public void TestPrefixAndSuffixMatches()
{
string[] peptides =
{
"LATQSNEITIPVTFESRAqLGGPEAAK",
"LATqSNEITIPVTFESRAQLGGPEAAK",
"LATQSnEITIPVTFESRAQLGGPEAAK",
"LATQSnEITIPVTFESRAQLGGPEAAKSDETAAK",
"LATQSNEITIPVTFESRAQLGGPEAAK",
"LATQSNEITIPVTFESRAQLGGPEAAKSDETAAK",
"LATQSNEITIPVTFESRAqLGGPEAAKSDETAAK",
};
var uniquePrefixGenerator = new UniquePrefixGenerator(peptides.Select(
sequence => new Tuple <string, bool>(sequence, true)), 3);
Dictionary <string, string> peptideAbbreviations = new Dictionary <string, string>();
foreach (string peptide in peptides)
{
string abbreviation = uniquePrefixGenerator.GetUniquePrefix(peptide, true);
Assert.IsTrue(abbreviation.Length <= peptide.Length);
peptideAbbreviations.Add(peptide, abbreviation);
}
CollectionAssert.AllItemsAreUnique(peptideAbbreviations.Values);
}
private void UpdateGraph()
{
if (!IsHandleCreated)
{
return;
}
zedGraphControl.GraphPane.GraphObjList.Clear();
zedGraphControl.GraphPane.CurveList.Clear();
_barGraph = null;
_rows = null;
var points = new PointPairList();
var groupComparisonModel = FoldChangeBindingSource.GroupComparisonModel;
var groupComparisonDef = groupComparisonModel.GroupComparisonDef;
var document = groupComparisonModel.Document;
var sequences = new List <Tuple <string, bool> >();
foreach (var nodePep in document.Molecules)
{
sequences.Add(new Tuple <string, bool>(nodePep.ModifiedTarget.DisplayName, nodePep.IsProteomic));
}
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
var textLabels = new List <string>();
var rows = _bindingListSource.OfType <RowItem>()
.Select(rowItem => rowItem.Value)
.OfType <FoldChangeBindingSource.FoldChangeRow>()
.ToArray();
bool showLabelType = rows.Select(row => row.IsotopeLabelType).Distinct().Count() > 1;
bool showMsLevel = rows.Select(row => row.MsLevel).Distinct().Count() > 1;
bool showGroup = rows.Select(row => row.Group).Distinct().Count() > 1;
foreach (var row in rows)
{
var foldChangeResult = row.FoldChangeResult;
double error = Math.Log(foldChangeResult.MaxFoldChange / foldChangeResult.FoldChange, 2.0);
var point = MeanErrorBarItem.MakePointPair(points.Count, foldChangeResult.Log2FoldChange, error);
points.Add(point);
string label;
if (null != row.Peptide)
{
try
{
label = uniquePrefixGenerator.GetUniquePrefix(
row.Peptide.GetDocNode().ModifiedTarget.DisplayName, row.Peptide.GetDocNode().IsProteomic);
}
catch
{
// Peptide must have been deleted.
label = row.Peptide.GetDocNode().ModifiedTarget.DisplayName;
}
}
else
{
label = ProteinMetadataManager.ProteinModalDisplayText(row.Protein.DocNode);
}
if (showMsLevel && row.MsLevel.HasValue)
{
label += @" MS" + row.MsLevel; //;
}
if (showLabelType && row.IsotopeLabelType != null)
{
label += @" (" + row.IsotopeLabelType.Title + @")";
}
if (showGroup && !Equals(row.Group, default(GroupIdentifier)))
{
label += @" " + row.Group;
}
textLabels.Add(label);
if (IsSelected(row))
{
double y, height;
if (foldChangeResult.Log2FoldChange >= 0)
{
y = foldChangeResult.Log2FoldChange + error;
height = y;
}
else
{
y = 0;
height = error - foldChangeResult.Log2FoldChange;
}
zedGraphControl.GraphPane.GraphObjList.Add(new BoxObj(point.X + .5, y, .99, height)
{
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true
});
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = groupComparisonDef.PerProtein ? GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Protein : GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Peptide;
zedGraphControl.GraphPane.YAxis.Title.Text = GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Log_2_Fold_Change;
var barGraph = new MeanErrorBarItem(null, points, Color.Black, Color.Blue);
zedGraphControl.GraphPane.CurveList.Add(barGraph);
zedGraphControl.GraphPane.XAxis.Scale.MinAuto = zedGraphControl.GraphPane.XAxis.Scale.MaxAuto =
zedGraphControl.GraphPane.YAxis.Scale.MinAuto = zedGraphControl.GraphPane.YAxis.Scale.MaxAuto = true;
zedGraphControl.GraphPane.XAxis.Type = AxisType.Text;
zedGraphControl.GraphPane.XAxis.Scale.TextLabels = textLabels.ToArray();
_axisLabelScaler.ScaleAxisLabels();
zedGraphControl.GraphPane.AxisChange();
zedGraphControl.Invalidate();
_barGraph = barGraph;
_rows = rows;
}
public void TestUniquePrefix()
{
var testSequences = new[, ]
{
// Original name on left, expected result on right.
{ null, null },
{ "", "" },
{ "A", "A" },
{ "A", "A" }, // duplicate name (on purpose)
{ "AB", "AB" },
{ "ABC", "ABC" },
{ "ABCD", "ABCD" },
{ "ABCDE", "ABCDE" },
{ "ABCDEF", "ABCDEF" },
{ "ABCDEFG", "ABCDEFG" },
{ "ABCDEFG", "ABCDEFG" }, // duplicate name (on purpose)
{ "ABCDEFGH", "ABC…FGH" },
{ "ABCDEFGHI", "ABC…GHI" },
{ "ABCE", "ABCE" },
{ "ABDEFGHI", "ABD…" },
{ "ABEFGHI", "ABEFGHI" },
{ "ABEFGHIJ", "ABE…HIJ" },
{ "ABEFHI", "ABEFHI" },
{ "ABFFFGHI", "ABF(5)" },
{ "ABFFFFGHI", "ABF(6)" },
{ "ABFFFFAFGHI", "ABF…FA…" },
{ "ABFFFAFFGHI", "ABF…A…" },
{ "ABGAABAABAGHI", "ABG…B…B…" },
{ "ABGAAbAABAGHI", "ABG…b…B…" },
{ "ABGAABAAbAGHI", "ABG…B…b…" },
{ "ABGAAB[80]AAB[99]AGHI", "ABG…b…b…" }
};
var testCustomIons = new[, ]
{
// Original name on left, expected result on right.
{ "C32:0", "C32:0" },
{ "C32:1", "C32:1" },
{ "C32:2", "C32:2" },
{ "C32:2", "C32:2" }, // Duplicated on purpose
{ "C30:0", "C30:0" },
{ "C[30]:0", "C[30]:0" },
{ "C[400]:0", "C[4…" },
{ "C12:0 fish breath", "C12…" },
{ "C15:0 fish breath", "C15(14)" },
{ "C15:0 doggy breath", "C15(15)" },
{ "C16:0 fishy breath", "C16…f…" },
{ "C16:0 doggy breath", "C16…d…" },
{ "C14", "C14" },
{ "C14:1", "C14:1" },
{ "C14:1-OH", "C14:1…" },
{ "C14:2", "C14:2" },
{ "C14:2-OH", "C14:2…" }
};
for (var loop = 2; loop > 0; loop--)
{
var strings = new List <Tuple <string, bool> >();
var commontext = (loop == 1) ? String.Empty : "Delta Niner Foxtrot "; // non-peptides should strip leading common text
for (int i = 0; i < testSequences.GetLength(0); i++)
{
strings.Add(new Tuple <string, bool>(testSequences[i, 0], true));
}
for (int i = 0; i < testCustomIons.GetLength(0); i++)
{
strings.Add(new Tuple <string, bool>(commontext + testCustomIons[i, 0], false));
}
var prefixGenerator = new UniquePrefixGenerator(strings, 3);
for (int i = 0; i < testSequences.GetLength(0); i++)
{
var expected = testSequences[i, 1];
var uniquePrefix = prefixGenerator.GetUniquePrefix(testSequences[i, 0], true);
Assert.AreEqual(expected, uniquePrefix);
}
for (int i = 0; i < testCustomIons.GetLength(0); i++)
{
var expected = testCustomIons[i, 1];
var uniquePrefix = prefixGenerator.GetUniquePrefix(commontext + testCustomIons[i, 0], false);
Assert.AreEqual(expected, uniquePrefix);
}
}
}
