public UserControl2(UIParameters up)
{
InitializeComponent();
Name = "UserControl2";
Up = up;
Up.FastaFile = "";
}
public UserControl10(UIParameters up)
{
InitializeComponent();
Name = "UserControl10";
Up = up;
Up.CxmlFile = "";
}
private void fileProcessor_DoWork(object sender, System.ComponentModel.DoWorkEventArgs e)
{
double currProgress;
BackgroundWorker worker = sender as BackgroundWorker;
UIParameters parameters = (UIParameters)e.Argument;
Dictionary <string, bool> staticLaunch = new Dictionary <string, bool>();
Dictionary <string, bool> dynamicLaunch = new Dictionary <string, bool>();
foreach (CheckBox box in parameters.groupBoxStatic.Controls)
{
staticLaunch.Add(box.Text, box.Checked);
}
foreach (CheckBox box in parameters.groupBoxDynamic.Controls)
{
dynamicLaunch.Add(box.Text, box.Checked);
}
ParserParent parserClass = new ParserParent(worker);
parserClass.dynamicLaunch = dynamicLaunch;
parserClass.staticLaunch = staticLaunch;
parserClass.parameters = parameters;
if (UsePatterns.Checked)
{
parserClass.SplitFiles(PatternStorage);
}
else
{
parserClass.InOneGo();
}
}
}; // 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 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 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 UserControl1(UIParameters up)
{
InitializeComponent();
Name = "UserControl1";
Up = up;
Up.ProjectDir = Environment.GetFolderPath(Environment.SpecialFolder.Desktop);
projectDirTextBox.Text = Up.ProjectDir;
}
public UserControl4(UIParameters up)
{
InitializeComponent();
Name = "UserControl4";
Up = up;
BlastDatabase.ItemsSource = proteinDatabases;
BlastAlgorithm.ItemsSource = proteinAlgorithms;
BlastDatabase.SelectedIndex = 0;
BlastAlgorithm.SelectedIndex = 0;
}
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 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 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));
}
private void ChangeValues(UIParameters vp, Plugin p)
{
if (pm != null)
{
pm = (UIParameters)vp.Clone();
statLabel.Font = vp.TextFont;
statLabel.ForeColor = vp.TextColor;
BackColor = vp.Color;
Opacity = vp.Opacity;
}
if (p != null)
{
this.p = p;
statLabel.Text = p.Update();
}
}
private void SetUIParameters_VisibleChanged(object sender, EventArgs e)
{
if (Visible == false)
{
if (DialogResult == DialogResult.OK)
{
v1 = (UIParameters)v2.Clone();
}
else
{
v2 = (UIParameters)v1.Clone();
}
}
else
{
ChangeValues(v2);
}
}
public static void ExecuteLogcat(object parameter)
{
UIParameters parameters = (UIParameters)parameter;
Context = parameters.Context;
BackgroundWorker worker = new BackgroundWorker();
worker.DoWork += async(sender, args) =>
{
await Context.Dispatcher.InvokeAsync(() => { _adb = new AdbTools(Context); });
await
Task.Run(
async() =>
await _adb.Logcat(parameters.Context2, parameters.Bool, parameters.Target));
};
worker.RunWorkerCompleted += (sender, args) => worker.Dispose();
worker.RunWorkerAsync();
}
public static void ExecuteToken(object parameter)
{
UIParameters parameters = (UIParameters)parameter;
Context = parameters.Context;
BackgroundWorker worker = new BackgroundWorker();
worker.DoWork += async(sender, args) =>
{
await Context.Dispatcher.InvokeAsync(() => { Fastboot = new FastbootTools(Context); });
await
Task.Run(
async() =>
await Fastboot.GetIdentiferToken(parameters.Context2, parameters.Bool));
};
worker.RunWorkerCompleted += (sender, args) => worker.Dispose();
worker.RunWorkerAsync();
}
private void ChangeValues(UIParameters v)
{
v2 = (UIParameters)v.Clone();
color1ChooseButton.BackColor = v.DesktopLabelColor1;
color1ChooseButton.ForeColor = (colorDialog.Color.GetBrightness() < 0.5) ? Color.White : Color.Black;
color2ChooseButton.BackColor = v.DesktopLabelColor2;
color2ChooseButton.ForeColor = (colorDialog.Color.GetBrightness() < 0.5) ? Color.White : Color.Black;
colorChooseButton.BackColor = v.Color;
colorChooseButton.ForeColor = (colorDialog.Color.GetBrightness() < 0.5) ? Color.White : Color.Black;
mainTextColorChooseButton.BackColor = v.TextColor;
mainTextColorChooseButton.ForeColor = (colorDialog.Color.GetBrightness() < 0.5) ? Color.White : Color.Black;
mainTextFontChooseButton.Font = new Font(v.TextFont.FontFamily, 8.25F, v.TextFont.Style, GraphicsUnit.Point, (byte)204);
desktopChooseFontButton.Font = new Font(v.DesktopLabelFont.FontFamily, 8.25F, v.DesktopLabelFont.Style, GraphicsUnit.Point, (byte)204);
opacityNumeric.Value = (decimal)v2.Opacity;
deskXnumeric.Value = (decimal)v2.DesktopLabelCoordinates.X;
deskYnumeric.Value = (decimal)v2.DesktopLabelCoordinates.Y;
switch (v2.DesktopLabelEffect)
{
case LinearGradientMode.BackwardDiagonal:
desktopLabelEffectListBox.SelectedIndex = 0;
break;
case LinearGradientMode.ForwardDiagonal:
desktopLabelEffectListBox.SelectedIndex = 1;
break;
case LinearGradientMode.Horizontal:
desktopLabelEffectListBox.SelectedIndex = 2;
break;
case LinearGradientMode.Vertical:
desktopLabelEffectListBox.SelectedIndex = 3;
break;
}
}
public AdbViewModel()
{
ThreeTextCommandParameters = new ThreeTextCommandParameters();
FiveTextCommandParameters = new FiveTextCommandParameters();
InstallTwoCommandParameters = new TwoCommandParameters();
UninstallTwoCommandParameters = new TwoCommandParameters();
UiParameters = new UIParameters();
ExecuteSingleCommandParameters = new TwoCommandParameters();
CopyCommandParameters = new ThreeTextCommandParameters();
MoveCommandParameters = new ThreeTextCommandParameters();
DeleteCommandParameters = new TwoCommandParameters();
SideloadParameters = new TwoCommandParameters();
ExecuteCommandsParameters = new ExecuteCommandParameters();
BackupParameters = new BackupParameters();
RestoreParameters = new TwoCommandParameters();
RemoteConnectParameters = new ThreeTextCommandParameters();
RemoteDisconnectParameters = new SingleCommandParameters();
RemoteSaveParameters = new ThreeTextCommandParameters();
_remoteInfoRepository = ((ViewModelLocator)Application.Current.Resources["Locator"]).RemoteInfoRepository;
}
public static void ExecuteListDevices(object parameter)
{
UIParameters parameters = (UIParameters)parameter;
if (parameters != null)
{
Context = parameters.Context;
BackgroundWorker worker = new BackgroundWorker();
worker.DoWork += async(sender, args) =>
{
await Context.Dispatcher.InvokeAsync(async() =>
{
Fastboot = new FastbootTools(Context);
await Fastboot.ListDevices(parameters.Context2, parameters.Bool);
});
};
worker.RunWorkerCompleted += (sender, args) => worker.Dispose();
worker.RunWorkerAsync();
}
}
private void toExcel_Click(object sender, EventArgs e)
{
if (fileProcessor.IsBusy != true)
{
cancelWorker.Visible = true;
fileProgressBar.Visible = true;
UIParameters parameters = new UIParameters();
parameters.groupBoxStatic = groupBoxStatic;
parameters.groupBoxDynamic = groupBoxDynamic;
parameters.groupBoxCommon = groupBoxCommon;
parameters.fileList = fileList.Items.Cast <ListViewItem>().ToList();
parameters.ExportDir = saveTo.Text;
if (templateDirectory.Text == "")
{
selectFile.Title = "No Template selected please select one!";
selectFile.ShowDialog();
templateDirectory.Text = selectFile.FileName;
}
parameters.TemplateDir = templateDirectory.Text;
fileProcessor.RunWorkerAsync(parameters);
}
}
/// <summary>
/// Loads Next UI Menu
/// </summary>
/// <param name="menu"></param>
public static void LoadMenu(UIMenu menu, UIParameters parameters = null)
{
if (menu == null)
{
Debug.LogWarning("No UI Menu to load!");
return;
}
if (ActiveMenu != null)
{
ActiveMenu.DisableMenu();
ActiveMenu.gameObject.SetActive(false);
}
ActiveMenu = menu;
ActiveMenu.gameObject.SetActive(true);
if (parameters != null)
{
ActiveMenu.parameters = parameters;
}
ActiveMenu.InitializeMenu();
}
//TODO: Наклепать цветные кнопки
public SetUIParameters(UIParameters v)
{
InitializeComponent();
v2 = (UIParameters)v.Clone();
v1 = (UIParameters)v.Clone();
}
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);
}
//Creation Methods
public UIText2 createText2(UIParameters aArgs)
{
//Create the game object
GameObject uiGameObject = new GameObject("Sprite(Text2)");
Transform uiTransform = uiGameObject.GetComponent<Transform>();
uiTransform.rotation = Quaternion.identity;
uiTransform.position = Vector3.zero;
uiTransform.localRotation = Quaternion.identity;
uiTransform.localPosition = Vector3.zero;
uiTransform.localScale = new Vector3(0.0f, 0.0f, 1.0f);
uiTransform.parent = transform;
//Create the required Components
GUIText uiGUIText = uiGameObject.AddComponent<GUIText>();
//Create the UIText2 Component
UIText2 uiText = uiGameObject.AddComponent<UIText2>();
//Set the Defaults
uiGUIText.anchor = TextAnchor.LowerLeft;
uiGUIText.alignment = TextAlignment.Left;
uiText.setManager(this);
uiText.setDefault(true);
//Set the UIParamaters
uiText.toggleName = aArgs.toggleName;
uiText.isInteractive = aArgs.interactive;
uiText.text = aArgs.text;
uiText.font = aArgs.font;
uiText.fontSize = aArgs.fontSize;
uiText.fontStyle = aArgs.fontStyle;
uiText.fontColor = aArgs.color;
uiText.scale = new Vector2(aArgs.scale,aArgs.scale);
uiText.setBounds(aArgs.bounds.x, aArgs.bounds.y, aArgs.bounds.width, aArgs.bounds.height);
//Register the Control
registerToggle(uiText);
return uiText;
}
public UILabel createLabel2(UIParameters aArgs)
{
bool defaultInteractive = aArgs.interactive;
Texture defaultTexture = aArgs.texture;
//Create the GameObject
GameObject uiGO = new GameObject("Sprite (Label 2)");
Transform uiTransform = uiGO.transform;
uiTransform.rotation = Quaternion.identity;
uiTransform.position = Vector3.zero;
uiTransform.localRotation = Quaternion.identity;
uiTransform.localPosition = Vector3.zero;
uiTransform.localScale = new Vector3(0.0f, 0.0f, 1.0f);
uiTransform.parent = transform;
//Create Text2 && Texture2
aArgs.interactive = true;
UIText2 text2 = createText2(aArgs);
aArgs.interactive = false;
aArgs.texture = null;
UITexture2 texture2 = createTexture2(aArgs);
//Create UILabel
UILabel label = uiGO.AddComponent<UILabel>();
label.uiText = text2;
label.uiTexture = texture2;
text2.setHandler(label);
texture2.setHandler(label);
text2.transform.parent = label.transform;
texture2.transform.parent = label.transform;
aArgs.interactive = defaultInteractive;
aArgs.texture = defaultTexture;
return null;
}
public UITexture2 createTexture2(UIParameters aArgs)
{
//Create the Game Object
GameObject uiGameObject = new GameObject("Sprite(Texture2)");
Transform uiTransform = uiGameObject.GetComponent<Transform>();
uiTransform.rotation = Quaternion.identity;
uiTransform.position = Vector3.zero;
uiTransform.localRotation = Quaternion.identity;
uiTransform.localPosition = Vector3.zero;
uiTransform.localScale = new Vector3(0.0f, 0.0f, 1.0f);
uiTransform.parent = transform;
//Create the required Components
GUITexture uiGUITexture = uiGameObject.AddComponent<GUITexture>();
//Create the UITexture2 Component
UITexture2 uiTexture = uiGameObject.AddComponent<UITexture2>();
//Set the Defaults
uiTexture.setManager(this);
uiTexture.setDefault(true);
//Set the UIParameters
uiTexture.toggleName = aArgs.toggleName;
uiTexture.isInteractive = aArgs.interactive;
uiTexture.texture = aArgs.texture;
uiTexture.color = aArgs.color;
uiTexture.scale = new Vector2(aArgs.scale, aArgs.scale);
uiTexture.setBounds(aArgs.bounds.x, aArgs.bounds.y, aArgs.bounds.width, aArgs.bounds.height);
//Register the Control
registerToggle(uiTexture);
return uiTexture;
}
private void setUIParametersMenuItem_Click(object sender, EventArgs e)
{
s.ShowDialog();
pm = s.GetViewParameters();
ChangeValues(pm, null);
}
public UIText3 createText3(UIParameters aArgs)
{
//Create the Game Object
GameObject uiGameObject = new GameObject("Sprite(Text3)");
Transform uiTransform = uiGameObject.GetComponent<Transform>();
uiTransform.rotation = Quaternion.identity;
uiTransform.position = Vector3.zero;
uiTransform.localRotation = Quaternion.identity;
uiTransform.localPosition = Vector3.zero;
uiTransform.localScale = new Vector3(0.5f, 0.5f, 0.5f);
uiTransform.parent = transform;
//Create the required components
MeshRenderer uiMeshRenderer = uiGameObject.AddComponent<MeshRenderer>();
TextMesh uiTextMesh = uiGameObject.AddComponent<TextMesh>();
uiMeshRenderer.material = m_TextMaterial;
uiTextMesh.characterSize = 0.1f;
uiTextMesh.anchor = TextAnchor.MiddleCenter;
uiTextMesh.alignment = TextAlignment.Center;
//Create the UIText3 Component
UIText3 uiText = uiGameObject.AddComponent<UIText3>();
// set The default
uiText.setManager(this);
uiText.setDefault(true);
//set the UIParameters
uiText.toggleName = aArgs.toggleName;
uiText.isInteractive = aArgs.interactive;
uiText.text = aArgs.text;
uiText.font = aArgs.font;
uiText.fontSize = aArgs.fontSize;
uiText.fontStyle = aArgs.fontStyle;
uiText.color = aArgs.color;
uiText.position = aArgs.position;
uiText.rotation = aArgs.rotation;
uiTextMesh.font = aArgs.font;
//Register the Control
registerToggle(uiText);
uiText.updateTransform(false);
return uiText;
}
public UITexture3 createTexture3(UIParameters aArgs)
{
//Create the Game Object
GameObject uiGameObject = new GameObject("Sprite(Texture3)");
Transform uiTransform = uiGameObject.GetComponent<Transform>();
uiTransform.rotation = Quaternion.identity;
uiTransform.position = Vector3.zero;
uiTransform.localRotation = Quaternion.identity;
uiTransform.localPosition = Vector3.zero;
uiTransform.localScale = new Vector3(1.0f, 1.0f, 1.0f);
uiTransform.parent = transform;
//Create the required components
MeshRenderer uiMeshRenderer = uiGameObject.AddComponent<MeshRenderer>();
MeshFilter uiMeshFilter = uiGameObject.AddComponent<MeshFilter>();
uiMeshRenderer.material = m_TextureMaterial;
uiMeshFilter.mesh = m_PlaneMesh;
//Create the UIText3 Component
UITexture3 uiTexture = uiGameObject.AddComponent<UITexture3>();
// set The default
uiTexture.setManager(this);
uiTexture.setDefault(true);
//set the UIParameters
uiTexture.toggleName = aArgs.toggleName;
uiTexture.isInteractive = aArgs.interactive;
uiTexture.texture = aArgs.texture;
uiTexture.color = aArgs.color;
uiTexture.position = aArgs.position;
uiTexture.rotation = aArgs.rotation;
//Register the Control
registerToggle(uiTexture);
uiTexture.updateTransform(false);
return uiTexture;
}
public UserControl0(UIParameters up)
{
InitializeComponent();
Name = "UserControl0";
Up = up;
}
public UserControl7(UIParameters up)
{
InitializeComponent();
Up = up;
Name = "UserControl7";
}
public UILabel createLabel3(UIParameters aArgs)
{
return null;
}