public UserControl7(UIParameters up)
{
InitializeComponent();
Up = up;
Name = "UserControl7";
}
{ 1f, 0.9f, 0.1f, 0.2f }}; // 12
/*
private float[,] bgScRgb = {
{ 1f, 1f, 0.75f, 0.5f }, // 1
{ 0.7f, 0.8f, 0.5f, 0f }, // 2
{ 1f, 1f, 1f, 0.6f }, // 3
{ 1f, 1f, 1f, 0.2f }, // 4
{ 1f, 0.7f, 1f, 0.55f }, // 5
{ 0.7f, 0.2f, 1f, 0f }, // 6
{ 1f, 0.65f, 0.93f, 1f }, // 7
{ 0.7f, 0.1f, 0.7f, 1f }, // 8
{ 1f, 0.8f, 0.75f, 1f }, // 9
{ 0.7f, 0.4f, 0.3f, 1f }, // 10
{ 1f, 1f, 0.6f, 0.75f }, // 11
{ 0.7f, 0.9f, 0.1f, 0.2f }}; // 12
*/
public UserControl8(UIParameters up)
{
InitializeComponent();
this.KeyUp += new KeyEventHandler(FacetCategoryKeyUp);
Up = up;
Name = "UserControl8";
// Create Colors from the RGB values.
BgColors = new List<Color>();
for (int i = 0; i < bgScRgb.GetLength(0); i++)
{
Color bgC = Color.FromScRgb(bgScRgb[i, 0], bgScRgb[i, 1], bgScRgb[i, 2], bgScRgb[i, 3]);
BgColors.Add(bgC);
}
Up.BackgroundColorScheme = BgColors; // Set the scheme to the above colors.
ForeColorPicker.SelectedColor += SetForeColor;
//BackColorPicker.SelectedColor += SetBackColor;
foreach (FacetCategory f in Up.FacetCategories)
{
if ((f.Name == "Species") || (f.Name == "Genus"))
{
BackgroundFacet.Items.Add(f);
}
AvailableFacets.Items.Add(f);
}
// Set the scale factor for translating the coordinates from the final image to the preview image
Image.ScaleFactor = ImagePreview.Width / Image.Width;
ImagePreview.Background = Brushes.White; // Set the BG color to a default color.
CurrentBackgroundFacetCategory = (FacetCategory)BackgroundFacet.SelectedItem; // Set the current BG FacetCat to the selected item.
// Load FacetCategories for BG color that are of type String and are FilterVisible.
CurrentItemIndex = 0; // Set the current item to the first one in the collection.
CurrentItemTextBox.Text = "1";
FontFamilyBox.ItemsSource = Fonts.SystemFontFamilies; // Load fonts into pulldown
}
public UserControl10(UIParameters up)
{
InitializeComponent();
Name = "UserControl10";
Up = up;
Up.CxmlFile = "";
}
public UserControl1(UIParameters up)
{
InitializeComponent();
Name = "UserControl1";
Up = up;
Up.ProjectDir = Environment.GetFolderPath(Environment.SpecialFolder.Desktop);
projectDirTextBox.Text = Up.ProjectDir;
}
public UserControl2(UIParameters up)
{
InitializeComponent();
Name = "UserControl2";
Up = up;
Up.FastaFile = "";
}
public UserControl4(UIParameters up)
{
InitializeComponent();
Name = "UserControl4";
Up = up;
BlastDatabase.ItemsSource = proteinDatabases;
BlastAlgorithm.ItemsSource = proteinAlgorithms;
BlastDatabase.SelectedIndex = 0;
BlastAlgorithm.SelectedIndex = 0;
}
public static void RecordPivotParameters(UIParameters Up, string collectionName, string collectionTitle)
{
//Up.CollectionName = collectionName;
Up.CollectionName = "blip";
Up.CollectionTitle = collectionTitle;
//Up.CollectionUrl = @"file:///" + Up.CollectionPath + "\\" + Up.CollectionName + ".cxml";
Up.CollectionUid = GetUid();
Up.CollectionUrl = Up.CollectionPath + "\\" + Up.CollectionName + ".cxml";
Up.CollectionImagePath = Up.CollectionPath + "\\" + Up.CollectionUid + "_images";
Up.CollectionDeepzoomPath = Up.CollectionPath + "\\" + Up.CollectionUid + "_deepzoom";
}
public static void RecordBlastThresholds(UIParameters Up, UserControl4 uc4, string blastProgram, string blastDb, string blastAlgo)
{
Up.BlastProgram = blastProgram;
Up.BlastDatabase = blastDb;
Up.BlastAlgorithm = blastAlgo;
Up.BlastGeneticCode = (uc4.BlastDatabase.SelectedIndex + 1).ToString();
Up.BlastMinPercentQueryCoverage = uc4.QueryCoverageSlider.Value;
Up.BlastMinPercentIdentity = uc4.PercentIdSlider.Value;
Up.BlastMaxEvalue = Math.Pow(10, uc4.EvalueSlider.Value);
Up.BlastMaxNumHits = Convert.ToInt32(uc4.NumTopHitsSlider.Value);
}
public static void CreateFacetCategories(UIParameters Up)
{
// Query information
Up.FacetCategories.Add(new FacetCategory("InputOrder", "Number", "0", true));
Up.FacetCategories.Add(new FacetCategory("QueryLen", "Number", "0", true));
FacetCategory fc = new FacetCategory("QueryName", "String", false);
fc.IsMetaDataVisible = false;
fc.IsWordWheelVisible = true;
Up.FacetCategories.Add(fc);
FacetCategory fc_seq = new FacetCategory("QuerySequence", "String", false);
fc.IsMetaDataVisible = false;
fc.IsWordWheelVisible = false;
Up.FacetCategories.Add(fc_seq);
// BLAST alignment information
Up.FacetCategories.Add(new FacetCategory("Rank", "Number", "0", true));
Up.FacetCategories.Add(new FacetCategory("Annotated", "String", true));
Up.FacetCategories.Add(new FacetCategory("Score", "Number", "0.0", true));
Up.FacetCategories.Add(new FacetCategory("EValue", "String", false));
Up.FacetCategories.Add(new FacetCategory("Identity", "Number", "0.00", true));
Up.FacetCategories.Add(new FacetCategory("Span", "Number", "0.00", true));
Up.FacetCategories.Add(new FacetCategory("AlignLen", "Link", false));
Up.FacetCategories.Add(new FacetCategory("NextScore", "String", true));
Up.FacetCategories.Add(new FacetCategory("Strand", "String", false));
Up.FacetCategories.Add(new FacetCategory("SubjStart", "Number", "0", false));
Up.FacetCategories.Add(new FacetCategory("SubjLen", "Number", "0", false));
// Gene information
Up.FacetCategories.Add(new FacetCategory("Gene", "Link", false));
Up.FacetCategories.Add(new FacetCategory("GI", "Link", false));
Up.FacetCategories.Add(new FacetCategory("Accession", "Link", false));
Up.FacetCategories.Add(new FacetCategory("Definition", "LongString", false));
Up.FacetCategories.Add(new FacetCategory("Product", "LongString", false));
Up.FacetCategories.Add(new FacetCategory("Function", "LongString", false));
// Organism information
Up.FacetCategories.Add(new FacetCategory("Lineage", "LongString", false));
Up.FacetCategories.Add(new FacetCategory("Organism", "LongString", false));
Up.FacetCategories.Add(new FacetCategory("Species", "String", true));
Up.FacetCategories.Add(new FacetCategory("Genus", "String", true));
Up.FacetCategories.Add(new FacetCategory("Kingdom", "String", true));
Up.FacetCategories.Add(new FacetCategory("Phylum", "String", true));
Up.FacetCategories.Add(new FacetCategory("Class", "String", true));
Up.FacetCategories.Add(new FacetCategory("Order", "String", true));
Up.FacetCategories.Add(new FacetCategory("Family", "String", true));
// References
Up.FacetCategories.Add(new FacetCategory("RefCount", "Number", "0", true));
fc = new FacetCategory("References", "Link", false);
fc.IsMetaDataVisible = true;
fc.IsWordWheelVisible = false;
Up.FacetCategories.Add(fc);
Up.FacetCategories.Add(new FacetCategory("SubmissionDate", "DateTime", true));
}
public UserControl0(UIParameters up)
{
InitializeComponent();
Name = "UserControl0";
Up = up;
}
public static void writePairwiseAlignment(UIParameters Up, Hit blastHit, int blastHspId, int itemId)
{
string pa = BlastUtil.ToString(blastHit, blastHspId);
TextWriter tw = new StreamWriter(Up.ProjectDir + "\\txt\\" + itemId + ".txt");
tw.Write(pa);
tw.Close();
}
public static void writePairwiseAlignment(UIParameters Up, int itemId)
{
TextWriter tw = new StreamWriter(Up.ProjectDir + "\\txt\\" + itemId + ".txt");
tw.Write("No alignments for this query sequence.");
tw.Close();
}
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;
}
public static int[] GetBestAnnotatedIndex(UIParameters Up, int seqPos)
{
// BLAST reports are saved in individual files by query and
// numbered in the same order as they appear in the input FASTA file.
int[] annotatedIndex = new int[2];
annotatedIndex[0] = -1;
annotatedIndex[1] = -1;
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();
// 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 (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;
if ((percentId >= Up.BlastMinPercentIdentity) &&
(Up.BlastMaxEvalue >= blastHsp.EValue) &&
(queryCoverage >= Up.BlastMinPercentQueryCoverage) &&
(hitsProcessed < Up.BlastMaxNumHits))
{
rank += 1;
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";
try
{
Console.WriteLine("GB OK: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
ISequence gbRecord = gbParser.ParseOne(gbFile);
GenBankMetadata gbMeta = (GenBankMetadata)gbRecord.Metadata["GenBank"];
IList<FeatureItem> features = gbMeta.Features.All;
FeatureItem bestItem = getBestFeatureItem(features);
if (bestItem != null)
{
annotatedIndex[0] = i;
annotatedIndex[1] = j;
return annotatedIndex;
}
}
catch
{
Console.WriteLine("ISANNOTATED: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
}
hitsProcessed += 1;
}
}
}
}
}
}
return annotatedIndex;
}
