3 * Copyright (C) 2014 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
.editor
.molecular
;
13 import info
.bioinfweb
.libralign
.alignmentarea
.AlignmentArea
;
14 import info
.bioinfweb
.libralign
.alignmentarea
.selection
.SelectionModel
;
15 import info
.bioinfweb
.libralign
.dataarea
.implementations
.ConsensusSequenceArea
;
16 import info
.bioinfweb
.libralign
.dataarea
.implementations
.SequenceIndexArea
;
17 import info
.bioinfweb
.libralign
.dataarea
.implementations
.pherogram
.PherogramAlignmentModel
;
18 import info
.bioinfweb
.libralign
.dataarea
.implementations
.pherogram
.PherogramArea
;
19 import info
.bioinfweb
.libralign
.dataarea
.implementations
.pherogram
.ShiftChange
;
20 import info
.bioinfweb
.libralign
.editsettings
.EditSettingsChangeEvent
;
21 import info
.bioinfweb
.libralign
.editsettings
.EditSettingsListener
;
22 import info
.bioinfweb
.libralign
.multiplealignments
.AlignmentAreaList
;
23 import info
.bioinfweb
.libralign
.multiplealignments
.MultipleAlignmentsContainer
;
24 import info
.bioinfweb
.libralign
.pherogram
.provider
.BioJavaPherogramProvider
;
25 import info
.bioinfweb
.libralign
.pherogram
.provider
.PherogramProvider
;
26 import info
.bioinfweb
.libralign
.pherogram
.provider
.ReverseComplementPherogramProvider
;
27 import info
.bioinfweb
.libralign
.sequenceprovider
.SequenceDataChangeListener
;
28 import info
.bioinfweb
.libralign
.sequenceprovider
.SequenceDataProvider
;
29 import info
.bioinfweb
.libralign
.sequenceprovider
.SequenceUtils
;
30 import info
.bioinfweb
.libralign
.sequenceprovider
.adapters
.StringAdapter
;
31 import info
.bioinfweb
.libralign
.sequenceprovider
.events
.SequenceChangeEvent
;
32 import info
.bioinfweb
.libralign
.sequenceprovider
.events
.SequenceRenamedEvent
;
33 import info
.bioinfweb
.libralign
.sequenceprovider
.events
.TokenChangeEvent
;
34 import info
.bioinfweb
.libralign
.sequenceprovider
.implementations
.PackedSequenceDataProvider
;
35 import info
.bioinfweb
.libralign
.sequenceprovider
.tokenset
.BioJavaTokenSet
;
36 import info
.bioinfweb
.libralign
.sequenceprovider
.tokenset
.TokenSet
;
39 import java
.io
.IOException
;
40 import java
.io
.InputStream
;
42 import java
.util
.ArrayList
;
43 import java
.util
.Collection
;
44 import java
.util
.Collections
;
45 import java
.util
.Iterator
;
47 import java
.util
.TreeMap
;
49 import org
.biojava
.bio
.chromatogram
.ChromatogramFactory
;
50 import org
.biojava
.bio
.chromatogram
.UnsupportedChromatogramFormatException
;
51 import org
.biojava3
.core
.sequence
.compound
.DNACompoundSet
;
52 import org
.biojava3
.core
.sequence
.compound
.NucleotideCompound
;
53 import org
.eclipse
.core
.runtime
.IProgressMonitor
;
54 import org
.eclipse
.swt
.SWT
;
55 import org
.eclipse
.swt
.widgets
.Composite
;
56 import org
.eclipse
.ui
.IActionBars
;
57 import org
.eclipse
.ui
.IEditorInput
;
58 import org
.eclipse
.ui
.IEditorPart
;
59 import org
.eclipse
.ui
.IEditorSite
;
60 import org
.eclipse
.ui
.PartInitException
;
61 import org
.eclipse
.ui
.PlatformUI
;
62 import org
.eclipse
.ui
.commands
.ICommandService
;
63 import org
.eclipse
.ui
.part
.EditorPart
;
65 import eu
.etaxonomy
.cdm
.api
.conversation
.ConversationHolder
;
66 import eu
.etaxonomy
.cdm
.api
.service
.molecular
.ISequenceService
;
67 import eu
.etaxonomy
.cdm
.model
.media
.MediaUtils
;
68 import eu
.etaxonomy
.cdm
.model
.molecular
.Sequence
;
69 import eu
.etaxonomy
.cdm
.model
.molecular
.SequenceString
;
70 import eu
.etaxonomy
.cdm
.model
.molecular
.SingleRead
;
71 import eu
.etaxonomy
.cdm
.model
.molecular
.SingleReadAlignment
;
72 import eu
.etaxonomy
.taxeditor
.editor
.handler
.alignmenteditor
.ToggleInsertOverwriteHandler
;
73 import eu
.etaxonomy
.taxeditor
.editor
.handler
.alignmenteditor
.ToggleLeftRightInsertionHandler
;
74 import eu
.etaxonomy
.taxeditor
.store
.CdmStore
;
79 * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
80 * a consensus sequence.
82 * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
88 public class AlignmentEditor
extends EditorPart
{
89 public static final String ID
= "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
91 public static final int READS_AREA_INDEX
= 1;
92 public static final int CONSENSUS_AREA_INDEX
= READS_AREA_INDEX
+ 1;
93 public static final int PHEROGRAM_AREA_INDEX
= 0;
94 public static final String DEFAULT_READ_NAME_PREFIX
= "Read ";
95 public static final String CONSENSUS_NAME
= "Consensus";
98 private final ConversationHolder conversationHolder
;
100 private final SequenceDataChangeListener DIRTY_LISTENER
= new SequenceDataChangeListener() {
102 public <T
> void afterTokenChange(TokenChangeEvent
<T
> e
) {
107 public <T
> void afterSequenceRenamed(SequenceRenamedEvent
<T
> e
) {
112 public <T
> void afterSequenceChange(SequenceChangeEvent
<T
> e
) {
117 public <T
, U
> void afterProviderChanged(SequenceDataProvider
<T
> oldProvider
,
118 SequenceDataProvider
<U
> newProvider
) { // Not expected.
124 private MultipleAlignmentsContainer alignmentsContainer
= null;
125 private final Map
<Integer
, SingleReadAlignment
> cdmMap
= new TreeMap
<Integer
, SingleReadAlignment
>(); //TODO Move this to ContigSequenceDataProvider
126 private boolean dirty
= false;
128 public AlignmentEditor() {
129 conversationHolder
= CdmStore
.createConversation();
133 private void refreshToolbarElement(String id
) {
134 ICommandService commandService
=
135 (ICommandService
)PlatformUI
.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService
.class);
136 if (commandService
!= null) {
137 commandService
.refreshElements(id
, Collections
.EMPTY_MAP
);
142 private void registerEditSettingListener(MultipleAlignmentsContainer container
) {
143 container
.getEditSettings().addListener(new EditSettingsListener() {
145 public void workingModeChanged(EditSettingsChangeEvent e
) {} // Currently nothing to do
148 public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e
) {
150 refreshToolbarElement(ToggleLeftRightInsertionHandler
.COMMAND_ID
);
154 public void insertChanged(EditSettingsChangeEvent e
) {
156 refreshToolbarElement(ToggleInsertOverwriteHandler
.COMMAND_ID
);
162 private AlignmentArea
createIndexArea(MultipleAlignmentsContainer container
) {
163 AlignmentArea result
= new AlignmentArea(container
);
164 result
.setAllowVerticalScrolling(false);
165 result
.getDataAreas().getTopAreas().add(new SequenceIndexArea(result
.getContentArea()));
170 private AlignmentArea
createEditableAlignmentArea(MultipleAlignmentsContainer container
, boolean allowVerticalScrolling
) {
171 AlignmentArea result
= new AlignmentArea(container
);
172 result
.setAllowVerticalScrolling(allowVerticalScrolling
);
174 TokenSet
<NucleotideCompound
> tokenSet
= new BioJavaTokenSet
<NucleotideCompound
>(new DNACompoundSet(), true);
175 SequenceDataProvider
<NucleotideCompound
> provider
= new PackedSequenceDataProvider
<NucleotideCompound
>(tokenSet
);
176 result
.setSequenceProvider(provider
, false);
177 provider
.getChangeListeners().add(DIRTY_LISTENER
);
183 private AlignmentArea
createConsensusHintArea(MultipleAlignmentsContainer container
,
184 SequenceDataProvider
<?
> sequenceProvider
) {
186 AlignmentArea result
= new AlignmentArea(container
);
187 result
.setAllowVerticalScrolling(false);
188 result
.getDataAreas().getBottomAreas().add(
189 new ConsensusSequenceArea(result
.getContentArea(), sequenceProvider
));
194 private MultipleAlignmentsContainer
getAlignmentsContainer() {
195 if (alignmentsContainer
== null) {
196 alignmentsContainer
= new MultipleAlignmentsContainer();
198 AlignmentAreaList list
= alignmentsContainer
.getAlignmentAreas();
199 list
.add(createIndexArea(alignmentsContainer
));
200 AlignmentArea readsArea
= createEditableAlignmentArea(alignmentsContainer
, true);
201 list
.add(readsArea
); // Make sure READS_AREA_INDEX is correct.
202 list
.add(createEditableAlignmentArea(alignmentsContainer
, false)); // Make sure COMSENSUS_AREA_INDEX is correct.
203 list
.add(createConsensusHintArea(alignmentsContainer
,
204 readsArea
.getSequenceProvider()));
206 registerEditSettingListener(alignmentsContainer
);
208 return alignmentsContainer
;
212 private AlignmentArea
getReadsArea() {
213 return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX
);
217 private AlignmentArea
getConsensusArea() {
218 return getAlignmentsContainer().getAlignmentAreas().get(CONSENSUS_AREA_INDEX
);
222 private PherogramArea
getPherogramArea(int sequenceID
) {
223 return (PherogramArea
)getReadsArea().getDataAreas().getSequenceAreas(sequenceID
).get(PHEROGRAM_AREA_INDEX
);
227 private void createTestContents() {
230 addRead(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").toURI(), false);
231 addRead(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").toURI(), false);
233 // Add test consensus sequence:
234 SequenceDataProvider consensusProvider
= getConsensusArea().getSequenceProvider();
235 int id
= consensusProvider
.addSequence(CONSENSUS_NAME
);
236 Collection
<Object
> tokens
= new ArrayList
<Object
>(); // First save tokens in a collection to avoid GUI updated for each token.
237 tokens
.add(consensusProvider
.getTokenSet().tokenByKeyChar('A'));
238 tokens
.add(consensusProvider
.getTokenSet().tokenByKeyChar('C'));
239 tokens
.add(consensusProvider
.getTokenSet().tokenByKeyChar('G'));
240 tokens
.add(consensusProvider
.getTokenSet().tokenByKeyChar('T'));
241 consensusProvider
.insertTokensAt(id
, 0, tokens
);
243 catch (Exception e
) {
244 throw new RuntimeException(e
);
249 private void readCDMData(Sequence sequenceNode
) {
250 //TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated).
253 for (SingleReadAlignment singleReadAlignment
: sequenceNode
.getSingleReadAlignments()) {
255 SingleRead pherogramInfo
= singleReadAlignment
.getSingleRead();
256 int id
= addRead(pherogramInfo
.getPrimer().getLabel(), //TODO Should the sequence name contain other/additional/alternative data? Can the same string as in the derivative tree be used here?
257 MediaUtils
.getFirstMediaRepresentationPart(pherogramInfo
.getPherogram()).getUri(),
258 singleReadAlignment
.isReverseComplement(),
259 singleReadAlignment
.getEditedSequence(),
260 singleReadAlignment
.getShifts());
261 cdmMap
.put(id
, singleReadAlignment
);
263 catch (IOException e
) {
264 e
.printStackTrace(); //TODO Output to user (Possibly collect for all pherograms and display in the end.)
266 catch (UnsupportedChromatogramFormatException e
) {
267 e
.printStackTrace(); //TODO Output to user (Possibly collect for all pherograms and display in the end.)
271 // Set consensus sequence:
272 SequenceDataProvider consensusProvider
= getConsensusArea().getSequenceProvider();
273 int id
= consensusProvider
.addSequence(CONSENSUS_NAME
);
274 consensusProvider
.insertTokensAt(id
, 0, SequenceUtils
.stringToTokenList(
275 sequenceNode
.getConsensusSequence().getString(), consensusProvider
.getTokenSet()));
276 //TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?
281 * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
284 public void createPartControl(Composite parent
) {
285 getAlignmentsContainer().createSWTWidget(parent
, SWT
.NONE
);
288 if (getEditorInput() instanceof AlignmentEditorInput
) {
289 if (((AlignmentEditorInput
)getEditorInput()).getSequenceNode() != null) {
290 Sequence sequenceNode
= ((AlignmentEditorInput
)getEditorInput()).getSequenceNode();
291 //re-load into the current session if it is already persisted in the DB
292 if(sequenceNode
!=null && sequenceNode
.getId()!=0){
293 sequenceNode
= CdmStore
.getService(ISequenceService
.class).load(sequenceNode
.getUuid());
295 readCDMData(sequenceNode
);
298 createTestContents(); // This case will removed after the test phase and an exception should probably be thrown.
302 throw new IllegalArgumentException("The editor input must have the type " +
303 AlignmentEditorInput
.class.getCanonicalName()); //TODO What should be done here?
308 private void updateStatusBar() {
309 IActionBars bars
= getEditorSite().getActionBars();
310 bars
.getStatusLineManager().setMessage("Edit mode: " +
311 (getReadsArea().getEditSettings().isInsert() ?
"Insert" : "Overwrite") + " " +
312 "Insertion in pherogram: " +
313 (getReadsArea().getEditSettings().isInsertLeftInDataArea() ?
"Left" : "Right"));
317 private SingleReadAlignment
.Shift
[] convertToCDMShifts(PherogramAlignmentModel alignmentModel
) {
318 SingleReadAlignment
.Shift
[] result
= new SingleReadAlignment
.Shift
[alignmentModel
.getShiftChangeCount()];
319 Iterator
<ShiftChange
> iterator
= alignmentModel
.shiftChangeIterator();
321 while (iterator
.hasNext()) {
322 ShiftChange shiftChange
= iterator
.next();
323 result
[pos
] = new SingleReadAlignment
.Shift(shiftChange
.getBaseCallIndex(), shiftChange
.getShiftChange());
330 * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
333 public void doSave(IProgressMonitor monitor
) {
334 if (getEditorInput() instanceof AlignmentEditorInput
) {
335 String taskName
= "Saving alignment";
336 monitor
.beginTask(taskName
, 3);
338 Sequence sequenceNode
= ((AlignmentEditorInput
)getEditorInput()).getSequenceNode();
339 StringAdapter stringProvider
= new StringAdapter(getConsensusArea().getSequenceProvider(), false); // Throws an exception if a token has more than one character.
341 // Write consensus sequence:
342 SequenceString consensusSequenceObj
= sequenceNode
.getConsensusSequence();
343 String newConsensusSequence
= stringProvider
.getSequence(
344 getConsensusArea().getSequenceProvider().sequenceIDByName(CONSENSUS_NAME
));
345 if (consensusSequenceObj
== null) {
346 sequenceNode
.setConsensusSequence(SequenceString
.NewInstance(newConsensusSequence
));
349 consensusSequenceObj
.setString(newConsensusSequence
);
352 // Write single reads:
353 stringProvider
.setUnderlyingProvider(getReadsArea().getSequenceProvider());
354 sequenceNode
.getSingleReadAlignments().retainAll(cdmMap
.values()); // Remove all reads that are not in the alignment anymore.
355 Iterator
<Integer
> iterator
= getReadsArea().getSequenceProvider().sequenceIDIterator();
356 while (iterator
.hasNext()) {
357 int id
= iterator
.next();
358 SingleReadAlignment singleRead
= cdmMap
.get(id
);
359 if (singleRead
== null) {
360 //TODO Create new read object. => Shall it be allowed to add reads in the alignment editor which are not represented in the CDM tree before the alignment editor is saved?
361 //singleRead = SingleReadAlignment.NewInstance(consensusSequence, singleRead, shifts, editedSequence);
364 singleRead
.setEditedSequence(stringProvider
.getSequence(id
));
365 singleRead
.setReverseComplement(getPherogramArea(id
).getProvider() instanceof ReverseComplementPherogramProvider
); // Works only if ReverseComplementPherogramProvider instances are not nested.
366 singleRead
.setShifts(convertToCDMShifts(getPherogramArea(id
).getAlignmentModel()));
369 if (!conversationHolder
.isBound()) {
370 conversationHolder
.bind();
374 // Commit the conversation and start a new transaction immediately:
375 conversationHolder
.commit(true);
381 firePropertyChange(PROP_DIRTY
);
384 //TODO Throw exception as soon as testing period which allows unlinked AlignmentEditor is over.
390 * @see org.eclipse.ui.part.EditorPart#doSaveAs()
393 public void doSaveAs() {}
397 * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
400 public void init(IEditorSite site
, IEditorInput input
) throws PartInitException
{
407 * @see org.eclipse.ui.part.EditorPart#isDirty()
410 public boolean isDirty() {
415 private void setDirty() {
417 firePropertyChange(IEditorPart
.PROP_DIRTY
);
422 * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
425 public boolean isSaveAsAllowed() {
426 return false; // "Save as" not allowed.
431 public void setFocus() {
432 if(conversationHolder
!=null){
433 conversationHolder
.bind();
438 public boolean isInsertMode() {
439 return getAlignmentsContainer().getEditSettings().isInsert();
443 public boolean isInsertLeftInPherogram() {
444 return getAlignmentsContainer().getEditSettings().isInsertLeftInDataArea();
448 public void toggleLeftRightInsertionInPherogram() {
449 getAlignmentsContainer().getEditSettings().toggleInsertLeftInDataArea();
453 public void toggleInsertOverwrite() {
454 getAlignmentsContainer().getEditSettings().toggleInsert();
458 public void reverseComplementSelection() {
459 SelectionModel selection
= getReadsArea().getSelection();
460 SequenceDataProvider
<?
> provider
= getReadsArea().getSequenceProvider();
461 for (int row
= selection
.getStartRow(); row
< selection
.getStartRow() + selection
.getCursorHeight(); row
++) {
462 int sequenceID
= getReadsArea().getSequenceOrder().idByIndex(row
);
463 //TODO rc edited sequence
465 if (getPherogramArea(sequenceID
).getProvider() instanceof ReverseComplementPherogramProvider
) {
466 //getPherogramArea(sequenceID).
467 //TODO Allow to set new provider in PherogramArea or create new PherogramArea
468 //TODO Reposition pherogram according to previous position in edited sequence and length
474 public static PherogramProvider
readPherogram(URI uri
) throws IOException
, UnsupportedChromatogramFormatException
{
475 PherogramProvider result
;
476 InputStream stream
= uri
.toURL().openStream();
478 result
= new BioJavaPherogramProvider(ChromatogramFactory
.create(stream
));
487 private String
newReadName() {
489 while (getReadsArea().getSequenceProvider().sequenceIDByName(DEFAULT_READ_NAME_PREFIX
+ index
)
490 != SequenceDataProvider
.NO_SEQUENCE_FOUND
) {
494 return DEFAULT_READ_NAME_PREFIX
+ index
;
498 public void addRead(URI pherogramURI
, boolean reverseComplemented
) throws IOException
, UnsupportedChromatogramFormatException
{
499 addRead(newReadName(), pherogramURI
, reverseComplemented
, null, null);
504 * Adds a new sequence with attached phergram data area to the reads alignment.
506 * If {@code null} is specified as {@code editedSequence} the base call sequence from the pherogram will
507 * be set as the edited sequence. If {@code null} is specified as {@code shifts} no shifts between the edited
508 * and the base calls sequence are assumed.
510 * @param name the name of the new sequence
511 * @param pherogramURI the URI where the associated pherogram file is located
512 * @param reverseComplemented Specify {@code true} here, if the reverse complement of the pherogram data should
513 * be added, {@code false} otherwise.
514 * @param editedSequence the edited version of the base call sequence (May be {@code null}.)
515 * @param shifts the alignment information that links the edited and the base call sequence (May be {@code null}.)
516 * @return the sequence ID of the added read
517 * @throws IOException if an error occurred when trying to read the pherogram file
518 * @throws UnsupportedChromatogramFormatException if the format of the pherogram file is not supported
520 public int addRead(String name
, URI pherogramURI
, boolean reverseComplemented
, String editedSequence
,
521 SingleReadAlignment
.Shift
[] shifts
) throws IOException
, UnsupportedChromatogramFormatException
{
523 SequenceDataProvider provider
= getReadsArea().getSequenceProvider();
524 PherogramProvider pherogramProvider
= readPherogram(pherogramURI
); // Must happen before a sequence is added, because it might throw an exception.
525 if (reverseComplemented
) {
526 pherogramProvider
= new ReverseComplementPherogramProvider(pherogramProvider
);
530 provider
.addSequence(name
);
531 int id
= provider
.sequenceIDByName(name
);
533 // Set edited sequence:
534 Collection
<Object
> tokens
; // First save tokens in a collection to avoid GUI updated for each token.
535 if (editedSequence
!= null) {
536 tokens
= SequenceUtils
.stringToTokenList(editedSequence
, provider
.getTokenSet());
538 else { // Copy base call sequence into alignment:
539 tokens
= new ArrayList
<Object
>();
540 for (int i
= 0; i
< pherogramProvider
.getSequenceLength(); i
++) {
541 tokens
.add(provider
.getTokenSet().tokenByKeyChar(
542 pherogramProvider
.getBaseCall(i
).getUpperedBase().charAt(0)));
546 provider
.insertTokensAt(id
, 0, tokens
);
548 // Create pherogram area:
549 PherogramArea pherogramArea
= new PherogramArea(getReadsArea().getContentArea(), pherogramProvider
);
552 if ((shifts
!= null) && (shifts
.length
> 0)) {
553 PherogramAlignmentModel alignmentModel
= pherogramArea
.getAlignmentModel();
554 for (int i
= 0; i
< shifts
.length
; i
++) {
555 alignmentModel
.addShiftChange(shifts
[i
].position
, shifts
[i
].shift
);
560 // Add pherogram area to GUI:
561 pherogramArea
.addMouseListener(new PherogramMouseListener(pherogramURI
));
562 getReadsArea().getDataAreas().getSequenceAreas(id
).add(pherogramArea
);