Example #1
0
        public void SetItemBgIndex(Collection collection)
        {
            foreach (FacetCategory fc in Up.FacetCategories)
            {
                if ((fc.Type == "String") && fc.IsFilterVisible)
                {
                    Dictionary<string, int> facetValues = new Dictionary<string, int>();
                    foreach (Item item in collection.Items)
                    {
                        foreach (Facet f in item.Facets)
                        {
                            if (f.Name == fc.Name)
                            {
                                if (!facetValues.ContainsKey(f[0].Value))
                                {
                                    facetValues[f[0].Value] = 1;
                                }
                                else
                                {
                                    facetValues[f[0].Value] += 1;
                                }
                            }
                        }
                    }

                    var sortedFacetValues = (from entry in facetValues orderby entry.Value descending select entry);
                    int rank = 0;
                    int lastCount = 0;
                    Dictionary<string, int> facetRank = new Dictionary<string, int>();
                    foreach (KeyValuePair<string, int> pair in sortedFacetValues)
                    {
                        if (pair.Value != lastCount)
                        {
                            rank += 1;
                        }
                        facetRank[pair.Key] = rank - 1;
                        lastCount = pair.Value;
                    }
                    foreach (Item item in collection.Items)
                    {
                        foreach (Facet f in item.Facets)
                        {
                            if (f.Name == fc.Name)
                            {
                                f.Rank = facetRank[f[0].Value];
                            }
                        }
                    }
                }
            }
        }
Example #2
0
        public void DrawImages(Collection collection)
        {
            Dictionary<string, int> facetValues = new Dictionary<string, int>();
            int ic = 0;

            foreach (Item item in collection.Items)
            {
                ic++;
                Dispatcher.Invoke(System.Windows.Threading.DispatcherPriority.Normal, new Action(delegate()
                {
                    int p = calcProgress(ic, collection.Items.Count());
                    progressBar1.Value = p;
                    progressText1.Text = "Drawing images (" + p + "%)";
                }));
                Image image = new Image(item, Up.FacetCategories);
                image.DrawAndSaveImage(Up.CollectionImagePath + "\\" + item.Id + ".png", Up.BackgroundFacetCategory, Up.BackgroundColorScheme);
            }
        }
Example #3
0
 /// <summary>
 /// Create the Pivot collection.
 /// Uses global parameters from UIParameters.
 /// </summary>
 /// <returns>Object representing a Pivot collection.</returns>
 public Collection CreateCollection()
 {
     
     // Create an empty collection
     string imgBase = Up.CollectionUid + "_deepzoom\\" + Up.CollectionUid + "_deepzoom.xml";
     Collection collection = new Collection(Up.CollectionTitle, imgBase);
     collection.FacetCategories = Up.FacetCategories;
     // Create output directories
     if (!Directory.Exists(Up.CollectionPath)) { Directory.CreateDirectory(Up.CollectionPath); }
     if (!Directory.Exists(Up.CollectionImagePath)) { Directory.CreateDirectory(Up.CollectionImagePath); }
     
     // Init current sequence position and item number.
     int seqPos = 0;
     int itemId = 0;
     
     // For each query sequence (parsed from FASTA file). 
     // I this version, the only property used from the query sequence is the displayID i.e. can be factored out.
     int progValue = 0;
     foreach (ISequence rec in Up.QuerySequences)
     {
         //GeneSequence gene = Collection.ParseGene(rec);
         // Update  the progress bar in the WPF app
         progValue = Convert.ToInt32(Math.Round((seqPos / (double)Up.QuerySequences.Count()), 2) * 100);
         UpdateProgressBar(progValue, "Generating Output");
         itemId = Pivot.CreateItems(Up, rec, itemId, seqPos, collection);
         // parse name from the query seq displayID property
         seqPos += 1;
     }
     //MessageBox.Show(collection.Items.Count().ToString());
     return collection;
     
 }
Example #4
0
        public static int CreateItems(UIParameters Up, ISequence rec, int itemId, int seqPos, Collection collection)
        {
            
            string queryName = rec.DisplayID.ToString().Split(' ')[0];

            // BLAST reports are saved in individual files by query and 
            // numbered in the same order as they appear in the input FASTA file.
            string blastFile = Up.ProjectDir + "\\xml\\" + seqPos + ".xml";
            if (!File.Exists(blastFile))
            {
                throw new Exception("File does not exist.");
            }
            BlastXmlParser blastParser = new BlastXmlParser();
            IList<BlastResult> blastResults = blastParser.Parse(blastFile);
            GenBankParser gbParser = new GenBankParser();

            int[] annotatedIndex = GetBestAnnotatedIndex(Up, seqPos);
            
            // iterate through the BLAST results.
            foreach (BlastResult blastResult in blastResults)
            {
                foreach (BlastSearchRecord record in blastResult.Records)
                {
                    int hitsProcessed = 0;
                    // If there are not hits in the BLAST result ...
                    int rank = 0;
                    if (record.Hits.Count() > 0)
                    {
                        // For each hit
                        for (int i = 0; i < record.Hits.Count(); i++)
                        {

                            Hit blastHit = record.Hits[i];
                            // For each HSP
                            for (int j = 0; j < blastHit.Hsps.Count(); j++)
                            {
                                
                                Hsp blastHsp = blastHit.Hsps[j];
                                double percentId = (blastHsp.IdentitiesCount / (double)blastHsp.AlignmentLength) * 100;
                                double queryCoverage = ((double)(blastHsp.QueryEnd - blastHsp.QueryStart + 1) / record.IterationQueryLength) * 100;
                                string txt = String.Format("{0} {1} {2} {3} {4} {5} {6} {7}", percentId, Up.BlastMinPercentIdentity,
                                    Up.BlastMaxEvalue, blastHsp.EValue, queryCoverage, Up.BlastMinPercentQueryCoverage,
                                    hitsProcessed, Up.BlastMaxNumHits);
                                // if HSP passes user-defined thresholds
                                if ((percentId >= Up.BlastMinPercentIdentity) &&
                                    (Up.BlastMaxEvalue >= blastHsp.EValue) &&
                                    (queryCoverage >= Up.BlastMinPercentQueryCoverage) &&
                                    (hitsProcessed < Up.BlastMaxNumHits))
                                {
                                    rank += 1;
                                    string nextScore = "no";
                                    if ((i + 1) < record.Hits.Count())
                                    {
                                        if (blastHsp.Score > record.Hits[i + 1].Hsps[0].Score)
                                        {
                                            nextScore = "less than";
                                        }
                                        else
                                        {
                                            nextScore = "equal";
                                        }
                                    }
                                    else
                                    {
                                        nextScore = "non existent";
                                    }

                                    // parse GI numner from hit
                                    long gi = Convert.ToInt64(blastHit.Id.Split('|')[1]);
                                    GenBankItem gitem = new GenBankItem(gi, blastHsp.HitStart, blastHsp.HitEnd);
                                    string gbFile = Up.ProjectDir + "\\gb\\" + gitem.Id.ToString();
                                    gbFile += "_" + gitem.HitStart.ToString();
                                    gbFile += "_" + gitem.HitEnd.ToString();
                                    gbFile += ".gb";
                                    // init item
                                    string img = "#" + itemId.ToString();
                                    Item item = new Item(itemId, img);
                                    string[] headerTokens = parseFastaHeader(rec.DisplayID.ToString());
                                    item.Name = headerTokens[0];
                                    item.Description = headerTokens[1];

                                    // write pairwise alignment
                                    writePairwiseAlignment(Up, blastHit, j, itemId);

                                    // try to parse the GB record associated with the hit and set facet values to data from BLAST/GB record
                                    try
                                    {
                                        Console.WriteLine("GB OK: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
                                        ISequence gbRecord = gbParser.ParseOne(gbFile);
                                        item.Href = GetNCBIUrl(Up.BlastProgram) + GetGenBankIdentifier(gbRecord);
                                        GenBankMetadata gbMeta = (GenBankMetadata)gbRecord.Metadata["GenBank"];
                                        CodingSequence bestCds = null;
                                        IList<FeatureItem> features = gbMeta.Features.All;
                                        FeatureItem bestItem = getBestFeatureItem(features);

                                        
                                        if (gbMeta.Features.CodingSequences.Count > 0)
                                        {
                                            bestCds = gbMeta.Features.CodingSequences[0];
                                        }
                                        
                                        for (int k = 1; k < gbMeta.Features.CodingSequences.Count; k++)
                                        {
                                            CodingSequence cds = gbMeta.Features.CodingSequences[k];
                                            //int bestSize = Math.Abs(bestCds.Location.End - bestCds.Location.Start);
                                            int bestSize = Math.Abs(bestItem.Location.End - bestItem.Location.Start);
                                            int cdsSize = Math.Abs(cds.Location.End - cds.Location.Start);
                                            if (cdsSize > bestSize)
                                            {
                                                bestCds = cds;
                                            }
                                        }
                                        foreach (FacetCategory f in Up.FacetCategories)
                                        {
                                            Facet facet = new Facet();
                                            switch (f.Name)
                                            {
                                                case "InputOrder":
                                                    facet = new Facet(f.Name, f.Type, seqPos);
                                                    break;
                                                case "QuerySequence":
                                                    facet = new Facet(f.Name, f.Type, rec.ToString());
                                                    break;
                                                case "NextScore":
                                                    facet = new Facet(f.Name, f.Type, nextScore);
                                                    break;
                                                case "Annotated":
                                                    string value = "na";
                                                    if ((annotatedIndex[0] == i) && (annotatedIndex[1] == j))
                                                    {
                                                        value = "top_annotated";
                                                    }
                                                    else
                                                    {
                                                        if ((i == 0) && (j == 0) && (annotatedIndex[0] == -1) && (annotatedIndex[1] == -1))
                                                        {
                                                            value = "top_unannotated";
                                                        }else{
                                                            if (bestItem != null)
                                                            {
                                                                value = "annotated";
                                                            }else{
                                                                value = "unannotated";
                                                            }
                                                        }
                                                    }
                                                    facet = new Facet(f.Name, f.Type, value);
                                                    break;
                                                default:
                                                    //facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item, GetNCBIUrl(Up.BlastProgram), bestCds, rank);
                                                    facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item, GetNCBIUrl(Up.BlastProgram), bestItem, rank);
                                                    break;
                                            }
                                            /*
                                            if (f.Name == "InputOrder")
                                            {
                                                facet = new Facet(f.Name, f.Type, seqPos);
                                            }

                                            else
                                            {
                                                facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item);
                                            }
                                            */
                                            item.Facets.Add(facet);
                                        }

                                    }
                                    //catch (System.NullReferenceException e) // if parsing failed init the item w/ default values (similar to 'no hit' above)
                                    catch
                                    {

                                        Console.WriteLine("GB ERROR: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
                                        item.Href = "#";
                                        foreach (FacetCategory f in Up.FacetCategories)
                                        {
                                            Facet facet = new Facet();
                                            switch (f.Name)
                                            {
                                                case ("InputOrder"):
                                                    facet = new Facet(f.Name, f.Type, seqPos);
                                                    break;
                                                case "QuerySequence":
                                                    facet = new Facet(f.Name, f.Type, rec.ToString());
                                                    break;
                                                case ("NextScore"):
                                                    facet = new Facet(f.Name, f.Type, "no");
                                                    break;
                                                case "Annotated":
                                                    string value = "na";
                                                    if ((annotatedIndex[0] == i) && (annotatedIndex[1] == j))
                                                    {
                                                        value = "top_annotated";
                                                    }
                                                    else
                                                    {
                                                        if ((i == 0) && (j == 0) && (annotatedIndex[0] == -1) && (annotatedIndex[1] == -1))
                                                        {
                                                            value = "top_unannotated";
                                                        }
                                                        else
                                                        {
                                                            value = "unannotated";
                                                        }
                                                    }
                                                    facet = new Facet(f.Name, f.Type, value);
                                                    break;
                                                default:
                                                    facet = CreateGBErrorFacet(f.Name, f.Type, record, i, j, item, GetNCBIUrl(Up.BlastProgram), rank);
                                                    break;
                                            }
                                            item.Facets.Add(facet);
                                        }
                                        //throw (e);
                                    }
                                    // Add item to collection, increment to next item, 
                                    collection.Items.Add(item);
                                    hitsProcessed += 1;
                                    itemId += 1;
                                }
                            }
                        }
                    }
                    if ((record.Hits.Count()) == 0 || (hitsProcessed == 0))
                    {
                        // Init Pivot item
                        string img = "#" + itemId.ToString();
                        Item item = new Item(itemId, img);
                        item.Href = "#";
                        string[] headerTokens = parseFastaHeader(rec.DisplayID.ToString());
                        item.Name = headerTokens[0];
                        item.Description = headerTokens[1];

                        // Write pairwise alignment to file.
                        writePairwiseAlignment(Up, itemId);

                        // Set facet values for each facet category to default values
                        foreach (FacetCategory f in Up.FacetCategories)
                        {
                            Facet facet = new Facet();
                            switch (f.Name)
                            {
                                case ("InputOrder"):
                                    facet = new Facet(f.Name, f.Type, seqPos);
                                    break;
                                case ("QuerySequence"):
                                    facet = new Facet(f.Name, f.Type, rec.ToString());
                                    break;
                                default:
                                    facet = CreateFacet(f.Name, f.Type, record, item, 0);
                                    break;
                            }
                            item.Facets.Add(facet);
                        }

                        // Add item to collection, increment to next item, skip remaining code
                        collection.Items.Add(item);
                        itemId += 1;
                        hitsProcessed += 1;
                    }
                }
            }
            return itemId;
        }