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; }