java.io.Serializable
, TableReport
public class LinkageDisequilibrium extends java.lang.Thread implements java.io.Serializable, TableReport
Modifier and Type | Field | Description |
---|---|---|
protected Alignment |
theAlignment |
|
protected AnnotationAlignment |
theAnnotationAlignment |
Constructor | Description |
---|---|
LinkageDisequilibrium(Alignment alignment) |
compute LD based on an alignment.
|
LinkageDisequilibrium(Alignment alignment,
boolean rapidPermute,
int numberOfPermutations) |
compute LD based on an alignment
|
Modifier and Type | Method | Description |
---|---|---|
AnnotationAlignment |
getAnnotatedAlignment() |
Returns an annotated aligment if one was used for this LD
this could be used to access information of locus position
|
double |
getDPrime(int r,
int c) |
Returns D' estimate for a given pair of sites
|
int |
getN(int r,
int c) |
Get number of gametes included in LD calculations (after missing data was excluded)
|
double |
getP(int r,
int c) |
Returns P-value estimate for a given pair of sites.
|
double |
getRSqr(int r,
int c) |
Returns r^2 estimate for a given pair of sites
|
int |
getSiteCount() |
Returns the counts of the sites in the alignment
|
java.lang.Object[] |
getTableColumnNames() |
get the names of the columns
|
java.lang.Object[][] |
getTableData() |
get the data elements
|
java.lang.String |
getTableTitle() |
get the title of the table
|
void |
print(LinkageDisequilibrium ld,
java.io.PrintWriter out) |
print the LD to the PrintWrite
|
void |
run() |
starts the thread to calculate LD
|
java.lang.String |
toString() |
returns representation of the LD results as a string
|
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, yield
protected Alignment theAlignment
protected AnnotationAlignment theAnnotationAlignment
public LinkageDisequilibrium(Alignment alignment)
alignment
- Alignment or AnnotationAlignment (this should only contain
polymorphic sites)public LinkageDisequilibrium(Alignment alignment, boolean rapidPermute, int numberOfPermutations)
alignment
- Alignment or AnnotationAlignment (this should only contain
polymorphic sites)rapidPermute
- Use a rapid approach to P-value estimation (see Contigency Table)numberOfPermutations
- The number of permutations to determine P valuespublic void run()
run
in class java.lang.Thread
public double getP(int r, int c)
r
- is site 1c
- is site 2public int getN(int r, int c)
r
- is site 1c
- is site 2public double getDPrime(int r, int c)
r
- is site 1c
- is site 2public double getRSqr(int r, int c)
r
- is site 1c
- is site 2public int getSiteCount()
public AnnotationAlignment getAnnotatedAlignment()
public java.lang.String toString()
toString
in class java.lang.Thread
public void print(LinkageDisequilibrium ld, java.io.PrintWriter out)
public java.lang.Object[] getTableColumnNames()
TableReport
getTableColumnNames
in interface TableReport
public java.lang.Object[][] getTableData()
TableReport
getTableData
in interface TableReport
public java.lang.String getTableTitle()
TableReport
getTableTitle
in interface TableReport