TissueInfo API 20130530171129

edu.cornell.med.icb.tissueinfo.similarity
Interface EstMatch2Counts

All Known Implementing Classes:
EstMatch2CuratedCancerTissueCounts, EstMatch2CuratedCancerTissueOnlyCounts, EstMatch2CuratedNormalTissueOnlyCounts, EstMatch2CuratedTissueCounts, EstMatch2RawTissueCounts

public interface EstMatch2Counts

Author:
Fabien Campagne Date: Aug 8, 2007 Time: 2:08:00 PM

Method Summary
 void convert(String queryAccessionCode, TissueInfo engine, TissueESTCountsWriter countWriter, String[] estAccessionCodes)
          Write tissue EST counts to the writer, for each tissue/condition pair.
 ObjectList<String> tissue2TissueConditionPairName(TissueInfo engine, ObjectSet<String> tissues)
          Returns a unique name for each tissue condition pair known to this converter.
 

Method Detail

tissue2TissueConditionPairName

ObjectList<String> tissue2TissueConditionPairName(TissueInfo engine,
                                                  ObjectSet<String> tissues)
Returns a unique name for each tissue condition pair known to this converter. The list of condition is implicitely defined by the implementation of this converter. For instance, it is possible to condition a given tissue on the attribute cancer/not cancer, or on the attribute embryo/not embryo, or any other attribute. This method returns a list of names that can be used to register the tissue/condition pair with the count writer.

Parameters:
tissues - The list of tissues to consider.
engine - TissueInfo engine.
Returns:
List of tissue/condition pair names.

convert

void convert(String queryAccessionCode,
             TissueInfo engine,
             TissueESTCountsWriter countWriter,
             String[] estAccessionCodes)
             throws TissueInfoNotAvailableException,
                    IOException
Write tissue EST counts to the writer, for each tissue/condition pair. If the TissueInfo implementation is not ready.

Parameters:
countWriter - Writer for EST count data.
engine - TissueInfo engine that may be used to calculate EST counts for the tissue/condition.
estAccessionCodes - Set of EST accession codes for a given transcript.
queryAccessionCode - Accession code of sequence for which tissue EST counts are sought.
Throws:
TissueInfoNotAvailableException - If the TissueInfo implementation is not ready.
IOException - If an error occurs writing counts.

TissueInfo API 20130530171129

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