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java.lang.Objectuk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
public class ChromatogramServiceImpl
This class handles rendering of chromatogram graphics.
Field Summary | |
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protected org.apache.commons.logging.Log |
log
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Constructor Summary | |
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ChromatogramServiceImpl()
Creates a new instance of ChromatogramServiceImpl |
Method Summary | |
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java.awt.image.BufferedImage |
generateComplexVariantView(ChromRenderBean varCrb,
ChromRenderBean wtCrb,
boolean reverseChromObject)
Generates images required for the complex variant view. |
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. |
java.awt.image.BufferedImage |
renderChromatogram(ChromRenderBean crb,
boolean revCompChromatogram)
Generates a simple variant or full trace image. |
void |
resetPreviousRendered()
Resets the set of files that have been previously rendered and written to a file. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected org.apache.commons.logging.Log log
Constructor Detail |
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public ChromatogramServiceImpl()
Method Detail |
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public java.awt.image.BufferedImage generateVariantViewSingle(java.lang.String pathRoot, ExperimentBean expBean, boolean writeToFile, boolean drawBaseChar)
ChromatogramService
ExperimentBean.getVariantToRender()
must not be nullwriteToFile
is false pathRoot can be null
generateVariantViewSingle
in interface ChromatogramService
pathRoot
- directory to write image toexpBean
- the experiment to use when rendering this variantwriteToFile
- indicates if writing to a file should be attempteddrawBaseChar
- true when base character should be rendered over the change
public java.awt.image.BufferedImage[] generateVariantViewSet(java.lang.String pathRoot, ExperimentBean expBean, ExperimentBean wtExp, boolean drawBaseChar, boolean writeToFile)
ChromatogramService
ExperimentBean.getVariantToRender()
must not be null
generateVariantViewSet
in interface ChromatogramService
pathRoot
- directory to write image toexpBean
- the variant experiment to use when rendering this variantwtExp
- the wildtype experiment to use when rendering this variantdrawBaseChar
- true when base character should be rendered over the changewriteToFile
- indicates if writing to a file should be attempted
public java.awt.image.BufferedImage generateComplexVariantView(java.lang.String pathRoot, ExperimentBean expBean, ExperimentBean wtExp, boolean drawBaseChar, boolean writeToFile)
ChromatogramService
ExperimentBean.getVariantToRender()
must not be null
generateComplexVariantView
in interface ChromatogramService
pathRoot
- directory to write image toexpBean
- the variant experiment to use when rendering this variantwtExp
- the wildtype experiment to use when rendering this variantdrawBaseChar
- true when base character should be rendered over the changewriteToFile
- indicates if writing to a file should be attempted
public java.awt.image.BufferedImage generateComplexVariantView(ChromRenderBean varCrb, ChromRenderBean wtCrb, boolean reverseChromObject)
ChromatogramService
varCrb.getFeatures()
generateComplexVariantView
in interface ChromatogramService
varCrb
- the crb for the variant chromatogramwtCrb
- the crb for the wildtype chromatogramreverseChromObject
- indicate if the chromatogram object needs to be reversed, also affects the alignment of the variant call
public java.awt.image.BufferedImage renderChromatogram(ChromRenderBean crb, boolean revCompChromatogram) throws CsaRenderException
ChromatogramService
crb.getFeatures()
crb.getStartRenderAtBase() == 0 && crb.getStopRenderAtBase() == 0
renderChromatogram
in interface ChromatogramService
crb
- object to be renderedrevCompChromatogram
- indicate if the chromatogram object needs to be reversed
CsaRenderException
- reports a rendering problem, normally due to inputs errorspublic java.awt.image.BufferedImage generateFullChrom(java.lang.String pathStub, ExperimentBean expBean, boolean writeImage, boolean drawBaseChar)
ChromatogramService
generateFullChrom
in interface ChromatogramService
pathStub
- directory to write image toexpBean
- the experiment containing the chromatogram to be renderedwriteImage
- true if the image should be written to filedrawBaseChar
- true if the character of the DNA change should be rendered when a variant is provided
public void resetPreviousRendered()
ChromatogramService
resetPreviousRendered
in interface ChromatogramService
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