Ejemplo n.º 1
0
        public List <SearchSiteCollection> FetchSearchSiteData(GeneCollection geneCollection, string originSequence, string[] siteArray)
        {
            Dictionary <string, string> iupacTable    = CreateIupacTable();
            List <SearchSiteCollection> finalSiteList = new List <SearchSiteCollection>();
            List <string> nonMatchedSites             = new List <string>();
            string        upperOriginSequence         = originSequence.ToUpper();

            foreach (string site in siteArray)
            {
                SearchSiteCollection searchSiteCollection = new SearchSiteCollection();
                string[]             nucleotideSites      = site.Split();
                List <string>        targetSequences      = new List <string>();
                bool isMatch = false;
                foreach (char nucleotideSite in site)
                {
                    string nucSite = nucleotideSite.ToString();
                    if (iupacTable.ContainsKey(nucSite))
                    {
                        String newNucleotides = iupacTable[nucSite];
                        String regex          = "[" + newNucleotides + "]";
                        foreach (char newNuc in newNucleotides)
                        {
                            string nuc            = newNuc.ToString();
                            string targetSequence = site.Replace(nucSite, nuc);
                            targetSequences.Add(targetSequence);
                        }
                        searchSiteCollection.searchSiteRegexMessage = "site search: " + nucSite + " (regex: " + nucSite.Replace(nucSite, regex) + ")";
                    }
                }
                foreach (String targetSequence in targetSequences)
                {
                    int index = 0;
                    while (index >= 0 && index != upperOriginSequence.Length)
                    {
                        index++;
                        index = upperOriginSequence.IndexOf(targetSequence, index);
                        String strIndex = "" + (index + 1);
                        if (index != -1)
                        {
                            String geneName = "INTERGENIC";
                            foreach (Gene gene in geneCollection.collection)
                            {
                                if (index >= gene.StartCoordinate && index <= gene.EndCoordinate)
                                {
                                    //Index + 1 because coding index starts at zero and sequence index starts at 1.
                                    if (gene.ID != "")
                                    {
                                        geneName = gene.ID;
                                    }
                                    else
                                    {
                                        geneName = gene.LocusTag;
                                    }
                                    isMatch = true;
                                }
                            }
                            SearchSite searchSite = new SearchSite(strIndex, targetSequence, geneName);
                            if (searchSiteCollection.collection.Any())
                            {
                                bool newEntry = true;
                                foreach (SearchSite siteEntry in searchSiteCollection.collection)
                                {
                                    if (siteEntry.StartPosition.Equals(strIndex))
                                    {
                                        if (siteEntry.Site.Equals("INTERGENIC") && !geneName.Equals("INTERGENIC"))
                                        {
                                            siteEntry.GeneName = geneName;
                                            newEntry           = false;
                                            break;
                                        }
                                    }
                                }
                                if (newEntry)
                                {
                                    searchSiteCollection.AddSearchSite(searchSite);
                                }
                            }
                            else
                            {
                                searchSiteCollection.AddSearchSite(searchSite);
                            }
                        }
                    }
                }
                finalSiteList.Add(searchSiteCollection);
                if (!isMatch)
                {
                    nonMatchedSites.Add(site);
                }
            }
            //If all site entries did not match:
            if (nonMatchedSites.Any())
            {
                //Display list of nucleotide site entries that did not match.
                String message = "";
                foreach (String site in nonMatchedSites)
                {
                    if (message == "")
                    {
                        message += "Some of the provided entries could not be found. Here is the list of nucleotide sites; ";
                        message += site;
                    }
                    else
                    {
                        message += ", " + site;
                    }
                }
                Console.WriteLine("\n" + message);
            }
            return(finalSiteList);
        }
Ejemplo n.º 2
0
 public void AddSearchSite(SearchSite site)
 {
     collection.Add(site);
 }