eu.etaxonomy.taxeditor.molecular.editor.e4

Class AlignmentEditorE4

java.lang.Object

eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4

public class AlignmentEditorE4
extends java.lang.Object

Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to a consensus sequence.

The contained GUI components used to edit the alignment come from LibrAlign.

Author:

Ben Stöver, pplitzner

Field Summary

Fields

Modifier and Type	Field and Description
org.eclipse.swt.dnd.Clipboard	CLIPBOARD
static int	CONSENSUS_DATA_AREA_INDEX
static int	CONSENSUS_HINT_AREA_INDEX
static java.lang.String	CONSENSUS_NAME
static java.lang.String	DEFAULT_READ_NAME_PREFIX
static int	EDITABLE_CONSENSUS_AREA_INDEX
static java.lang.String	ID
static int	PHEROGRAM_AREA_INDEX
static int	READS_AREA_INDEX

Constructor Summary

Constructors

Constructor and Description
AlignmentEditorE4()

Method Summary

Modifier and Type	Method and Description
java.lang.String	addRead(java.lang.String name, java.net.URI pherogramURI, boolean reverseComplemented, java.lang.String editedSequence, java.lang.Integer firstSeqPos, java.lang.Integer leftCutPos, java.lang.Integer rightCutPos, eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift[] shifts) Adds a new sequence with attached phergram data area to the reads alignment.
void	addRead(java.net.URI pherogramURI, boolean reverseComplemented)
<T> void	createConsensusSequence() Recreates the whole consensus sequence from all single read sequences.
void	createPartControl(org.eclipse.swt.widgets.Composite parent)
java.lang.String	cutPherogramLeft()
java.lang.String	cutPherogramRight()
void	dispose()
void	doSave(org.eclipse.core.runtime.IProgressMonitor monitor)
info.bioinfweb.libralign.alignmentarea.AlignmentArea	getEditableConsensusArea()
info.bioinfweb.libralign.alignmentarea.AlignmentArea	getFocusedArea() Checks whether getReadsArea() or getEditableConsensusArea() currently have the user focus and returns the according component.
info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea	getPherogramArea(java.lang.String sequenceID)
static java.net.URI	getPherogramURI(eu.etaxonomy.cdm.model.molecular.SingleRead pherogramInfo)
info.bioinfweb.libralign.alignmentarea.AlignmentArea	getReadsArea()
boolean	hasPherogram(java.lang.String sequenceID)
void	init(AlignmentEditorInput input)
boolean	isDirty()
boolean	isInsertLeftInPherogram()
boolean	isInsertMode()
static info.bioinfweb.libralign.pherogram.provider.PherogramProvider	readPherogram(java.net.URI uri)
void	reverseComplementSelectedSequences()
void	setFocus()
void	toggleInsertOverwrite()
void	toggleLeftRightInsertionInPherogram()
<T> void	updateConsensusSequence() Updates the current consensus sequence by replacing gaps by the according consensus tokens calculated from the single read sequences and extends the consensus sequence if necessary.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ID

public static final java.lang.String ID

See Also:

Constant Field Values

READS_AREA_INDEX

public static final int READS_AREA_INDEX

See Also:

Constant Field Values

EDITABLE_CONSENSUS_AREA_INDEX

public static final int EDITABLE_CONSENSUS_AREA_INDEX

See Also:

Constant Field Values

CONSENSUS_HINT_AREA_INDEX

public static final int CONSENSUS_HINT_AREA_INDEX

See Also:

Constant Field Values

PHEROGRAM_AREA_INDEX

public static final int PHEROGRAM_AREA_INDEX

See Also:

Constant Field Values

CONSENSUS_DATA_AREA_INDEX

public static final int CONSENSUS_DATA_AREA_INDEX

See Also:

Constant Field Values

DEFAULT_READ_NAME_PREFIX

public static final java.lang.String DEFAULT_READ_NAME_PREFIX

See Also:

Constant Field Values

CONSENSUS_NAME

public static final java.lang.String CONSENSUS_NAME

See Also:

Constant Field Values

CLIPBOARD

public final org.eclipse.swt.dnd.Clipboard CLIPBOARD

Constructor Detail

AlignmentEditorE4

@Inject
public AlignmentEditorE4()

Method Detail

getReadsArea

public info.bioinfweb.libralign.alignmentarea.AlignmentArea getReadsArea()

getEditableConsensusArea

public info.bioinfweb.libralign.alignmentarea.AlignmentArea getEditableConsensusArea()

getFocusedArea

public info.bioinfweb.libralign.alignmentarea.AlignmentArea getFocusedArea()

Checks whether getReadsArea() or getEditableConsensusArea() currently have the user focus and returns the according component.

Returns:

either the reads or the consensus alignment area or null if none of these components is currently focused

hasPherogram

public boolean hasPherogram(java.lang.String sequenceID)

getPherogramArea

public info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea getPherogramArea(java.lang.String sequenceID)

createPartControl

@PostConstruct
public void createPartControl(org.eclipse.swt.widgets.Composite parent)

dispose

@PreDestroy
public void dispose()

doSave

@Persist
public void doSave(org.eclipse.core.runtime.IProgressMonitor monitor)

init

public void init(AlignmentEditorInput input)
          throws org.eclipse.ui.PartInitException

Throws:

org.eclipse.ui.PartInitException

isDirty

public boolean isDirty()

setFocus

@Focus
public void setFocus()

isInsertMode

public boolean isInsertMode()

isInsertLeftInPherogram

public boolean isInsertLeftInPherogram()

toggleLeftRightInsertionInPherogram

public void toggleLeftRightInsertionInPherogram()

toggleInsertOverwrite

public void toggleInsertOverwrite()

cutPherogramLeft

public java.lang.String cutPherogramLeft()

cutPherogramRight

public java.lang.String cutPherogramRight()

reverseComplementSelectedSequences

public void reverseComplementSelectedSequences()

createConsensusSequence

public <T> void createConsensusSequence()

Recreates the whole consensus sequence from all single read sequences. The previous consensus sequence is overwritten.

updateConsensusSequence

public <T> void updateConsensusSequence()

Updates the current consensus sequence by replacing gaps by the according consensus tokens calculated from the single read sequences and extends the consensus sequence if necessary.

readPherogram

public static info.bioinfweb.libralign.pherogram.provider.PherogramProvider readPherogram(java.net.URI uri)
                                                                                   throws java.io.IOException,
                                                                                          org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException

Throws:

java.io.IOException

org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException

addRead

public void addRead(java.net.URI pherogramURI,
                    boolean reverseComplemented)
             throws java.io.IOException,
                    org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException

Throws:

java.io.IOException

org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException

addRead

public java.lang.String addRead(java.lang.String name,
                                java.net.URI pherogramURI,
                                boolean reverseComplemented,
                                java.lang.String editedSequence,
                                java.lang.Integer firstSeqPos,
                                java.lang.Integer leftCutPos,
                                java.lang.Integer rightCutPos,
                                eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift[] shifts)
                         throws java.io.IOException,
                                org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException

Adds a new sequence with attached phergram data area to the reads alignment.

If null is specified as editedSequence the base call sequence from the pherogram will be set as the edited sequence. If null is specified as shifts no shifts between the edited and the base calls sequence are assumed.

Parameters:

name - the name of the new sequence

pherogramURI - the URI where the associated pherogram file is located

reverseComplemented - Specify true here, if the reverse complement of the pherogram data should be added, false otherwise.

editedSequence - the edited version of the base call sequence (May be null.)

shifts - the alignment information that links the edited and the base call sequence (May be null.)

Returns:

the sequence ID of the added read

Throws:

java.io.IOException - if an error occurred when trying to read the pherogram file

org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException - if the format of the pherogram file is not supported

getPherogramURI

public static java.net.URI getPherogramURI(eu.etaxonomy.cdm.model.molecular.SingleRead pherogramInfo)