StrippedAlignment

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

All Implemented Interfaces:

java.io.Serializable, Alignment, IdGroup, Report

Direct Known Subclasses:

StrippedAnnotatedAlignment
```
public class StrippedAlignment
extends AbstractAlignment
```
takes an alignment and repeatedly removes sites

Version:

$Id: StrippedAlignment.java,v 1.6 2002/02/27 22:25:59 matt Exp $

Author:

Korbinian Strimmer

See Also:

Serialized Form

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

Field Summary

Fields
Modifier and Type Field and Description

protected int[] alias

protected boolean[] notDropped

protected Alignment rawAlignment

protected int rawNumSites
- 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 and Description

StrippedAlignment(Alignment raw)
Constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`dropSite(int s)` drop a site
`char`	`getData(int seq, int site)` sequence alignment at (sequence, site)
`void`	`removeConstantSites()` remove constant sites
`void`	`removeGaps()` remove sites with gaps
`void`	`removeNoninformativeSites()` remove noninformative sites
`void`	`removeSites(char c)` remove site that contain a specified character
`void`	`removeUnknowns()` remove sites with unknowns

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

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

- Field Detail
  - rawAlignment
```
protected Alignment rawAlignment
```
  - rawNumSites
```
protected int rawNumSites
```
  - alias
```
protected int[] alias
```
  - notDropped
```
protected boolean[] notDropped
```
- Constructor Detail
  - StrippedAlignment
```
public StrippedAlignment(Alignment raw)
```
    Constructor
    
    Parameters:
    
    raw - original alignment
- 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
  - dropSite
```
public void dropSite(int s)
```
    drop a site
    
    Parameters:
    
    s - site of original alignment
  - removeSites
```
public void removeSites(char c)
```
    remove site that contain a specified character
    
    Parameters:
    
    c - character that will cause the removal of a site
  - removeGaps
```
public void removeGaps()
```
    remove sites with gaps
  - removeUnknowns
```
public void removeUnknowns()
```
    remove sites with unknowns
  - removeConstantSites
```
public void removeConstantSites()
```
    remove constant sites
  - removeNoninformativeSites
```
public void removeNoninformativeSites()
```
    remove noninformative sites

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