Пример #1
0
 internal SelectomeGene(Dictionary <SelectomeTaxaGroup, SelectomeQuerySubResult> initiatingResults, string label)
 {
     if (!initiatingResults.ContainsKey(SelectomeTaxaGroup.Euteleostomi))
     {
         throw new FormatException("Could not parse the vertebrate group data from the XML received from selectome.\n");
     }
     this.Label = label;
     this.vetebrateQueryResult = initiatingResults[SelectomeTaxaGroup.Euteleostomi];
 }
Пример #2
0
 internal SelectomeGene(Dictionary<SelectomeTaxaGroup,SelectomeQuerySubResult> initiatingResults, string label)
 {
     if (!initiatingResults.ContainsKey(SelectomeTaxaGroup.Euteleostomi))
     {
         throw new FormatException("Could not parse the vertebrate group data from the XML received from selectome.\n");
     }
     this.Label = label;
     this.vetebrateQueryResult = initiatingResults[SelectomeTaxaGroup.Euteleostomi];
 }
Пример #3
0
        /// <summary>
        /// Parses one line from the note section of the XML into a SelectomeResultObject
        /// </summary>
        /// <param name="data"></param>
        /// <returns></returns>
        private static SelectomeQuerySubResult ProcessSelectomeData(string data)
        {
            //First assign taxa to a group
            SelectomeTaxaGroup group = SelectomeTaxaGroup.NotSet;

            foreach (var kv in SelectomeConstantsAndEnums.GroupToNameList)
            {
                if (data.Contains(kv.Value))
                {
                    group = kv.Key;
                    break;
                }
            }

            //Now determine if positive seleciton has occurred.
            bool positiveSelectionSignature = false;

            if (data.Contains("Positive selection found"))
            {
                positiveSelectionSignature = true;
            }
            else if (data.Contains("No positive selection found"))
            {
                positiveSelectionSignature = false;
            }
            else if (data.Contains("Branch(es) under positive selection BUT no site found"))
            {
                positiveSelectionSignature = true;
            }
            else
            {
                throw new FormatException("Could not determine whether gene was under positive selection.\n XML was:" + data);
            }
            var result = new SelectomeQuerySubResult(group, positiveSelectionSignature);

            return(result);
        }
Пример #4
0
        /// <summary>
        /// Parses one line from the note section of the XML into a SelectomeResultObject
        /// </summary>
        /// <param name="data"></param>
        /// <returns></returns>
       private static SelectomeQuerySubResult ProcessSelectomeData(string data)
       {
           //First assign taxa to a group
           SelectomeTaxaGroup group=SelectomeTaxaGroup.NotSet;
           foreach(var kv in SelectomeConstantsAndEnums.GroupToNameList)
           {
               if(data.Contains(kv.Value))
               {
                   group=kv.Key;
                   break;
               }
           }

           //Now determine if positive seleciton has occurred.           
           bool positiveSelectionSignature = false;
           if (data.Contains("Positive selection found"))
           {
               positiveSelectionSignature = true;
           }
           else if (data.Contains("No positive selection found"))
           {
               positiveSelectionSignature = false;
           }
           else if (data.Contains("Branch(es) under positive selection BUT no site found"))
           {
               positiveSelectionSignature=true;
           }
           else
           {
               throw new FormatException("Could not determine whether gene was under positive selection.\n XML was:" + data);
           }
           var result = new SelectomeQuerySubResult(group,positiveSelectionSignature);
           return result;

       }