Package de.julielab.genemapper.evaluation.tools

Class Stats

  • public class Stats
extends Object

    • Constructor Detail

      • Stats

        public Stats()

    • Method Detail

      • incNumFpMentions

        public void incNumFpMentions()

      • incNumUncertainAndWrong

        public void incNumUncertainAndWrong()

      • incNumUncertainAndCorrect

        public void incNumUncertainAndCorrect()

      • incNumCorrectHighestMentionScoreGeneId

        public void incNumCorrectHighestMentionScoreGeneId​(boolean b)

      • incNumCorrectFirstGeneId

        public void incNumCorrectFirstGeneId​(boolean b)

      • incNumCorrectMajorityGeneId

        public void incNumCorrectMajorityGeneId​(boolean b)

      • incTotalNumberCandidates

        public void incTotalNumberCandidates​(int size)

      • getTotalNumberCandidates

        public int getTotalNumberCandidates()

      • incNoCorrectAfterExactSearch

        public void incNoCorrectAfterExactSearch​(boolean b)

      • incNoCorrectAfterRelaxed1

        public void incNoCorrectAfterRelaxed1​(boolean b)

      • incNoCorrectAfterRelaxed2

        public void incNoCorrectAfterRelaxed2​(boolean b)

      • incNoCorrectAfterRelaxed3

        public void incNoCorrectAfterRelaxed3​(boolean b)

      • incNumCorrectInInitialSearchNotInOrthologs

        public void incNumCorrectInInitialSearchNotInOrthologs​(boolean correctInOrthologs,
                                                       boolean correctBeforeOrthologsResolution)

      • incCorrectGeneIdAfterRelaxed1

        public void incCorrectGeneIdAfterRelaxed1​(boolean b)

      • incNumExcactMatchWithOrthologResolution

        public void incNumExcactMatchWithOrthologResolution​(boolean b)
        Exact matches which didn't have an entry for the given tax ID but did have an ortholog for this tax ID
        Parameters:
        b -

      • getNumCorrectGenesInOrthologsOfExactMatch

        public int getNumCorrectGenesInOrthologsOfExactMatch()

      • incNumCorrectGenesInOrthologsOfExactMatchIfTrue

        public void incNumCorrectGenesInOrthologsOfExactMatchIfTrue​(boolean orthologsEmpty,
                                                            boolean correctInOrthologs)

      • getNumCorrectGenesInCandidateListAfterSpeciesRestriction

        public int getNumCorrectGenesInCandidateListAfterSpeciesRestriction()

      • incNumCorrectGenesInCandidateListAfterSpeciesRestrictionIfTrue

        public void incNumCorrectGenesInCandidateListAfterSpeciesRestrictionIfTrue​(boolean b)

      • getNumExactMatchAfterSpeciesRestriction

        public int getNumExactMatchAfterSpeciesRestriction()

      • incNumExactMatchAfterSpeciesRestrictionIfTrue

        public void incNumExactMatchAfterSpeciesRestrictionIfTrue​(Boolean b)

      • incExactMatchFirstTryIfTrue

        public void incExactMatchFirstTryIfTrue​(boolean b)

      • getNumGenesRecognized

        public int getNumGenesRecognized()

      • getNumApprxGenesRecognized

        public int getNumApprxGenesRecognized()

      • getNumExactGenesRecognized

        public int getNumExactGenesRecognized()

      • getReport

        public String getReport()

      • getNumExactGoldOverlappingMentions

        public int getNumExactGoldOverlappingMentions()

      • getNumApprxGoldOverlappingMentions

        public int getNumApprxGoldOverlappingMentions()

      • getNumCorrectExactTop3WithGold

        public int getNumCorrectExactTop3WithGold()

      • getNumCorrectExactTop5WithGold

        public int getNumCorrectExactTop5WithGold()

      • getNumCorrectApprxTop3WithGold

        public int getNumCorrectApprxTop3WithGold()

      • getNumCorrectApprxTop5WithGold

        public int getNumCorrectApprxTop5WithGold()

      • getNumCorrectExactTop10WithGold

        public int getNumCorrectExactTop10WithGold()

      • getNumCorrectExactTop15WithGold

        public int getNumCorrectExactTop15WithGold()

      • getNumCorrectApprxTop10WithGold

        public int getNumCorrectApprxTop10WithGold()

      • getNumCorrectApprxTop15WithGold

        public int getNumCorrectApprxTop15WithGold()

      • incNumPerfectMatchFirstTry

        public void incNumPerfectMatchFirstTry()

      • incNumCorrectGenesInCandidateListExactMatchFirstTry

        public void incNumCorrectGenesInCandidateListExactMatchFirstTry()

      • incNumCorrectGenesInCandidateListExactMatchFirstTryIfTrue

        public void incNumCorrectGenesInCandidateListExactMatchFirstTryIfTrue​(boolean b)

      • getNumExactMatchFirstTry

        public int getNumExactMatchFirstTry()

      • getNumCorrectGenesInCandidateListExactMatchFirstTry

        public int getNumCorrectGenesInCandidateListExactMatchFirstTry()

      • getNumGenes

        public int getNumGenes()

      • getCorrectGenesInCandidateList

        public int getCorrectGenesInCandidateList()

      • incNumGenes

        public void incNumGenes()

      • incCorrectGenesInCandidateList

        public void incCorrectGenesInCandidateList()

      • incCorrectGenesInCandidateList

        public void incCorrectGenesInCandidateList​(Boolean hasCorrectEntryInOrthologs)

      • incCorrectGeneIdAfterRelaxed2

        public void incCorrectGeneIdAfterRelaxed2​(Boolean b)

      • incCorrectGeneIdAfterRelaxed3

        public void incCorrectGeneIdAfterRelaxed3​(Boolean b)

      • incNumGenesRecognized

        public void incNumGenesRecognized()

      • incNumCertainAndWrong

        public void incNumCertainAndWrong()

      • incMissedMentions

        public void incMissedMentions()

      • incNumGoldOverlappingGenesRecognized

        public void incNumGoldOverlappingGenesRecognized()

      • incCorrectGeneIdInBestCandidates

        public void incCorrectGeneIdInBestCandidates()

      • incUnambiguousCorrectGeneInBestCandidates

        public void incUnambiguousCorrectGeneInBestCandidates()

      • incBestCandidateHasCorrectId

        public void incBestCandidateHasCorrectId()

      • incBestCandidateHasCorrectTaxId

        public void incBestCandidateHasCorrectTaxId()

      • incBestCandidateWithCorrectIdIsAmbiguous

        public void incBestCandidateWithCorrectIdIsAmbiguous()

      • incAmbiguousBestCandidateHasCorrectIdSelected

        public void incAmbiguousBestCandidateHasCorrectIdSelected()

      • incNumAmbiguous

        public void incNumAmbiguous()

      • incDisambiguated

        public void incDisambiguated()

      • incCorrectlyDisambiguated

        public void incCorrectlyDisambiguated()

      • incExactCorrectlyDisambiguated

        public void incExactCorrectlyDisambiguated()

      • incApprxCorrectlyDisambiguated

        public void incApprxCorrectlyDisambiguated()

      • incNumCorrectExactHightestMentionScoreGeneId

        public void incNumCorrectExactHightestMentionScoreGeneId​(Boolean b)

      • incNumCorrectApprxHightestMentionScoreGeneId

        public void incNumCorrectApprxHightestMentionScoreGeneId​(Boolean b)

      • incNotGoldOverlappingMatchType

        public void incNotGoldOverlappingMatchType​(boolean exactMatch)

      • incNumCorrectExactMatchesTop3

        public void incNumCorrectExactMatchesTop3​(Boolean b)

      • incNumCorrectExactMatchesTop5

        public void incNumCorrectExactMatchesTop5​(Boolean b)

      • incNumCorrectApprxMatchesTop3

        public void incNumCorrectApprxMatchesTop3​(Boolean b)

      • incNumCorrectApprxMatchesTop5

        public void incNumCorrectApprxMatchesTop5​(Boolean b)

      • incNumCorrectExactMatchesTop10

        public void incNumCorrectExactMatchesTop10​(Boolean b)

      • incNumCorrectExactMatchesTop15

        public void incNumCorrectExactMatchesTop15​(Boolean b)

      • incNumCorrectApprxMatchesTop10

        public void incNumCorrectApprxMatchesTop10​(Boolean b)

      • incNumCorrectApprxMatchesTop15

        public void incNumCorrectApprxMatchesTop15​(Boolean b)

      • incCorrectGeneIdInExactBestCandidates

        public void incCorrectGeneIdInExactBestCandidates()

      • incCorrectGeneIdInApprxBestCandidates

        public void incCorrectGeneIdInApprxBestCandidates()

      • incExactBestCandidateHasCorrectId

        public void incExactBestCandidateHasCorrectId()

      • incApprxBestCandidateHasCorrectId

        public void incApprxBestCandidateHasCorrectId()

      • incNumExactGoldOverlappingGenesRecognized

        public void incNumExactGoldOverlappingGenesRecognized()

      • incNumApprxGoldOverlappingGenesRecognized

        public void incNumApprxGoldOverlappingGenesRecognized()

      • incNumExactAmbiguous

        public void incNumExactAmbiguous()

      • incNumApprxAmbiguous

        public void incNumApprxAmbiguous()

      • incExactBestCandidateWithCorrectIdIsAmbiguous

        public void incExactBestCandidateWithCorrectIdIsAmbiguous()

      • incApprxBestCandidateWithCorrectIdIsAmbiguous

        public void incApprxBestCandidateWithCorrectIdIsAmbiguous()

      • incAmbiguousExactBestCandidateHasCorrectIdSelected

        public void incAmbiguousExactBestCandidateHasCorrectIdSelected()

      • incAmbiguousApprxBestCandidateHasCorrectIdSelected

        public void incAmbiguousApprxBestCandidateHasCorrectIdSelected()

      • incBestExactCandidateHasCorrectTaxId

        public void incBestExactCandidateHasCorrectTaxId()

      • incBestApprxCandidateHasCorrectTaxId

        public void incBestApprxCandidateHasCorrectTaxId()

      • incNumExactGenesRecognized

        public void incNumExactGenesRecognized()

      • incNumApprxGenesRecognized

        public void incNumApprxGenesRecognized()

      • incNumCandidateSearches

        public void incNumCandidateSearches()

      • getNumCandidateSearches

        public int getNumCandidateSearches()