public void LoadSearch(IGraphScene <IVisual, IVisualEdge> scene, IGraphSceneLayout <IVisual, IVisualEdge> layout, object name)
{
var graph = scene.Graph.Source <IVisual, IVisualEdge, IThing, ILink>();
if (graph == null)
{
throw new ArgumentException("Search works only on ThingGraphs");
}
scene.CleanScene();
var visuals = scene.Graph.ThingGraph()
.Search(name, false)
.Select(t => graph.Get(t));
new GraphSceneFacade <IVisual, IVisualEdge>(() => scene, layout)
.Add(visuals, false, false);
var aligner = new Aligner <IVisual, IVisualEdge>(scene, layout);
aligner.FullLayout(null, new Point(layout.Border.Width, layout.Border.Height), layout.Options(), new VisualComparer());
aligner.Commit();
scene.ClearSpatialIndex();
}
public Controller(FrmMain form)
{
formClass = form;
drawerClass = new Drawer(form);
AlignerClass = new Aligner();
selected = 0;
}
/// <inheritdoc/>
protected override IEnumerable <Segment> Render(RenderContext context, int maxWidth)
{
if (context is null)
{
throw new ArgumentNullException(nameof(context));
}
if (_lines.Count == 0)
{
return(Array.Empty <Segment>());
}
var lines = context.SingleLine
? new List <SegmentLine>(_lines)
: SplitLines(maxWidth);
// Justify lines
var justification = context.Justification ?? Alignment ?? Justify.Left;
if (justification != Justify.Left)
{
foreach (var line in lines)
{
Aligner.Align(line, justification, maxWidth);
}
}
if (context.SingleLine)
{
// Return the first line
return(lines[0].Where(segment => !segment.IsLineBreak));
}
return(new SegmentLineEnumerator(lines));
}
public Goto(MyGridProgram argPg, Grid argG, Mover m, Aligner a)
{
pg = argPg;
g = argG;
mover = m;
aligner = a;
rc = new RemoteControl(g);
}
public void SetAligner_Pivot()
{
Aligner_Pivot aligner = new Aligner_Pivot();
aligner = new Aligner_Pivot();
aligner.panel = this;
this.aligner = aligner;
}
public MAlignerViewer()
{
InitializeComponent();
KeyValuePair <int[, ], Dictionary <char, int> > m = MAligner.Utils.LoadSubstitutionMatrixFromString(PepExplorer2.Properties.Resources.PAM30MS);
mAligner = new Aligner(m);
}
public void SetAligner_FixedTile(Vector2 tileSize)
{
Aligner_FixedTile aligner = new Aligner_FixedTile();
aligner = new Aligner_FixedTile();
aligner.panel = this;
aligner.SetTileSize(tileSize);
this.aligner = aligner;
}
public void SetAligner_AdaptiveTile(int linesCount, int tilesCountInLine)
{
Aligner_AdaptiveTile aligner = new Aligner_AdaptiveTile();
aligner = new Aligner_AdaptiveTile();
aligner.panel = this;
aligner.SetGrid(linesCount, tilesCountInLine, this);
this.aligner = aligner;
}
public AlignmentForm()
{
InitializeComponent();
examplesComboBox.SelectedIndex = 0;
examplesComboBox_SelectedIndexChanged(null, null);
aligner = new Aligner();
globalAlignmentButton_Click(null, null);
}
public IEnumerable <IModListingGetter> Get()
{
var mods = RawListingsReader.Read(ListingsPathProvider.Path);
return(Aligner.AlignToTimestamps(
mods,
DirectoryProvider.Path,
throwOnMissingMods: Prefs.ThrowOnMissingMods));
}
public MainForm()
{
InitializeComponent();
// initialize
this.detector = new Detector("data\\models\\Detector2.0.ats");
this.aligner = new Aligner("data\\models\\PointDetector2.0.pts5.ats");
this.recognizer = new Recognizer("data\\models\\Recognizer2.0.ats");
}
public static SyntaxNode AlignIndents(this SyntaxNode root, Action<int, string> onLineVisualized = null)
{
if (Runtime.Settings.AlignIndents)
try
{
root = new Aligner(onLineVisualized).AlignIndents(root);
}
catch { }
return root;
}
public MaintainPrealignerTabPanel()
{
InitializeComponent();
comboBoxMode.DataSource = System.Enum.GetValues(typeof(AlignerCommand.MainTainMovingMode));
if (AppData.IsRuntime)
{
preAligner = ATSCore.Instance.Aligner;
}
}
public void Test4()
{
// Batch.exe --highlight-spaces xx.in xx.in xx.in 01.in xx.in xx.in ex08.out 80
string[] files = new string[] { "01.in", "01.in", "01.in" };
IReader reader = new MultifileReader(files);
Aligner aligner = new Aligner(reader, "ex12_actual.out", 17, false);
aligner.Process();
Assert.AreEqual(ReadFile("ex12.out"), ReadFile("ex12_actual.out"));
}
public string GetString(int MatchNumber, int RefMatchNumber /* if no refs =-1 */)
{
string comment = ""; //comment сейчас вообще никак не работает
QMatch Match, Refs;
PeptidePair Pair;
if (Aligner != null)
{
Pair = Aligner.GetPeptPair(this, MatchNumber, RefMatchNumber);
Match = Pair.LeftMatch;
Refs = Pair.RightMatch;
}
else
{
Match = Matches[MatchNumber];
Refs = null;
Pair = null;
}
string Out =
((ReportString[0] != '1')?"":String.Format("{0:20} \t", (Sequence ?? "NOSEQUENCE"))) +
((ReportString[1] != '1')?"":String.Format("{0:f4}\t", MascotRT)) +
((ReportString[2] != '1')?"":String.Format("{0:f4}\t", (Match != null)?Match.ApexRT:0.0)) +
((ReportString[3] != '1')?"":String.Format("{0}\t", MascotScan)) +
((ReportString[4] != '1')?"":String.Format("{0:F6}\t", (Match != null)?Match.RTDisp:0.0)) +
((ReportString[5] != '1')?"":String.Format("{0}\t", (Pair != null)?Pair.Shift:0.0)) +
((ReportString[6] != '1')?"":String.Format("{0}\t", (Pair != null)?Pair.MaxConv:0.0)) +
((ReportString[7] != '1')?"":String.Format("{0}\t", (Match != null && Refs != null)?Match.RTDisp / Refs.RTDisp:0.0)) +
((ReportString[8] != '1')?"":String.Format("{0:f4}\t", (Pair != null)?Pair.ESIFactor:0.0)) +
((ReportString[9] != '1')?"":String.Format("{0:f2}\t", (Match != null)?Match.Score:0.0)) +
((ReportString[10] != '1')?"":String.Format("{0}\t", (Refs != null)?Refs.Score:0.0)) +
((ReportString[11] != '1')?"":String.Format("{0}\t", (Match != null)?Math.Log10(Match.Score):0.0)) +
((ReportString[12] != '1')?"":String.Format("{0}\t", (Refs != null)?Math.Log10(Refs.Score):0.0)) +
((ReportString[13] != '1')?"":String.Format("{0:f2}\t", (Match != null)?Match.ApexScore:0.0)) +
((ReportString[14] != '1')?"":String.Format("{0:f5}\t", MascotMZ)) +
((ReportString[15] != '1')?"":String.Format("{0:f5}\t", (Match != null)?Match.ApexMZ:0.0)) +
((ReportString[16] != '1')?"":String.Format("{0}\t", Charge)) +
((ReportString[17] != '1')?"":String.Format("{0}\t", PI)) +
((ReportString[18] != '1')?"":String.Format("{0}\t", Sequence == null?"NOSEQUENCE":Fragmentation.Peptide.CalcElemComp(Sequence))) +
((ReportString[19] != '1')?"":String.Format("{0}\t", Match == null || Match.MSMatches == null?0:Match.MSMatches.Count - 2)) +
((ReportString[20] != '1')?"":String.Format("{0}\t", (IPI ?? "NOPROTEIN"))) +
((ReportString[21] != '1')?"":String.Format("{0}\t", (PartOfProtein != null ? PartOfProtein.Desc : "NOPROTEIN"))) +
((ReportString[22] != '1')?"":(Utils.IPIListtoString(IPIs)) + "\t") +
((ReportString[23] != '1')?"":String.Format("{0:f2}\t", MascotScore)) +
((ReportString[24] != '1')?"":String.Format("{0:f5}\t", ModMass)) +
((ReportString[25] != '1')?"":String.Format("{0:f5}\t", (Match != null)?Match.IsotopeRatio:0.0)) +
((ReportString[26] != '1')?"":String.Format("{0:f5}\t", TheorIsotopeRatio)) +
((ReportString[27] != '1')?"":String.Format("{0}\t", ModDesk)) +
((ReportString[28] != '1')?"":String.Format("{0}\t", Case)) +
((ReportString[29] != '1')?"":String.Format("{0}", comment));
// Out = String.Format("{0}\t{1}\t"+Out,RTNumber,MascotScan);
return(Out);
}
public void DistanceEst(object IndexObj)
{
int Index = (IndexObj as IntArg).Arg;
int UpperIndex = Math.Min(Index + 1000, Aligners.Count);
for (int i = Index; i < UpperIndex; i++)
{
//для каждого спектра - проходим вних и вверх считая спектры не на месте
//на полную длинну файла???
int Count = 0;
double MinRT = Aligners[i].Best.RT - RTMin * 2.0;
double MaxRT = Aligners[i].Best.RT + RTMin * 2.0;
for (int k = i - 1; k >= 0; k--)
{
if (Aligners[k].Best.RT < MinRT)
{
break;
}
for (int l = 0; l < FileCount; l++)
{
if (Aligners[i].Indexes[l] != -1 &&
Aligners[k].Indexes[l] != -1 &&
Aligners[i].Indexes[l] < Aligners[k].Indexes[l])
{
Count--;
}
}
}
for (int k = i + 1; k < Aligners.Count; k++)
{
if (Aligners[k].Best.RT > MaxRT)
{
break;
}
for (int l = 0; l < FileCount; l++)
{
if (Aligners[i].Indexes[l] != -1 &&
Aligners[k].Indexes[l] != -1 &&
Aligners[i].Indexes[l] > Aligners[k].Indexes[l])
{
Count++;
}
}
}
lock (Als){
Aligner Al = Aligners[i];
Al.Equalizer = Count;
Aligners[i] = Al;
}
}
lock (ForCountLock){
ExecCount++;
}
}
public void TestMethod1()
{
Bitmap bmp1 = (Bitmap)Bitmap.FromFile("2.jpg");
Bitmap bmp2 = (Bitmap)Bitmap.FromFile("6.jpg");
Face.Aligner aligner = new Aligner("models\\pd_2_00_pts5.dat");
Face.Detector detector = new Detector("models\\fd_2_00.dat");
Face.Recognizer recognizer = new Recognizer("models\\fr_2_10.dat");
Face.Assessor assessor = new Assessor();
Stopwatch sw = new Stopwatch();
sw.Start();
List <Rectangle> faces1 = detector.Detect(bmp1);
List <Rectangle> faces2 = detector.Detect(bmp2);
sw.Stop();
long detect = sw.ElapsedMilliseconds;
sw.Restart();
List <PointF> pt1 = aligner.Align(bmp1, faces1[0]);
List <PointF> pt2 = aligner.Align(bmp2, faces2[0]);
sw.Stop();
long align = sw.ElapsedMilliseconds;
sw.Restart();
double s = recognizer.Verify(bmp1, pt1, bmp2, pt2);
sw.Stop();
long recognize = sw.ElapsedMilliseconds;
for (int i = 0; i < faces1.Count; i++)
{
Console.WriteLine(faces1[i].X + "\t" + faces1[i].Y + "\t" + faces1[i].Width + "\t" + faces1[i].Height);
}
sw.Restart();
double score = assessor.Evaluate(bmp2, faces2[0], pt2);
sw.Stop();
long assert = sw.ElapsedMilliseconds;
Console.WriteLine(s);
Console.WriteLine(score);
Console.WriteLine("detect:" + detect);
Console.WriteLine("align:" + align);
Console.WriteLine("recognize:" + recognize);
Console.WriteLine("assert:" + assert);
}
private void globalAlignmentButton_Click(object sender, EventArgs e)
{
try
{
Aligner aligner = new Aligner();
aligner.Input = inputRichTextBox.Text;
aligner.Parameters = parametersRichTextBox.Text;
at = aligner.getGlobalAlignmentTable();
generateAndDisplayAlignments();
}
catch (Exception ex) { MessageBox.Show("Invalid parameter or input data:\r\n" + ex.Message); }
}
public void TestExpand()
{
var options = new AlignerOptions {
AlignX = Alignment.Start,
AlignY = Alignment.Center,
Dimension = Dimension.X,
PointOrder = PointOrder.XY,
};
var worker = SceneWorkerWithTestData2(3, options);
options.Distance = worker.Layout.Distance;
var origins = new IVisual [] { worker.Scene.Focused };
var aligner = new Aligner <IVisual, IVisualEdge> (worker.Scene, worker.Layout);
var deep = false;
var graphView = worker.Scene.Graph as SubGraph <IVisual, IVisualEdge>;
var affected = new SubGraphWorker <IVisual, IVisualEdge>
(graphView).Expand(origins, deep);
var walk = graphView.Walk();
origins.ForEach(origin => {
var route = (deep ? walk.DeepWalk(origin, 1) : walk.ExpandWalk(origin, 1))
.Where(l => !(l.Node is IVisualEdge)).ToArray();
var bounds = new Rectangle(aligner.Locator.GetLocation(origin), aligner.Locator.GetSize(origin));
options.Collisions = Collisions.None;
var cols = aligner.MeasureWalk(route, ref bounds, options);
var removeCol = cols.Dequeue();
if (options.Dimension == Dimension.X)
{
var adjust = options.AlignY.Delta(bounds.Height, removeCol.Item2.Height);
bounds.Location = new Point(bounds.X + removeCol.Item2.Width + options.Distance.Width, bounds.Y - adjust);
}
else
{
var adjust = options.AlignX.Delta(bounds.Width, removeCol.Item2.Width);
bounds.Location = new Point(bounds.X + adjust, bounds.Y + removeCol.Item2.Height + options.Distance.Height);
}
options.Collisions = Collisions.NextFree | Collisions.PerColumn | Collisions.Toggle;
aligner.LocateColumns(cols, bounds, options);
});
aligner.Commit();
worker.Modeller.Perform();
worker.Modeller.Finish();
ReportPainter.PushPaint(ctx => worker.Painter.Paint(ctx));
WritePainter();
}
public void Test1()
{
// Batch.exe --highlight-spaces 01.in ex01.out 17
string[] files = new string[] { "01.in" };
IReader reader = new MultifileReader(files);
Aligner aligner = new Aligner(reader, "ex01_actual.out", 17, true);
aligner.Process();
Assert.AreEqual(ReadFile("ex01.out"), ReadFile("ex01_actual.out"));
}
private void lcsButton_Click(object sender, EventArgs e)
{
try
{
Aligner aligner = new Aligner();
aligner.Input = this.inputRichTextBox.Text;
at = aligner.getLcsTable();
selectedPath = 0;
generateAndDisplayAlignments();
}
catch (Exception ex) { MessageBox.Show("Invalid parameter or input data:\r\n" + ex.Message); }
}
/*
* (non-Javadoc)
*
* @see edu.cmu.sphinx.decoder.ResultListener#newResult(edu.cmu.sphinx.result.Result)
*/
public override void NewResult(Result result)
{
String @ref = result.ReferenceText;
if (result.IsFinal() && @ref != null)
{
String hyp = result.GetBestResultNoFiller();
Aligner.Align(@ref, hyp);
ShowFullPath(result);
ShowDetails(result.ToString());
}
}
public static SyntaxNode AlignIndents(this SyntaxNode root, string singleIndent, Action <int, string> onLineVisualized = null)
{
if (Runtime.Settings.AlignIndents)
{
try
{
// todo add parameter and read value her from caller
root = new Aligner(singleIndent, onLineVisualized).AlignIndents(root);
}
catch { }
}
return(root);
}
public string CalculateLocalCharacteristicsSimilarityMatrix(
int taskId,
Aligner aligner,
DistanceCalculator distanceCalculator,
Aggregator aggregator)
{
var data = TaskManager.Instance.GetTaskData(taskId);
var characteristicsObject = JsonConvert.DeserializeObject <Dictionary <string, dynamic> >(data);
var characteristics = characteristicsObject["characteristics"];
LocalCharacteristicsData[] chars = characteristics.ToObject <LocalCharacteristicsData[]>();
var series = new double[chars.Length][];
for (int i = 0; i < chars.Length; i++)
{
series[i] = chars[i].FragmentsData.Select(fd => fd.Characteristics[0]).ToArray();
}
var alignersFactory = new AlignersFactory();
var calculatorsFactory = new DistanceCalculatorsFactory();
var aggregatorsFactory = new AggregatorsFactory();
var comparer = new OneDimensionalTimeSeriesComparer(
alignersFactory.GetAligner(aligner),
calculatorsFactory.GetDistanceCalculator(distanceCalculator),
aggregatorsFactory.GetAggregator(aggregator));
var result = new double[series.Length, series.Length];
for (int i = 0; i < series.Length - 1; i++)
{
for (int j = i + 1; j < series.Length; j++)
{
result[i, j] = comparer.GetDistance(series[i], series[j]);
result[j, i] = comparer.GetDistance(series[i], series[j]);
}
}
var response = new Dictionary <string, object>
{
{ "aligner", aligner },
{ "distanceCalculator", distanceCalculator },
{ "aggregator", aggregator },
{ "result", result }
};
return(JsonConvert.SerializeObject(response));
}
/// <inheritdoc/>
public IEnumerable <Segment> Render(RenderContext context, int maxWidth)
{
var alignment = Alignment ?? Justify.Left;
var rootStyle = RootStyle ?? Style.Plain;
var separatorStyle = SeparatorStyle ?? Style.Plain;
var stemStyle = StemStyle ?? Style.Plain;
var leafStyle = LeafStyle ?? Style.Plain;
var fitted = Fit(context, maxWidth);
var parts = new List <Segment>();
foreach (var(_, first, last, item) in fitted.Enumerate())
{
// Leaf?
if (last)
{
parts.Add(new Segment(item, leafStyle));
}
else
{
if (first && _rooted)
{
// Root
parts.Add(new Segment(item, rootStyle));
if (_windows)
{
// Windows root has a slash
parts.Add(new Segment("/", separatorStyle));
}
}
else
{
// Normal path segment
parts.Add(new Segment(item, stemStyle));
parts.Add(new Segment("/", separatorStyle));
}
}
}
// Align the result
Aligner.Align(parts, Alignment, maxWidth);
// Insert a line break
parts.Add(Segment.LineBreak);
return(parts);
}
public Attendance()
{
InitializeComponent();
this.BindWindowsUIButtonEvents();
this.DisposeNeeded = true;
this.RefreshNeeded = true;
// initialize
this.detector = new Detector("data\\models\\Detector2.0.ats");
this.aligner = new Aligner("data\\models\\PointDetector2.0.pts5.ats");
this.recognizer = new Recognizer("data\\models\\Recognizer2.0.ats");
}
/*
* (non-Javadoc)
*
* @see edu.cmu.sphinx.util.props.Configurable#newProperties(edu.cmu.sphinx.util.props.PropertySheet)
*/
public override void NewProperties(PropertySheet ps)
{
base.NewProperties(ps);
InitRecognizer((Recognizer)ps.GetComponent(PropRecognizer));
_showSummary = ps.GetBoolean(PropShowSummary);
_showDetails = ps.GetBoolean(PropShowDetails);
_showResults = ps.GetBoolean(PropShowResults);
_showAlignedResults = ps.GetBoolean(PropShowAlignedResults);
_showRaw = ps.GetBoolean(PropShowRawResults);
Aligner.SetShowResults(_showResults);
Aligner.SetShowAlignedResults(_showAlignedResults);
}
protected void Align(Aligner aligner)
{
Vector2 pos = aligner.OriginalPos;
if (Mode == PositionMode.Percent)
{
pos = PercentToPixels(pos);
}
Rectangle bounds = aligner.Child.LocalBounds;
switch (aligner.XAlignment)
{
case Alignment.Center:
pos.X = 0.5f * LocalBounds.Width - bounds.Width * 0.5f;
break;
case Alignment.Left:
pos.X = 0;
break;
case Alignment.Right:
pos.X = LocalBounds.Width - bounds.Width;
break;
default:
break;
}
switch (aligner.YAlignment)
{
case Alignment.Center:
pos.Y = 0.5f * LocalBounds.Height - bounds.Height * 0.5f;
break;
case Alignment.Bottom:
pos.Y = LocalBounds.Height - bounds.Height;
break;
case Alignment.Top:
pos.Y = 0;
break;
default:
break;
}
aligner.Child.LocalBounds = new Rectangle((int)pos.X, (int)pos.Y, bounds.Width, bounds.Height);
}
protected virtual void AfterEdit()
{
var scene = Scene;
if (focusAfterEdit)
{
scene.Selected.Clear();
scene.SetFocused(Current);
}
if (Current != null)
{
var aligner = new Aligner <IVisual, IVisualEdge>(scene, this.Layout);
aligner.Justify(new IVisual[] { Current });
aligner.Commit();
}
}
public void Call(IGraphSceneDisplay <IVisual, IVisualEdge> display, Action <Aligner <IVisual, IVisualEdge>, IEnumerable <IVisual> > call, IEnumerable <IVisual> items)
{
if (display == null)
{
return;
}
var aligner = new Aligner <IVisual, IVisualEdge> (display.Data, display.Layout);
call(aligner, items);
aligner.Locator.Commit(aligner.GraphScene.Requests);
StoreUndo(display, aligner, items);
display.Perform();
}
