@Entity public class SingleReadAlignment extends VersionableEntity implements java.io.Serializable
Modifier and Type | Class and Description |
---|---|
static class |
SingleReadAlignment.Shift |
CLOB_LENGTH, uuid
Modifier | Constructor and Description |
---|---|
protected |
SingleReadAlignment() |
Modifier and Type | Method and Description |
---|---|
java.lang.Object |
clone()
Clones this versionable entity.
|
Sequence |
getConsensusSequence() |
java.lang.String |
getEditedSequence() |
java.lang.Integer |
getFirstSeqPosition()
Returns the position in the
sequence
this single read align is attached to
where the output of the visible part of the pherogram starts. |
java.lang.Integer |
getLeftCutPosition()
Returns the first base call index of the pherogram which has not been cut off.
|
java.lang.Integer |
getRightCutPosition()
Returns the first base call index of the pherogram that has been cut off (so that the length of the visible
area of the pherogram can be calculated as getRightCutPosition()
|
SingleReadAlignment.Shift[] |
getShifts() |
SingleRead |
getSingleRead() |
boolean |
isReverseComplement() |
static SingleReadAlignment |
NewInstance(Sequence consensusSequence,
SingleRead singleRead) |
static SingleReadAlignment |
NewInstance(Sequence consensusSequence,
SingleRead singleRead,
SingleReadAlignment.Shift[] shifts,
java.lang.String editedSequence) |
void |
setConsensusAlignment(Sequence consensusAlignment) |
void |
setEditedSequence(java.lang.String editedSequence) |
void |
setFirstSeqPosition(java.lang.Integer firstSeqPosition) |
void |
setLeftCutPosition(java.lang.Integer leftCutPosition) |
void |
setReverseComplement(boolean reverseComplement) |
void |
setRightCutPosition(java.lang.Integer rightCutPosition) |
void |
setShifts(SingleReadAlignment.Shift[] shifts) |
void |
setSingleRead(SingleRead singleRead) |
cloneLanguageString, equals, getUpdated, getUpdatedBy, setUpdated, setUpdatedBy
addPropertyChangeListener, addPropertyChangeListener, addToSetWithChangeEvent, deproxy, deproxy, fireOnCreateEvent, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getCreated, getCreatedBy, getId, getUserFriendlyDescription, getUserFriendlyFieldName, getUserFriendlyTypeName, getUuid, hashCode, hasListeners, initListener, instanceToString, invokeSetMethod, invokeSetMethodWithNull, isBlank, isInstanceOf, isNotBlank, isPersited, removeFromSetWithChangeEvent, removePropertyChangeListener, removePropertyChangeListener, replaceInList, setCreated, setCreatedBy, setId, setNewEntityListener, setUuid, toString
finalize, getClass, notify, notifyAll, wait, wait, wait
getCreated, getCreatedBy, getId, getUuid, isInstanceOf, isPersited, setCreated, setCreatedBy, setId, setUuid
public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead)
public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead, SingleReadAlignment.Shift[] shifts, java.lang.String editedSequence)
public Sequence getConsensusSequence()
public void setConsensusAlignment(Sequence consensusAlignment)
public SingleRead getSingleRead()
public void setSingleRead(SingleRead singleRead)
public SingleReadAlignment.Shift[] getShifts()
public void setShifts(SingleReadAlignment.Shift[] shifts)
public java.lang.String getEditedSequence()
public void setEditedSequence(java.lang.String editedSequence)
public boolean isReverseComplement()
public void setReverseComplement(boolean reverseComplement)
public java.lang.Object clone() throws java.lang.CloneNotSupportedException
VersionableEntity
clone
in class VersionableEntity
java.lang.CloneNotSupportedException
Object.clone()
public java.lang.Integer getFirstSeqPosition()
sequence
this single read align
is attached to
where the output of the visible part of the pherogram starts.http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/dataarea/implementations/pherogram/PherogramArea.html#getFirstSeqPos
public void setFirstSeqPosition(java.lang.Integer firstSeqPosition)
getFirstSeqPosition()
public java.lang.Integer getLeftCutPosition()
http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/pherogram/PherogramComponent.html#getLeftCutPosition
public void setLeftCutPosition(java.lang.Integer leftCutPosition)
see
- getLeftCutPosition()
public java.lang.Integer getRightCutPosition()
http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/pherogram/PherogramComponent.html#getRightCutPosition
public void setRightCutPosition(java.lang.Integer rightCutPosition)
see
- getRightCutPosition()
Copyright © 2007-2020 EDIT. All Rights Reserved.