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public interface ChromatogramService
This interface provides access to all the methods that a view should require for rendering chromatogram graphics.
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 imageLoc,
ExperimentBean expBean,
boolean writeImage,
boolean drawBaseChar)
Generates a full chromatogram image. |
java.awt.image.BufferedImage[] |
generateVariantViewSet(java.lang.String imageLoc,
ExperimentBean expBean,
ExperimentBean normExp,
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. |
Method Detail |
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java.awt.image.BufferedImage generateFullChrom(java.lang.String imageLoc, ExperimentBean expBean, boolean writeImage, boolean drawBaseChar)
imageLoc
- 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
java.awt.image.BufferedImage[] generateVariantViewSet(java.lang.String imageLoc, ExperimentBean expBean, ExperimentBean normExp, boolean drawBaseChar, boolean writeToFile)
ExperimentBean.getVariantToRender()
must not be null
writeToFile
- indicates if writing to a file should be attemptedimageLoc
- directory to write image toexpBean
- the variant experiment to use when rendering this variantnormExp
- the wildtype experiment to use when rendering this variantdrawBaseChar
- true when base character should be rendered over the change
java.awt.image.BufferedImage generateVariantViewSingle(java.lang.String pathRoot, ExperimentBean expBean, boolean writeToFile, boolean drawBaseChar)
ExperimentBean.getVariantToRender()
must not be nullwriteToFile
is false pathRoot can be null
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
java.awt.image.BufferedImage generateComplexVariantView(java.lang.String pathRoot, ExperimentBean expBean, ExperimentBean wtExp, boolean drawBaseChar, boolean writeToFile)
ExperimentBean.getVariantToRender()
must not be null
writeToFile
- indicates if writing to a file should be attemptedpathRoot
- 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 change
java.awt.image.BufferedImage generateComplexVariantView(ChromRenderBean varCrb, ChromRenderBean wtCrb, boolean reverseChromObject)
varCrb.getFeatures()
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
java.awt.image.BufferedImage renderChromatogram(ChromRenderBean crb, boolean revCompChromatogram) throws CsaRenderException
crb.getFeatures()
crb.getStartRenderAtBase() == 0 && crb.getStopRenderAtBase() == 0
crb
- object to be renderedrevCompChromatogram
- indicate if the chromatogram object needs to be reversed
CsaRenderException
- reports a rendering problem, normally due to inputs errorsvoid resetPreviousRendered()
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