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];
}
}
}
}
}
}
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);
}
}
/// <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;
}
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;
}