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.gui.sequence
Class GappedRenderer

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.gui.sequence.SequenceRendererWrapper
              org.biojava.bio.gui.sequence.GappedRenderer

All Implemented Interfaces:
  Serializable, SequenceRenderer, Changeable

    public class GappedRenderer

extends SequenceRendererWrapper

A renderer that will display a gapped sequence as a discontinuous series of regions.

Each ungapped block in the gapped symbol list will be displayed as a contiguous region by this renderer. Where there are gaps, this renderer will display nothing. Then, when the gaps are over, it will continue to render the ungapped sequence. This has the effect of snapping the image of the ungapped sequence where there are gaps, so as to allow it to be viewed in the gapped co-ordinate system.

Author:
  Matthew Pocock
See Also:
  Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderer
`SequenceRenderer.RendererForwarder`

Field Summary

Fields inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper
`RENDERER`

Constructor Summary
`GappedRenderer()`
`GappedRenderer(SequenceRenderer renderer)`

Method Summary
`double` | `getDepth(SequenceRenderContext src)` Retrieve the depth of this renderer when rendering src.
`double` | `getMinimumLeader(SequenceRenderContext src)` Retrieve the minimum leading distance for this renderer when rendering src.
`double` | `getMinimumTrailer(SequenceRenderContext src)` Retrieve the minimum trailing distance for this renderer when rendering src.
`protected SequenceRenderContext` | `makeContext(SequenceRenderContext src, RangeLocation loc)`
`void` | `paint(Graphics2D g, SequenceRenderContext src)` Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.

Methods inherited from class org.biojava.bio.gui.sequence.SequenceRendererWrapper
`getChangeSupport, getRenderer, processMouseEvent, setRenderer`

Methods inherited from class org.biojava.utils.AbstractChangeable
`addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener`

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

Constructor Detail

### GappedRenderer

    public GappedRenderer()

### GappedRenderer

    public GappedRenderer(SequenceRenderer renderer)

Method Detail

### getDepth

    public double getDepth(SequenceRenderContext src)

  Description copied from interface: `SequenceRenderer`
  Retrieve the depth of this renderer when rendering src.

  The depth may vary between sequence panels - for example based upon sequence length. Each line of information in the SequenceRendererContext only renders a region of the sequence. The depth for one complete line may be different from that for another due to the sequence having more or less information in that region to show. For example, a feature renderer implementation may chose to collapse down to a depth of zero pixels if there are no features to render within a region.

  Specified by:
    `getDepth` in interface `SequenceRenderer`
  Overrides:
    `getDepth` in class `SequenceRendererWrapper`
  Parameters:
    `src` - the SequenceRenderContext to return info for
  Returns:
    the depth of the renderer for that sequence panel

### getMinimumLeader

    public double getMinimumLeader(SequenceRenderContext src)

  Description copied from interface: `SequenceRenderer`
  Retrieve the minimum leading distance for this renderer when rendering src.

  The leading distance may vary between sequence panels - for example based upon sequence length.

  Specified by:
    `getMinimumLeader` in interface `SequenceRenderer`
  Overrides:
    `getMinimumLeader` in class `SequenceRendererWrapper`
  Parameters:
    `src` - the SequenceRenderContext to return info for
  Returns:
    the leading distance of the renderer for that sequence panel

### getMinimumTrailer

    public double getMinimumTrailer(SequenceRenderContext src)

  Description copied from interface: `SequenceRenderer`
  Retrieve the minimum trailing distance for this renderer when rendering src.

  The trailing distance may vary between sequence panels - for example based upon sequence length.

  Specified by:
    `getMinimumTrailer` in interface `SequenceRenderer`
  Overrides:
    `getMinimumTrailer` in class `SequenceRendererWrapper`
  Parameters:
    `src` - the SequenceRenderContext to return info for
  Returns:
    the trailing distance of the renderer for that sequence panel

### paint

    public void paint(Graphics2D g,
                      SequenceRenderContext src)

  Description copied from interface: `SequenceRenderer`
  Render a portion (possibly all) of the information for src to g, displaying all of the data that would fall within seqBox.

  Specified by:
    `paint` in interface `SequenceRenderer`
  Overrides:
    `paint` in class `SequenceRendererWrapper`
  Parameters:
    `g` - the Graphics2D to render to
    `src` - the SequenceRenderContext that encapsulates the information to render

### makeContext

    protected SequenceRenderContext makeContext(SequenceRenderContext src,
                                                RangeLocation loc)

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