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

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

All Implemented Interfaces:

ViewService

public class ViewServiceImpl
extends java.lang.Object
implements ViewService

This method handles all things view related. This includes generation of chromatograms and html output.

Author:

Original: kr2, $Author: kr2 $

Field Summary

protected ChromatogramService	cs
protected static org.apache.commons.logging.Log	log

Constructor Summary

ViewServiceImpl()
Creates a new instance of FileLocatorServiceImpl

Method Summary

void	renderAmplimer(AmplimerBean amp) Generates the amplimer html page.
java.io.File	renderIndex(java.util.Map amplimers, java.lang.String csvLoc) Generates the index html page.
void	renderTraceInfo(TraceGroupBean tgb) Generates variant trace html page.
void	renderTraceSummary(TraceGroupBean tgb) Generates the variant trace summary html page.
void	renderVariantTraceResults(TraceGroupBean traceGroup) Generate the called variant html pages.
void	renderWildtypePanel(TraceGroupBean tgb) Generates wildtype trace html page.
void	resetService() Resets the chromatogram service.

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

cs

protected ChromatogramService cs

Constructor Detail

ViewServiceImpl

public ViewServiceImpl()

Creates a new instance of FileLocatorServiceImpl

Method Detail

renderTraceInfo

public void renderTraceInfo(TraceGroupBean tgb)

Description copied from interface: ViewService

Generates variant trace html page. This method should render an html page displaying the results of all variant traces and the best normal for each sequencing direction.

Specified by:

renderTraceInfo in interface ViewService

Parameters:

tgb - the TraceGroup to get the traces from

renderTraceSummary

public void renderTraceSummary(TraceGroupBean tgb)

Description copied from interface: ViewService

Generates the variant trace summary html page. This method should render an html page displaying the results of variant traces where variants have been called, and the best normal for each sequencing direction.

Specified by:

renderTraceSummary in interface ViewService

Parameters:

tgb - the TraceGroup to get the traces from

renderWildtypePanel

public void renderWildtypePanel(TraceGroupBean tgb)

Description copied from interface: ViewService

Generates wildtype trace html page. This method should render an html page displaying the results of just wildtype traces, indicating the best normal for each sequencing direction.

Specified by:

renderWildtypePanel in interface ViewService

Parameters:

tgb - the TraceGroup to get the traces from

renderIndex

public java.io.File renderIndex(java.util.Map amplimers,
                                java.lang.String csvLoc)

Description copied from interface: ViewService

Generates the index html page. Render the index page for the view. If a results.csv file is present provide a link.

Specified by:

renderIndex in interface ViewService

Parameters:

amplimers - map of amplimerName and number of variants found

csvLoc - the location of the results.csv file

Returns:

the location of the index page

renderAmplimer

public void renderAmplimer(AmplimerBean amp)

Description copied from interface: ViewService

Generates the amplimer html page. This method should cause the generation of an html page containing information on this amplimer.

Specified by:

renderAmplimer in interface ViewService

Parameters:

amp - the amplimer to be rendered as html

renderVariantTraceResults

public void renderVariantTraceResults(TraceGroupBean traceGroup)

Description copied from interface: ViewService

Generate the called variant html pages. Render the variant view for each variant on each variant experiment. Includes generation of images and adding to the csv output file.

Specified by:

renderVariantTraceResults in interface ViewService

Parameters:

traceGroup - the trace group to get the variant traces from

resetService

public void resetService()

Description copied from interface: ViewService

Resets the chromatogram service. See ChromatogramService.resetPreviousRendered().

Specified by:

resetService in interface ViewService