Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD

## org.biojava.bio.seq.projection
Class ProjectionUtils

    java.lang.Object
      org.biojava.bio.seq.projection.ProjectionUtils

    public class ProjectionUtils

extends Object

Some common things you want to do while projecting features.

Since:
  1.3
Author:
  Thomas Down, Matthew Pocock

Constructor Summary
`ProjectionUtils()`

Method Summary
`static Location` | `flipLocation(Location oldLoc, int translation)` Flip a location.
`static StrandedFeature.Strand` | `flipStrand(StrandedFeature.Strand s)`
`static Location` | `revertLocation(Location oldLoc, int translation, boolean oppositeStrand)` Revert a location, translating and flipping as required.
`static Location` | `transformLocation(Location oldLoc, int translation, boolean oppositeStrand)` Transform a location, translating and flipping as required.

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

Constructor Detail

### ProjectionUtils

    public ProjectionUtils()

Method Detail

### transformLocation

    public static Location transformLocation(Location oldLoc,
                                             int translation,
                                             boolean oppositeStrand)

  Transform a location, translating and flipping as required.

  If oppositeStrand is false, this is equivalent to translating the location. If it is true, this is equivalent to flipping it.

  Parameters:
    `oldLoc` - the Location to transform
    `translation` - the translation to apply
    `oppositeStrand` - wether or not this is a flip
  Returns:
    the transformed location

### revertLocation

    public static Location revertLocation(Location oldLoc,
                                          int translation,
                                          boolean oppositeStrand)

  Revert a location, translating and flipping as required.

  If oppositeStrand is false, this is equivalent to un-translating the location. If it is true, this is equivalent to (un)flipping it.

  Parameters:
    `oldLoc` - the Location to revert
    `translation` - the translation to unapply
    `oppositeStrand` - wether or not this is a flip
  Returns:
    the reverted location

### flipLocation

    public static Location flipLocation(Location oldLoc,
                                        int translation)

  Flip a location.

  All points `p` map to `translation - p`. Clearly, this mapping is its own inverse. If you wish to flip all locations between 1 and length, you should use a translation of length + 1. In general, if you wish to flip all features between x and y, you should use a translation of x + y.

  Parameters:
    `oldLoc` - the Location to flip
    `translation` - the translation to use
  Returns:
    the flipped Location

### flipStrand

    public static StrandedFeature.Strand flipStrand(StrandedFeature.Strand s)

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD