java.lang.Object
- pal.alignment.AbstractAlignment
- - pal.alignment.ConcatenatedAnnotatedAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, AnnotationAlignment, IdGroup, Report
```
public class ConcatenatedAnnotatedAlignment
extends AbstractAlignment
implements AnnotationAlignment
```
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences. It will merge by either union or intersection. Missing taxa will return missing values on getData.

Version:

$Id:

Author:

Ed Buckler

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.misc.IdGroup
  IdGroup.Utils

Field Summary
- Fields inherited from class pal.alignment.AbstractAlignment
  idGroup, numSeqs, numSites
- Fields inherited from interface pal.alignment.Alignment
  GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA

Constructor Summary

Constructors
Constructor	Description
`ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list, boolean mergeByID, boolean union)`	concatenate alignments

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getChromosome(int site)`	Returns chromosome
`float`	`getChromosomePosition(int site)`	Return the position along chromosome
`char`	`getData(int seq, int site)`	sequence alignment at (sequence, site)
`DataType`	`getDataType(int site)`	Return the datatype for a given site, which can differ between source alignments
`java.lang.String`	`getLocusName(int site)`	Returns the name of the locus
`int`	`getLocusPosition(int site)`	Return the position along the locus (ignores gaps)
`char`	`getPositionType(int site)`	Returns position type (eg.
`float`	`getWeightedLocusPosition(int site)`	Return the weighted position along the gene (handles gaps)
`void`	`report(java.io.PrintWriter out)`	print human readable report (e.g., on parameters and associated model)
`void`	`sortSites()`	sort the sites by chromosome, then by chromosomal location, and final locusPosition

Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, setDataType, setIdentifier, toString, whichIdNumber

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pal.alignment.Alignment
getAlignedSequenceString, getDataType, getSequenceCount, getSiteCount

Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber

- Constructor Detail
  - ConcatenatedAnnotatedAlignment
```
public ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list,
                                      boolean mergeByID,
                                      boolean union)
                               throws java.lang.IllegalArgumentException
```
    concatenate alignments
    
    Parameters:
    
    list - array with alignments to concatenate
    
    mergeByID - if true it will be by ID name
    
    union - if true it will create the union of the list, if false the intersection will be produced
    
    Throws:
    
    java.lang.IllegalArgumentException
- Method Detail
  - getData
```
public char getData(int seq,
                    int site)
```
    sequence alignment at (sequence, site)
    
    Specified by:
    
    getData in interface Alignment
    
    Specified by:
    
    getData in class AbstractAlignment
  - getDataType
```
public DataType getDataType(int site)
```
    Return the datatype for a given site, which can differ between source alignments
    
    Specified by:
    
    getDataType in interface AnnotationAlignment
  - getChromosomePosition
```
public float getChromosomePosition(int site)
```
    Return the position along chromosome
    
    Specified by:
    
    getChromosomePosition in interface AnnotationAlignment
  - getChromosome
```
public int getChromosome(int site)
```
    Returns chromosome
    
    Specified by:
    
    getChromosome in interface AnnotationAlignment
  - getWeightedLocusPosition
```
public float getWeightedLocusPosition(int site)
```
    Return the weighted position along the gene (handles gaps)
    
    Specified by:
    
    getWeightedLocusPosition in interface AnnotationAlignment
  - getLocusPosition
```
public int getLocusPosition(int site)
```
    Return the position along the locus (ignores gaps)
    
    Specified by:
    
    getLocusPosition in interface AnnotationAlignment
  - getPositionType
```
public char getPositionType(int site)
```
    Returns position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.
    
    Specified by:
    
    getPositionType in interface AnnotationAlignment
  - getLocusName
```
public java.lang.String getLocusName(int site)
```
    Returns the name of the locus
    
    Specified by:
    
    getLocusName in interface AnnotationAlignment
  - sortSites
```
public void sortSites()
```
    sort the sites by chromosome, then by chromosomal location, and final locusPosition
  - report
```
public void report(java.io.PrintWriter out)
```
    Description copied from interface: Report
    
    print human readable report (e.g., on parameters and associated model)
    
    Specified by:
    
    report in interface AnnotationAlignment
    
    Specified by:
    
    report in interface Report
    
    Overrides:
    
    report in class AbstractAlignment
    
    Parameters:
    
    out - output stream

Class ConcatenatedAnnotatedAlignment

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

Field Summary

Fields inherited from class pal.alignment.AbstractAlignment

Fields inherited from interface pal.alignment.Alignment

Constructor Summary

Method Summary

Methods inherited from class pal.alignment.AbstractAlignment

Methods inherited from class java.lang.Object

Methods inherited from interface pal.alignment.Alignment

Methods inherited from interface pal.misc.IdGroup

Constructor Detail

ConcatenatedAnnotatedAlignment

Method Detail

getData

getDataType

getChromosomePosition

getChromosome

getWeightedLocusPosition

getLocusPosition

getPositionType

getLocusName

sortSites

report