Created the GetUserGenomeLocusValuesMapFromProfile function and used it to remove some duplicated code.
This commit is contained in:
Simon Sarasova
parent
b6f5612bbc
commit
39c4edbe2f
4 changed files with 21 additions and 252 deletions
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@ -6,6 +6,7 @@ Small and insignificant changes may not be included in this log.
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## Unversioned Changes
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* Created the GetUserGenomeLocusValuesMapFromProfile function and used it to remove some duplicated code. - *Simon Sarasova*
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* Added new genetic attributes to the calculatedAttributes package. Added the ability to view and sort by these attributes in the GUI. - *Simon Sarasova*
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* Upgraded Golang to version 1.23. - *Simon Sarasova*
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* Added the Obesity disease to genetic analyses. - *Simon Sarasova*
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@ -9,4 +9,4 @@ Many other people have written code for modules which are imported by Seekia. Th
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Name | Date Of First Commit | Number Of Commits
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--- | --- | ---
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Simon Sarasova | June 13, 2023 | 281
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Simon Sarasova | June 13, 2023 | 282
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@ -3033,45 +3033,8 @@ func setViewMateProfilePage_PolygenicDiseases(window fyne.Window, userOrOffsprin
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diseaseNameLabel := getBoldLabelCentered(diseaseName)
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// Map Structure: Locus rsID -> Locus Value
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userDiseaseLocusValuesMap := make(map[int64]locusValue.LocusValue)
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for _, locusRSID := range diseaseLociList{
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locusRSIDString := helpers.ConvertInt64ToString(locusRSID)
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locusValueAttributeName := "LocusValue_rs" + locusRSIDString
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userLocusValueExists, _, userLocusValue, err := getAnyUserProfileAttributeFunction(locusValueAttributeName)
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if (err != nil) { return nil, err }
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if (userLocusValueExists == false){
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continue
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}
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userLocusBase1, userLocusBase2, semicolonFound := strings.Cut(userLocusValue, ";")
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if (semicolonFound == false){
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return nil, errors.New("Database corrupt: Contains profile with invalid " + locusValueAttributeName + " value: " + userLocusValue)
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}
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userLocusIsPhasedAttributeName := "LocusIsPhased_rs" + locusRSIDString
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userLocusIsPhasedExists, _, userLocusIsPhasedString, err := getAnyUserProfileAttributeFunction(userLocusIsPhasedAttributeName)
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if (err != nil) { return nil, err }
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if (userLocusIsPhasedExists == false){
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return nil, errors.New("Database corrupt: Contains profile with locusValue but not locusIsPhased status for locus: " + locusRSIDString)
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}
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userLocusIsPhased, err := helpers.ConvertYesOrNoStringToBool(userLocusIsPhasedString)
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if (err != nil) { return nil, err }
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userLocusValueObject := locusValue.LocusValue{
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Base1Value: userLocusBase1,
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Base2Value: userLocusBase2,
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LocusIsPhased: userLocusIsPhased,
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}
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userDiseaseLocusValuesMap[locusRSID] = userLocusValueObject
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}
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userDiseaseLocusValuesMap, err := calculatedAttributes.GetUserGenomeLocusValuesMapFromProfile(diseaseLociList, getAnyUserProfileAttributeFunction)
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if (err != nil) { return nil, err }
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if (userOrOffspring == "User"){
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@ -3372,45 +3335,9 @@ func setViewMateProfilePage_DiscreteGeneticTraits(window fyne.Window, userOrOffs
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viewTraitDetailsButtonsColumn.Add(viewTraitDetailsButton)
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// We construct the user's trait locus values map
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// Map Structure: Locus rsID -> locusValue.LocusValue
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userTraitLocusValuesMap := make(map[int64]locusValue.LocusValue)
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for _, rsID := range traitLociList{
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rsIDString := helpers.ConvertInt64ToString(rsID)
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userLocusValueAttributeName := "LocusValue_rs" + rsIDString
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userLocusValueIsKnown, _, userLocusValue, err := getAnyUserProfileAttributeFunction(userLocusValueAttributeName)
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if (err != nil) { return nil, err }
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if (userLocusValueIsKnown == false){
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continue
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}
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userLocusBase1, userLocusBase2, semicolonFound := strings.Cut(userLocusValue, ";")
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if (semicolonFound == false){
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return nil, errors.New("Database corrupt: Contains profile with invalid " + userLocusValueAttributeName + " value: " + userLocusValue)
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}
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userLocusIsPhasedAttributeName := "LocusIsPhased_rs" + rsIDString
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userLocusIsPhasedExists, _, userLocusIsPhasedString, err := getAnyUserProfileAttributeFunction(userLocusIsPhasedAttributeName)
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if (err != nil) { return nil, err }
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if (userLocusIsPhasedExists == false){
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return nil, errors.New("Database corrupt: Contains profile with locusValue but not locusIsPhased status for locus: " + rsIDString)
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}
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userLocusIsPhased, err := helpers.ConvertYesOrNoStringToBool(userLocusIsPhasedString)
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if (err != nil) { return nil, err }
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userLocusValueObject := locusValue.LocusValue{
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Base1Value: userLocusBase1,
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Base2Value: userLocusBase2,
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LocusIsPhased: userLocusIsPhased,
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}
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userTraitLocusValuesMap[rsID] = userLocusValueObject
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}
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userTraitLocusValuesMap, err := calculatedAttributes.GetUserGenomeLocusValuesMapFromProfile(traitLociList, getAnyUserProfileAttributeFunction)
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if (err != nil) { return nil, err }
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if (userOrOffspring == "User"){
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@ -3737,45 +3664,10 @@ func setViewMateProfilePage_DiscreteTraitRules(window fyne.Window, traitName str
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getUserTraitLocusValuesMap := func()(bool, map[int64]locusValue.LocusValue, error){
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// We construct the user's trait locus values map
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// Map Structure: Locus rsID -> locusValue.LocusValue
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userTraitLocusValuesMap := make(map[int64]locusValue.LocusValue)
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for _, rsID := range traitLociList_Rules{
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userTraitLocusValuesMap, err := calculatedAttributes.GetUserGenomeLocusValuesMapFromProfile(traitLociList_Rules, getAnyUserProfileAttributeFunction)
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if (err != nil) { return false, nil, err }
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rsIDString := helpers.ConvertInt64ToString(rsID)
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userLocusValueAttributeName := "LocusValue_rs" + rsIDString
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userLocusValueIsKnown, _, userLocusValue, err := getAnyUserProfileAttributeFunction(userLocusValueAttributeName)
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if (err != nil) { return false, nil, err }
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if (userLocusValueIsKnown == false){
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continue
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}
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userLocusBase1, userLocusBase2, semicolonFound := strings.Cut(userLocusValue, ";")
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if (semicolonFound == false){
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return false, nil, errors.New("Database corrupt: Contains profile with invalid " + userLocusValueAttributeName + " value: " + userLocusValue)
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}
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userLocusIsPhasedAttributeName := "LocusIsPhased_rs" + rsIDString
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userLocusIsPhasedExists, _, userLocusIsPhasedString, err := getAnyUserProfileAttributeFunction(userLocusIsPhasedAttributeName)
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if (err != nil) { return false, nil, err }
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if (userLocusIsPhasedExists == false){
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return false, nil, errors.New("Database corrupt: Contains profile with locusValue but not locusIsPhased status for locus: " + rsIDString)
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}
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userLocusIsPhased, err := helpers.ConvertYesOrNoStringToBool(userLocusIsPhasedString)
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if (err != nil) { return false, nil, err }
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userLocusValueObject := locusValue.LocusValue{
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Base1Value: userLocusBase1,
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Base2Value: userLocusBase2,
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LocusIsPhased: userLocusIsPhased,
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}
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userTraitLocusValuesMap[rsID] = userLocusValueObject
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}
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if (len(userTraitLocusValuesMap) == 0){
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return false, nil, nil
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}
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@ -4235,45 +4127,9 @@ func setViewMateProfilePage_NumericGeneticTraits(window fyne.Window, userOrOffsp
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traitNameText := getBoldLabelCentered(translate(traitName))
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// We construct the user's trait locus values map
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// Map Structure: Locus rsID -> locusValue.LocusValue
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userTraitLocusValuesMap := make(map[int64]locusValue.LocusValue)
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for _, rsID := range traitLociList{
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rsIDString := helpers.ConvertInt64ToString(rsID)
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userLocusValueAttributeName := "LocusValue_rs" + rsIDString
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userLocusValueIsKnown, _, userLocusValue, err := getAnyUserProfileAttributeFunction(userLocusValueAttributeName)
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if (err != nil) { return nil, err }
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if (userLocusValueIsKnown == false){
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continue
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}
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userLocusBase1, userLocusBase2, semicolonFound := strings.Cut(userLocusValue, ";")
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if (semicolonFound == false){
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return nil, errors.New("Database corrupt: Contains profile with invalid " + userLocusValueAttributeName + " value: " + userLocusValue)
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}
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userLocusIsPhasedAttributeName := "LocusIsPhased_rs" + rsIDString
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userLocusIsPhasedExists, _, userLocusIsPhasedString, err := getAnyUserProfileAttributeFunction(userLocusIsPhasedAttributeName)
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if (err != nil) { return nil, err }
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if (userLocusIsPhasedExists == false){
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return nil, errors.New("Database corrupt: Contains profile with locusValue but not locusIsPhased status for locus: " + rsIDString)
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}
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userLocusIsPhased, err := helpers.ConvertYesOrNoStringToBool(userLocusIsPhasedString)
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if (err != nil) { return nil, err }
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userLocusValueObject := locusValue.LocusValue{
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Base1Value: userLocusBase1,
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Base2Value: userLocusBase2,
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LocusIsPhased: userLocusIsPhased,
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}
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userTraitLocusValuesMap[rsID] = userLocusValueObject
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}
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userTraitLocusValuesMap, err := calculatedAttributes.GetUserGenomeLocusValuesMapFromProfile(traitLociList, getAnyUserProfileAttributeFunction)
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if (err != nil) { return nil, err }
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getPredictedOutcomeLabel := func(analysisExists bool, predictedOutcome float64)(fyne.Widget, error){
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@ -707,56 +707,12 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
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// Each risk score is a number between 0 and 1
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allDiseasesAverageRiskScoreNumerator := float64(0)
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// Map Structure: Locus rsID -> Locus Value
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userDiseaseLocusValuesMap := make(map[int64]locusValue.LocusValue)
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for _, diseaseObject := range polygenicDiseaseObjectsList{
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diseaseLociList := diseaseObject.LociList
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for _, locusRSID := range diseaseLociList{
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_, exists := userDiseaseLocusValuesMap[locusRSID]
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if (exists == true){
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// We already added this locus
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// This can happen if two diseases share the same locus
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continue
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}
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locusRSIDString := helpers.ConvertInt64ToString(locusRSID)
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locusValueAttributeName := "LocusValue_rs" + locusRSIDString
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userLocusValueExists, _, userLocusValue, err := getProfileAttributesFunction(locusValueAttributeName)
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if (err != nil) { return false, 0, "", err }
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if (userLocusValueExists == false){
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continue
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}
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userLocusBase1, userLocusBase2, semicolonFound := strings.Cut(userLocusValue, ";")
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if (semicolonFound == false){
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return false, 0, "", errors.New("Database corrupt: Contains profile with invalid " + locusValueAttributeName + " value: " + userLocusValue)
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}
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userLocusIsPhasedAttributeName := "LocusIsPhased_rs" + locusRSIDString
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userLocusIsPhasedExists, _, userLocusIsPhasedString, err := getProfileAttributesFunction(userLocusIsPhasedAttributeName)
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if (err != nil) { return false, 0, "", err }
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if (userLocusIsPhasedExists == false){
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return false, 0, "", errors.New("Database corrupt: Contains profile with locusValue but not locusIsPhased status for locus: " + locusRSIDString)
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}
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userLocusIsPhased, err := helpers.ConvertYesOrNoStringToBool(userLocusIsPhasedString)
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if (err != nil) { return false, 0, "", err }
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userLocusValueObject := locusValue.LocusValue{
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Base1Value: userLocusBase1,
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Base2Value: userLocusBase2,
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LocusIsPhased: userLocusIsPhased,
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}
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userDiseaseLocusValuesMap[locusRSID] = userLocusValueObject
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}
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userDiseaseLocusValuesMap, err := GetUserGenomeLocusValuesMapFromProfile(diseaseLociList, getProfileAttributesFunction)
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if (err != nil) { return false, 0, "", err }
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neuralNetworkExists, anyLocusTested, userDiseaseRiskScore, _, _, _, err := createPersonGeneticAnalysis.GetPersonGenomePolygenicDiseaseAnalysis(diseaseObject, userDiseaseLocusValuesMap, true)
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if (err != nil) { return false, 0, "", err }
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@ -828,56 +784,12 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
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// Each risk score is a number between 0 and 1
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allDiseasesAverageRiskScoreNumerator := float64(0)
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// Map Structure: rsID -> Locus Value
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userDiseaseLocusValuesMap := make(map[int64]locusValue.LocusValue)
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for _, diseaseObject := range polygenicDiseaseObjectsList{
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diseaseLociList := diseaseObject.LociList
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for _, locusRSID := range diseaseLociList{
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_, exists := userDiseaseLocusValuesMap[locusRSID]
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if (exists == true){
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// We already added this locus
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// This can happen if two diseases share the same locus
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continue
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}
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locusRSIDString := helpers.ConvertInt64ToString(locusRSID)
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locusValueAttributeName := "LocusValue_rs" + locusRSIDString
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userLocusValueExists, _, userLocusValue, err := getProfileAttributesFunction(locusValueAttributeName)
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if (err != nil) { return false, 0, "", err }
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if (userLocusValueExists == false){
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continue
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}
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userLocusBase1, userLocusBase2, semicolonFound := strings.Cut(userLocusValue, ";")
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if (semicolonFound == false){
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return false, 0, "", errors.New("GetAnyProfileAttributeIncludingCalculated called with profile containing invalid " + locusValueAttributeName + ": " + userLocusValue)
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}
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userLocusIsPhasedAttributeName := "LocusIsPhased_rs" + locusRSIDString
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userLocusIsPhasedExists, _, userLocusIsPhasedString, err := getProfileAttributesFunction(userLocusIsPhasedAttributeName)
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if (err != nil) { return false, 0, "", err }
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if (userLocusIsPhasedExists == false){
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return false, 0, "", errors.New("Database corrupt: Contains profile with locusValue but not locusIsPhased status for locus: " + locusRSIDString)
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}
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userLocusIsPhased, err := helpers.ConvertYesOrNoStringToBool(userLocusIsPhasedString)
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if (err != nil) { return false, 0, "", err }
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newLocusValueObject := locusValue.LocusValue{
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Base1Value: userLocusBase1,
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Base2Value: userLocusBase2,
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LocusIsPhased: userLocusIsPhased,
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}
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userDiseaseLocusValuesMap[locusRSID] = newLocusValueObject
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}
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userDiseaseLocusValuesMap, err := GetUserGenomeLocusValuesMapFromProfile(diseaseLociList, getProfileAttributesFunction)
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if (err != nil) { return false, 0, "", err }
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neuralNetworkExists, anyLocusValuesTested, offspringAverageRiskScore, _, _, _, _, err := createCoupleGeneticAnalysis.GetOffspringPolygenicDiseaseAnalysis(diseaseObject, myGenomeLocusValuesMap, userDiseaseLocusValuesMap)
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if (err != nil) { return false, 0, "", err }
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@ -921,7 +833,7 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
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diseaseLociList := diseaseObject.LociList
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userDiseaseLocusValuesMap, err := getUserGenomeLocusValuesMap(diseaseLociList, getProfileAttributesFunction)
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userDiseaseLocusValuesMap, err := GetUserGenomeLocusValuesMapFromProfile(diseaseLociList, getProfileAttributesFunction)
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if (err != nil) { return false, 0, "", err }
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neuralNetworkExists, anyLocusTested, userDiseaseRiskScore, _, _, _, err := createPersonGeneticAnalysis.GetPersonGenomePolygenicDiseaseAnalysis(diseaseObject, userDiseaseLocusValuesMap, true)
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@ -972,7 +884,7 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
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diseaseLociList := diseaseObject.LociList
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userDiseaseLocusValuesMap, err := getUserGenomeLocusValuesMap(diseaseLociList, getProfileAttributesFunction)
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userDiseaseLocusValuesMap, err := GetUserGenomeLocusValuesMapFromProfile(diseaseLociList, getProfileAttributesFunction)
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if (err != nil) { return false, 0, "", err }
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neuralNetworkExists, anyLocusValuesTested, offspringAverageRiskScore, _, _, _, _, err := createCoupleGeneticAnalysis.GetOffspringPolygenicDiseaseAnalysis(diseaseObject, myGenomeLocusValuesMap, userDiseaseLocusValuesMap)
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@ -1021,7 +933,7 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
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traitLociList := traitObject.LociList
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userTraitLocusValuesMap, err := getUserGenomeLocusValuesMap(traitLociList, getProfileAttributesFunction)
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userTraitLocusValuesMap, err := GetUserGenomeLocusValuesMapFromProfile(traitLociList, getProfileAttributesFunction)
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if (err != nil) { return false, 0, "", err }
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neuralNetworkExists, neuralNetworkOutcomeIsKnown, predictedOutcome, _, _, _, err := createPersonGeneticAnalysis.GetGenomeDiscreteTraitAnalysis_NeuralNetwork(traitObject, userTraitLocusValuesMap, true)
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@ -1117,7 +1029,7 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
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traitLociList := traitObject.LociList
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userTraitLocusValuesMap, err := getUserGenomeLocusValuesMap(traitLociList, getProfileAttributesFunction)
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userTraitLocusValuesMap, err := GetUserGenomeLocusValuesMapFromProfile(traitLociList, getProfileAttributesFunction)
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if (err != nil) { return false, 0, "", err }
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neuralNetworkExists, anyLociKnown, outcomeProbabilitiesMap, _, _, _, err := createCoupleGeneticAnalysis.GetOffspringDiscreteTraitAnalysis_NeuralNetwork(traitObject, myGenomeLocusValuesMap, userTraitLocusValuesMap)
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@ -1190,7 +1102,7 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
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traitLociList := traitObject.LociList
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userTraitLocusValuesMap, err := getUserGenomeLocusValuesMap(traitLociList, getProfileAttributesFunction)
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userTraitLocusValuesMap, err := GetUserGenomeLocusValuesMapFromProfile(traitLociList, getProfileAttributesFunction)
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if (err != nil) { return false, 0, "", err }
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traitNeuralNetworkExists, anyLocusValuesAreKnown, predictedOutcome, _, _, _, err := createPersonGeneticAnalysis.GetGenomeNumericTraitAnalysis(traitObject, userTraitLocusValuesMap, true)
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@ -1264,7 +1176,7 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
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traitLociList := traitObject.LociList
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userTraitLocusValuesMap, err := getUserGenomeLocusValuesMap(traitLociList, getProfileAttributesFunction)
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userTraitLocusValuesMap, err := GetUserGenomeLocusValuesMapFromProfile(traitLociList, getProfileAttributesFunction)
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if (err != nil) { return false, 0, "", err }
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neuralNetworkExists, anyLociKnown, predictedOutcome, _, _, _, _, err := createCoupleGeneticAnalysis.GetOffspringNumericTraitAnalysis(traitObject, userTraitLocusValuesMap, myGenomeLocusValuesMap)
|
||||
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|
@ -2070,7 +1982,7 @@ func GetAnyProfileAttributeIncludingCalculated(attributeName string, getProfileA
|
|||
//Outputs:
|
||||
// -map[int64]locusValue.LocusValue: Genome map for provided loci
|
||||
// -error
|
||||
func getUserGenomeLocusValuesMap(lociList []int64, getProfileAttributesFunction func(string)(bool, int, string, error))(map[int64]locusValue.LocusValue, error){
|
||||
func GetUserGenomeLocusValuesMapFromProfile(lociList []int64, getProfileAttributesFunction func(string)(bool, int, string, error))(map[int64]locusValue.LocusValue, error){
|
||||
|
||||
// We construct the user's locus values map
|
||||
// Map Structure: Locus rsID -> locusValue.LocusValue
|
||||
|
|
|
|||
Loading…
Reference in a new issue