
|
104
|
pherogramArea.setLeftCutPosition(13);
|
105
|
pherogramArea.setRightCutPosition(697);
|
106
|
pherogramArea.getAlignmentModel().setShiftChange(14, 1);
|
107
|
pherogramArea.getAlignmentModel().setShiftChange(35, 1);
|
108
|
result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea);
|
109
|
|
110
|
pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(
|
111
|
new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\AlignmentTestData\\JR444_JR-P05.ab1"))));
|
112
|
pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);
|
113
|
pherogramArea.setFirstSeqPos(1);
|
114
|
pherogramArea.setLeftCutPosition(267);
|
115
|
pherogramArea.getAlignmentModel().setShiftChange(273, -1);
|
116
|
pherogramArea.setVerticalScale(20 * pherogramArea.getVerticalScale());
|
117
|
result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea);
|
118
|
|
119
|
|
120
|
result.getContentArea().getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result.getContentArea()));
|
121
|
return result;
|
122
|
}
|
123
|
catch (Exception e) {
|
124
|
throw new RuntimeException(e);
|
125
|
}
|
126
|
|
127
|
// Alignment<DNASequence, NucleotideCompound> alignment =
|
128
|
// new SimpleAlignment<DNASequence, NucleotideCompound>();
|
129
|
// alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
|
130
|
// alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
|
131
|
// alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
|
132
|
//
|
133
|
// BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
|
134
|
// new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
|
135
|
// new BioJavaTokenSet<NucleotideCompound>(
|
136
|
// AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
|
137
|
// alignment);
|
138
|
//
|
139
|
// AlignmentArea result = new AlignmentArea();
|
140
|
// result.setSequenceProvider(sequenceProvider, false);
|
141
|
// SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
|
142
|
// //sequenceIndexArea.setFirstIndex(5);
|
143
|
// //sequenceIndexArea.setHeight(25);
|
144
|
// result.getDataAreas().getTopAreas().add(sequenceIndexArea);
|
145
|
// result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
|
146
|
// return result;
|
147
|
}
|
148
|
|
149
|
|
150
|
/* (non-Javadoc)
|
151
|
* @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
|
152
|
*/
|
153
|
@Override
|
154
|
public void createPartControl(Composite parent) {
|
155
|
alignmentArea = createAlignmentArea();
|
156
|
Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);
|
157
|
//getSite().setSelectionProvider(provider)
|
158
|
}
|
159
|
|
160
|
|
161
|
/* (non-Javadoc)
|
162
|
* @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
|
163
|
*/
|
164
|
@Override
|
165
|
public void doSave(IProgressMonitor monitor) {
|
166
|
// TODO Auto-generated method stub
|
167
|
|
168
|
}
|
169
|
|
170
|
|
171
|
/* (non-Javadoc)
|
172
|
* @see org.eclipse.ui.part.EditorPart#doSaveAs()
|
173
|
*/
|
174
|
@Override
|
175
|
public void doSaveAs() {
|
176
|
// TODO Auto-generated method stub
|
177
|
|
178
|
}
|
179
|
|
180
|
|
181
|
/* (non-Javadoc)
|
182
|
* @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
|
183
|
*/
|
184
|
@Override
|
185
|
public void init(IEditorSite site, IEditorInput input) throws PartInitException {
|
186
|
setSite(site);
|
187
|
setInput(input);
|
188
|
}
|
189
|
|
190
|
|
191
|
/* (non-Javadoc)
|
192
|
* @see org.eclipse.ui.part.EditorPart#isDirty()
|
193
|
*/
|
194
|
@Override
|
195
|
public boolean isDirty() {
|
196
|
// TODO Auto-generated method stub
|
197
|
return false;
|
198
|
}
|
199
|
|
200
|
|
201
|
/* (non-Javadoc)
|
202
|
* @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
|
203
|
*/
|
204
|
@Override
|
205
|
public boolean isSaveAsAllowed() {
|
206
|
// TODO Auto-generated method stub
|
207
|
return false;
|
208
|
}
|
209
|
|
210
|
|
211
|
/* (non-Javadoc)
|
212
|
* @see org.eclipse.ui.part.WorkbenchPart#setFocus()
|
213
|
*/
|
214
|
@Override
|
215
|
public void setFocus() {
|
216
|
//alignmentArea.getToolkitComponent().redistributeHeight();
|
217
|
}
|
218
|
}
|