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java.lang.Objectuk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
public class AmplimerBean
This object handles information pertaining to the amplimer and any associated mappings. In addition it will validate inputs such as amplimer sequence validity and coordinates
Field Summary | |
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static java.lang.String |
VALID_RESIDUES
Static list of valid residues for DNA sequence, including ambiguity codes. |
Constructor Summary | |
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protected |
AmplimerBean()
Creates a new instance of AmplimerBean, not for general use. |
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AmplimerBean(java.lang.String amplimerName,
java.lang.String amplimer,
int[] roi)
Generates a new AmplimerBean using the following parameters |
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AmplimerBean(java.lang.String amplimerName,
java.lang.String amplimer,
int[] roi,
CdsBean cds)
Generates a new AmplimerBean using the following parameters |
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AmplimerBean(java.lang.String amplimerName,
java.lang.String amplimer,
java.lang.Integer roiStart,
java.lang.Integer roiStop)
Generates a new AmplimerBean using the following parameters |
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AmplimerBean(java.lang.String amplimerName,
java.lang.String amplimer,
java.lang.Integer roiStart,
java.lang.Integer roiStop,
CdsBean cds)
Generates a new AmplimerBean using the following parameters |
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AmplimerBean(java.lang.String amplimerName,
java.lang.String amplimer,
java.lang.String roi,
CdsBean cds)
Generates a new AmplimerBean using the following parameters |
Method Summary | |
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java.lang.Integer |
getAmpLength()
Gets the length of the amplimer. |
java.lang.String |
getAmplimer()
Returns the currently set amplimer as a string. |
java.lang.String |
getAmplimer(int lineSize)
Returns the currently set amplimer as a formatted string with width as defined by lineSize. |
java.lang.String |
getAmplimerName()
Gets the amplimer name. |
java.lang.Boolean |
getAmplimerReversed()
Indicated if the amplimer need to be reverse complimented to match the CDS sequence. |
CdsBean |
getCds()
Gets the CdsBean object assigned to this amplimer. |
java.lang.Integer |
getCdsStart()
Gets the position of the cds that the amplimer starts to match (indexed from 1). |
java.lang.Integer |
getCdsStartIndex()
Gets the position of the cds that the amplimer starts to match (indexed from 0). |
java.lang.Integer |
getCodingStart()
Gets the start of the coding portion of the amplimer (indexed from 1). |
java.lang.Integer |
getCodingStartIndex()
Gets the start of the coding portion of the amplimer (indexed from 0). |
java.lang.Integer |
getCodingStop()
Gets the stop of the coding portion of the amplimer (indexed from 1). |
java.lang.Integer |
getCodingStopIndex()
Gets the stop of the coding portion of the amplimer (indexed from 0). |
java.lang.String |
getMapsToCds()
The name of the CDS that this amplimer should map to. |
int[] |
getRoi()
Gets the current region of interest. |
java.lang.Integer |
getRoiStart()
Gets the current start position of the ROI on the amplimer. |
java.lang.Integer |
getRoiStop()
Gets the current stop position of the ROI on the amplimer. |
void |
setAmplimer(java.lang.String amplimer)
Set the amplimer to the provided string. |
void |
setAmplimerName(java.lang.String amplimerName)
Sets the amplimer name. |
void |
setRoi(int[] roi)
int[] wrapper of setRoi(Integer roiStart, Integer roiStop) . |
protected void |
setRoi(java.lang.Integer roiStart,
java.lang.Integer roiStop)
Sets the region of interest to the provided values. |
protected void |
setRoi(java.lang.String roi)
String wrapper of setRoi(Integer roiStart, Integer roiStop) |
protected void |
setRoiStart(java.lang.Integer roiStart)
Sets the roi start position on the amplimer |
protected void |
setRoiStop(java.lang.Integer roiStop)
Sets the roi stop position on the amplimer |
java.lang.String |
toString()
Gives a basic string representation of this object. |
static boolean |
validateResidues(java.lang.String amplimer)
Validates that the input string only contains DNA residues recognised by AutoCSA. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final java.lang.String VALID_RESIDUES
Constructor Detail |
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protected AmplimerBean()
public AmplimerBean(java.lang.String amplimerName, java.lang.String amplimer, java.lang.String roi, CdsBean cds)
amplimerName
- the name for the amplimeramplimer
- the amplimer sequenceroi
- the region of interest as 2 comma separated values e.g. 15,70cds
- the CdsBean that this amplimer should map topublic AmplimerBean(java.lang.String amplimerName, java.lang.String amplimer, int[] roi)
amplimerName
- the name for the amplimeramplimer
- the amplimer sequenceroi
- the region of interest as a 2 value int[]public AmplimerBean(java.lang.String amplimerName, java.lang.String amplimer, int[] roi, CdsBean cds)
amplimerName
- the name for the amplimeramplimer
- the amplimer sequenceroi
- the region of interest as a 2 value int[]cds
- the CdsBean that this amplimer should map topublic AmplimerBean(java.lang.String amplimerName, java.lang.String amplimer, java.lang.Integer roiStart, java.lang.Integer roiStop)
amplimerName
- the name for the amplimeramplimer
- the amplimer sequenceroiStart
- start position for region of interestroiStop
- stop position for region of interestpublic AmplimerBean(java.lang.String amplimerName, java.lang.String amplimer, java.lang.Integer roiStart, java.lang.Integer roiStop, CdsBean cds)
amplimerName
- the name for the amplimeramplimer
- the amplimer sequenceroiStart
- start position for region of interestroiStop
- stop position for region of interestcds
- the CdsBean that this amplimer should map toMethod Detail |
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public java.lang.String getAmplimer()
public java.lang.String getAmplimer(int lineSize)
lineSize
- number of characters to each line
public void setAmplimer(java.lang.String amplimer)
amplimer
- the amplimer to be setpublic java.lang.Integer getAmpLength()
protected void setRoi(java.lang.Integer roiStart, java.lang.Integer roiStop)
setRoiStart(Integer roiStart)
and setRoiStop(Integer roiStop)
.
roiStart
- the start position for the region of interest within the amplimer (index from 1)roiStop
- the stop position for the region of interest within the amplimer (index from 1)protected void setRoi(java.lang.String roi)
setRoi(Integer roiStart, Integer roiStop)
roi
- the region of interest as 2 comma separated values e.g. 15,70public void setRoi(int[] roi)
setRoi(Integer roiStart, Integer roiStop)
.
roi
- the region of interest as 2 comma separated values e.g. 15,70public int[] getRoi()
public java.lang.Integer getRoiStart()
protected void setRoiStart(java.lang.Integer roiStart)
roiStart
- the start position on the amplimer (indexed from 1)public java.lang.Integer getRoiStop()
protected void setRoiStop(java.lang.Integer roiStop)
roiStop
- the stop position on the amplimer (indexed from 1)public java.lang.String getAmplimerName()
public void setAmplimerName(java.lang.String amplimerName)
amplimerName
- the name of the amplimerpublic java.lang.Integer getCodingStartIndex()
setupCds()
is called for lazy loading.
public java.lang.Integer getCodingStopIndex()
setupCds()
is called for lazy loading.
public java.lang.String getMapsToCds()
public static boolean validateResidues(java.lang.String amplimer)
amplimer
- the string to be checked for validity
public java.lang.Integer getCdsStartIndex()
setupCds()
is called for lazy loading.
public java.lang.Boolean getAmplimerReversed()
public CdsBean getCds()
public java.lang.Integer getCodingStart()
getCodingStartIndex()
is called.
public java.lang.Integer getCodingStop()
getCodingStopIndex()
is called.
public java.lang.Integer getCdsStart()
setupCds()
is called for lazy loading.
public java.lang.String toString()
toString
in class java.lang.Object
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