uk.ac.sanger.cgp.standalonecsa.interfaces
Interface ViewService

All Known Implementing Classes:
ViewServiceImpl

public interface ViewService

This interface handles all calls to the VelocityTemplate system when rendering output.

Author:
Original: kr2, $Author: kr2 $

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.
 

Method Detail

renderAmplimer

void renderAmplimer(AmplimerBean amp)
Generates the amplimer html page. This method should cause the generation of an html page containing information on this amplimer.

Parameters:
amp - the amplimer to be rendered as html

renderTraceInfo

void renderTraceInfo(TraceGroupBean tgb)
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.

Parameters:
tgb - the TraceGroup to get the traces from

renderTraceSummary

void renderTraceSummary(TraceGroupBean tgb)
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.

Parameters:
tgb - the TraceGroup to get the traces from

renderWildtypePanel

void renderWildtypePanel(TraceGroupBean tgb)
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.

Parameters:
tgb - the TraceGroup to get the traces from

renderIndex

java.io.File renderIndex(java.util.Map amplimers,
                         java.lang.String csvLoc)
Generates the index html page. Render the index page for the view. If a results.csv file is present provide a link.

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

renderVariantTraceResults

void renderVariantTraceResults(TraceGroupBean traceGroup)
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.

Parameters:
traceGroup - the trace group to get the variant traces from

resetService

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