uk.ac.sanger.cgp.standalonecsa.services
Class ChromatogramServiceImpl

java.lang.Object
  uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl

All Implemented Interfaces:

ChromatogramService

public class ChromatogramServiceImpl
extends java.lang.Object
implements ChromatogramService

This class handles rendering of chromatogram graphics.

Author:

Original: kr2, $Author: kr2 $

Field Summary

protected static org.apache.commons.logging.Log

log

Constructor Summary

ChromatogramServiceImpl()
Creates a new instance of ChromatogramServiceImpl

Method Summary

java.awt.image.BufferedImage	generateComplexVariantView(java.lang.String pathRoot, ExperimentBean expBean, ExperimentBean wtExp, boolean drawBaseChar, boolean writeToFile) Generates images required for the complex variant view.
java.awt.image.BufferedImage	generateFullChrom(java.lang.String pathStub, ExperimentBean expBean, boolean writeImage, boolean drawBaseChar) Generates a full chromatogram image.
java.awt.image.BufferedImage[]	generateVariantViewSet(java.lang.String pathRoot, ExperimentBean expBean, ExperimentBean wtExp, boolean drawBaseChar, boolean writeToFile) Generates images required for the simple variant view.
java.awt.image.BufferedImage	generateVariantViewSingle(java.lang.String pathRoot, ExperimentBean expBean, boolean writeToFile, boolean drawBaseChar) Generates an image as used in the simple variant view.
void	resetPreviousRendered() Resets the set of files that have been previously rendered and written to a file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log

protected static final org.apache.commons.logging.Log log

Constructor Detail

ChromatogramServiceImpl

public ChromatogramServiceImpl()

Creates a new instance of ChromatogramServiceImpl

Method Detail

generateVariantViewSingle

public java.awt.image.BufferedImage generateVariantViewSingle(java.lang.String pathRoot,
                                                              ExperimentBean expBean,
                                                              boolean writeToFile,
                                                              boolean drawBaseChar)

Description copied from interface: ChromatogramService

Generates an image as used in the simple variant view. Method should behave as follows:

- ExperimentBean.getVariantToRender() must not be null
- calculate where image should start and finish based on the length of the variant
- render and write to file (if indicated) the segment

If writeToFile is false pathRoot can be null

Specified by:

generateVariantViewSingle in interface ChromatogramService

Parameters:

pathRoot - directory to write image to

expBean - the experiment to use when rendering this variant

writeToFile - indicates if writing to a file should be attempted

drawBaseChar - true when base character should be rendered over the change

Returns:

to be used if further processing of image is required, or streaming

generateVariantViewSet

public java.awt.image.BufferedImage[] generateVariantViewSet(java.lang.String pathRoot,
                                                             ExperimentBean expBean,
                                                             ExperimentBean wtExp,
                                                             boolean drawBaseChar,
                                                             boolean writeToFile)

Description copied from interface: ChromatogramService

Generates images required for the simple variant view. Method should behave as follows:

- variant ExperimentBean.getVariantToRender() must not be null
- calculate where image should start and finish based on the length of the variant
- render and write to file (if indicated) the variant and wildtype segment
- if a compliment comparison was performed render these segments too

Specified by:

generateVariantViewSet in interface ChromatogramService

Parameters:

pathRoot - directory to write image to

expBean - the variant experiment to use when rendering this variant

wtExp - the wildtype experiment to use when rendering this variant

drawBaseChar - true when base character should be rendered over the change

writeToFile - indicates if writing to a file should be attempted

Returns:

array of BufferedImages, ordered {sample, reference, compliment sample, compliment reference}.

generateComplexVariantView

public java.awt.image.BufferedImage generateComplexVariantView(java.lang.String pathRoot,
                                                               ExperimentBean expBean,
                                                               ExperimentBean wtExp,
                                                               boolean drawBaseChar,
                                                               boolean writeToFile)

Description copied from interface: ChromatogramService

Generates images required for the complex variant view. Method should behave as follows:

- variant ExperimentBean.getVariantToRender() must not be null
- render full trace for both variant and wildtype traces, but not write to file
- calculate which image should be shifted to right to align variant location
- calculate the x offset for the shift
- create a new image with the wildtype displayed at the top and the variant trace on the bottom
- write this new image to file

Specified by:

generateComplexVariantView in interface ChromatogramService

Parameters:

pathRoot - directory to write image to

expBean - the variant experiment to use when rendering this variant

wtExp - the wildtype experiment to use when rendering this variant

drawBaseChar - true when base character should be rendered over the change

writeToFile - indicates if writing to a file should be attempted

Returns:

to be used if further processing of image is required, or streaming

generateFullChrom

public java.awt.image.BufferedImage generateFullChrom(java.lang.String pathStub,
                                                      ExperimentBean expBean,
                                                      boolean writeImage,
                                                      boolean drawBaseChar)

Description copied from interface: ChromatogramService

Generates a full chromatogram image. This method is expected to generate a full chromatogram image.

Specified by:

generateFullChrom in interface ChromatogramService

Parameters:

pathStub - directory to write image to

expBean - the experiment containing the chromatogram to be rendered

writeImage - true if the image should be written to file

drawBaseChar - true if the character of the DNA change should be rendered when a variant is provided

Returns:

to be used if further processing of image is required, or streaming

resetPreviousRendered

public void resetPreviousRendered()

Description copied from interface: ChromatogramService

Resets the set of files that have been previously rendered and written to a file. A list is kept to prevent images generated for a variant in one direction being regenerated when the same variant is called on the opposite comparison.

Use this method to empty this list at the end of each amplimer set to reduce memory footprint.

NOT NEEDED IF NOT WRITING TO FILE

Specified by:

resetPreviousRendered in interface ChromatogramService