OpenMS
Annotation1DPeakItem.h
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1 // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Johannes Veit $
6 // $Authors: Johannes Junker $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
12 
16 
17 #include <QtGui/QColor>
18 #include <QtGui/QFontMetricsF>
19 
20 namespace OpenMS
21 {
22 
26  template <class DataPoint> // e.g. Peak1D
28  public Annotation1DItem
29  {
30 public:
32  Annotation1DPeakItem(const DataPoint& peak_position, const QString& text, const QColor& color) :
33  Annotation1DItem(text), peak_position_(peak_position), position_(peak_position), color_(color)
34  {
35  }
36 
39 
41  ~Annotation1DPeakItem() override = default;
42 
43  // Docu in base class
44  void draw(Plot1DCanvas* const canvas, QPainter& painter, bool flipped = false) override
45  {
46  painter.save();
47 
48  painter.setPen(color_);
49 
50  QPoint position_widget, peak_position_widget;
51 
52  // translate units to pixel coordinates
53  canvas->dataToWidget(canvas->getMapper().map(position_), position_widget, flipped);
54  canvas->dataToWidget(canvas->getMapper().map(peak_position_), peak_position_widget, flipped);
55 
56  // pre-compute bounding box of text_item
57  const QFontMetricsF fm(QApplication::font());
58  const auto prebox = fm.boundingRect(QRectF(position_widget.x(), position_widget.y(), 0, 0), Qt::AlignCenter, getText());
59  // Shift position of the widget/text, so it sits 'on top' of the peak
60  // We can only do that there, since we do not know the state of 'flipped' in general
61  // Compute the delta in data-units, NOT pixels, since the shift (up/down, or even left/right) depends on state of 'flipped' and axis
62  const auto deltaXY_in_units = canvas->widgetToDataDistance(prebox.width(), prebox.height()).abs(); // abs() to make sure y axis is not negative
63  const auto delta_gravity_in_units = canvas->getGravitator().swap().gravitateZero(deltaXY_in_units); // only keep gravity dim
64  // recompute 'position_widget', shifting the text up by 1/2 box
65  canvas->dataToWidget(canvas->getMapper().map(position_) + delta_gravity_in_units / 2, position_widget, flipped);
66  // re-compute bounding box of text_item on with new position!
67  bounding_box_ = fm.boundingRect(QRectF(position_widget.x(), position_widget.y(), 0, 0), Qt::AlignCenter, getText());
68 
69 
70  // draw connection line between anchor point and current position if pixel coordinates differ significantly
71  if ((position_widget - peak_position_widget).manhattanLength() > 2)
72  {
73  QPointF border_point = GUIHelpers::intersectionPoint(bounding_box_, peak_position_widget);
74  if (bounding_box_.center() != border_point)
75  {
76  painter.save();
77  painter.setPen(Qt::DashLine);
78  painter.drawLine(peak_position_widget, border_point);
79  painter.restore();
80  }
81  }
82 
83  // some pretty printing
84  QString text = text_;
85  if (!text.contains("<\\")) // don't process HTML strings again
86  {
87  // extract ion index
88  {
89  QRegularExpression reg_exp(R"(([abcdwxyz])(\d+))");
90  QRegularExpressionMatch match = reg_exp.match(text);
91  if (text.indexOf(reg_exp) == 0) // only process if at the beginning of the string
92  {
93  text.replace(reg_exp, "\\1<sub>\\2</sub>");
94  }
95  else // protein-protein XL specific ion names
96  { // e.g. "[alpha|ci$y1]"
97  QRegularExpression reg_exp_xlms(R"((ci|xi)[$][abcxyz](\d+))");
98  auto match_pos = text.indexOf(reg_exp_xlms);
99  if ((match_pos == 6) || (match_pos == 7))
100  {
101  // set the match_pos to the position of the ion index
102  match_pos += 3; // skip "ci$" or "xi$"
103  ++match_pos; // skip the ion type (=captured(1))
104  QString charge_str = match.captured(2);
105  // put sub html tag around number
106  text = text.left(match_pos) + QString("<sub>") + charge_str + QString("</sub>") + text.right(text.size() - match_pos - charge_str.size());
107  }
108  }
109  }
110 
111  // common losses
112  text.replace("H2O1", "H<sub>2</sub>O"); // mind the order with H2O substitution
113  text.replace("H2O", "H<sub>2</sub>O");
114  text.replace("NH3", "NH<sub>3</sub>");
115  text.replace("H3N1", "NH<sub>3</sub>");
116  text.replace("C1H4O1S1", "H<sub>4</sub>COS"); // methionine sulfoxide loss
117 
118  // nucleotide XL related losses
119  text.replace("H3PO4", "H<sub>3</sub>PO<sub>4</sub>");
120  text.replace("HPO3", "HPO<sub>3</sub>");
121  text.replace("C3O", "C<sub>3</sub>O");
122 
123  // charge format: +z
124  QRegularExpression charge_rx(R"([\+|\-](\d+)$)");
125  int match_pos = text.indexOf(charge_rx);
126  if (match_pos > 0)
127  {
128  text = text.left(match_pos) + QString("<sup>") + text[match_pos] // + or -
129  + charge_rx.match(text).captured(1) + QString("</sup>"); // charge
130  }
131 
132  // charge format: z+
133  charge_rx = QRegularExpression(R"((\d+)[\+|\-]$)");
134  match_pos = text.indexOf(charge_rx);
135  if (match_pos > 0)
136  {
137  auto charge_match = charge_rx.match(text).captured(1);
138  text = text.left(match_pos) + QString("<sup>") + charge_match // charge
139  + text[match_pos + charge_match.size()] + QString("</sup>"); // + or -
140  }
141 
142  text.replace(QRegularExpression(R"(\+\+$)"), "<sup>2+</sup>");
143  text.replace(QRegularExpression(R"(\+$)"), "");
144  text.replace(QRegularExpression(R"(\-\-$)"), "<sup>2-</sup>");
145  text.replace(QRegularExpression(R"(\-$)"), "");
146  }
147 
148  text = "<font color=\"" + color_.name() + "\">" + text + "</font>";
149 
150  // draw html text
151  {
152  QTextDocument td;
153  td.setHtml(text);
154  painter.save();
155  double w = td.size().width();
156  double h = td.size().height();
157  painter.translate(position_widget.x() - w / 2, position_widget.y() - h / 2);
158  td.drawContents(&painter);
159  painter.restore();
160  }
161 
162  if (selected_)
163  {
164  drawBoundingBox_(painter);
165  }
166 
167  painter.restore();
168  }
169 
170  // Docu in base class
171  void move(const PointXYType delta, const Gravitator& /*gr*/, const DimMapper<2>& dim_mapper) override
172  {
173  auto pos_xy = dim_mapper.map(position_);
174  pos_xy += delta;
175  dim_mapper.fromXY(pos_xy, position_);
176  }
177 
179  void setPosition(const DataPoint& position)
180  {
181  position_ = position;
182  }
183 
185  const DataPoint& getPosition() const
186  {
187  return position_;
188  }
189 
191  const DataPoint& getPeakPosition() const
192  {
193  return peak_position_;
194  }
195 
196  // Docu in base class
197  void ensureWithinDataRange(Plot1DCanvas* const canvas, const int layer_index) override
198  {
199  canvas->pushIntoDataRange(position_, layer_index);
200  }
201 
203  void setColor(const QColor& color)
204  {
205  color_ = color;
206  }
207 
209  const QColor& getColor() const
210  {
211  return color_;
212  }
213 
216  {
217  // add new fragment annotation
218  QString peak_anno = this->getText().trimmed();
219 
220  // check for newlines in the label and only continue with the first line for charge determination
221  peak_anno.remove('\r');
222  QStringList lines = peak_anno.split('\n', Qt::SkipEmptyParts);
223  if (lines.size() > 1)
224  {
225  peak_anno = lines[0];
226  }
227 
228  // regular expression for a charge at the end of the annotation
229  QRegularExpression reg_exp(R"(([\+|\-]\d+)$)");
230 
231  // read charge and text from annotation item string
232  // we support two notations for the charge suffix: '+2' or '++'
233  // cut and convert the trailing + or - to a proper charge
234  int match_pos = peak_anno.indexOf(reg_exp);
235  int tmp_charge(0);
236  if (match_pos >= 0)
237  {
238  tmp_charge = reg_exp.match(peak_anno).captured(1).toInt();
239  peak_anno = peak_anno.left(match_pos);
240  }
241  else
242  {
243  // count number of + and - in suffix (e.g., to support "++" as charge 2 annotation)
244  int plus(0), minus(0);
245 
246  for (int p = (int)peak_anno.size() - 1; p >= 0; --p)
247  {
248  if (peak_anno[p] == '+')
249  {
250  ++plus;
251  continue;
252  }
253  else if (peak_anno[p] == '-')
254  {
255  ++minus;
256  continue;
257  }
258  else // not '+' or '-'?
259  {
260  if (plus > 0 && minus == 0) // found pluses?
261  {
262  tmp_charge = plus;
263  peak_anno = peak_anno.left(peak_anno.size() - plus);
264  break;
265  }
266  else if (minus > 0 && plus == 0) // found minuses?
267  {
268  tmp_charge = -minus;
269  peak_anno = peak_anno.left(peak_anno.size() - minus);
270  break;
271  }
272  break;
273  }
274  }
275  }
276 
278  fa.charge = tmp_charge;
279  fa.mz = this->getPeakPosition().getMZ();
280  fa.intensity = this->getPeakPosition().getIntensity();
281  if (lines.size() > 1)
282  {
283  peak_anno.append("\n").append(lines[1]);
284  }
285  fa.annotation = peak_anno;
286 
287  return fa;
288  }
289 
290  // Docu in base class
291  Annotation1DItem* clone() const override
292  {
293  return new Annotation1DPeakItem(*this);
294  }
295 
296  protected:
298  DataPoint peak_position_;
299 
301  DataPoint position_;
302 
304  QColor color_;
305  };
306 } // namespace OpenMS
An abstract class acting as an interface for the different 1D annotation items.
Definition: Annotation1DItem.h:36
QRectF bounding_box_
The current bounding box of this item on the canvas where it has last been drawn.
Definition: Annotation1DItem.h:83
QString text_
The displayed text.
Definition: Annotation1DItem.h:89
void drawBoundingBox_(QPainter &painter)
Draws the bounding_box_.
const QString & getText() const
Returns the text of the item.
bool selected_
Determines whether this item is currently selected on the canvas.
Definition: Annotation1DItem.h:86
A peak annotation item.
Definition: Annotation1DPeakItem.h:29
const QColor & getColor() const
Returns the color of the label.
Definition: Annotation1DPeakItem.h:209
Annotation1DItem * clone() const override
Creates a copy of the item on the heap and returns a pointer.
Definition: Annotation1DPeakItem.h:291
~Annotation1DPeakItem() override=default
Destructor.
const DataPoint & getPosition() const
Returns the position of the label (peak)
Definition: Annotation1DPeakItem.h:185
void draw(Plot1DCanvas *const canvas, QPainter &painter, bool flipped=false) override
Draws the item on painter.
Definition: Annotation1DPeakItem.h:44
const DataPoint & getPeakPosition() const
Returns the position of the annotated peak.
Definition: Annotation1DPeakItem.h:191
QColor color_
The color of the label.
Definition: Annotation1DPeakItem.h:304
Annotation1DPeakItem(const Annotation1DPeakItem &rhs)=default
Copy constructor.
void ensureWithinDataRange(Plot1DCanvas *const canvas, const int layer_index) override
Ensures that the item has coordinates within the visible area of the canvas.
Definition: Annotation1DPeakItem.h:197
PeptideHit::PeakAnnotation toPeakAnnotation() const
Convert the 'text()' to a Peptide::PeakAnnotation.
Definition: Annotation1DPeakItem.h:215
DataPoint peak_position_
The position of the anchor (e.g. the Peak1D)
Definition: Annotation1DPeakItem.h:298
void setColor(const QColor &color)
Set the color of the label.
Definition: Annotation1DPeakItem.h:203
Annotation1DPeakItem(const DataPoint &peak_position, const QString &text, const QColor &color)
Constructor.
Definition: Annotation1DPeakItem.h:32
void setPosition(const DataPoint &position)
Sets the position of the label.
Definition: Annotation1DPeakItem.h:179
void move(const PointXYType delta, const Gravitator &, const DimMapper< 2 > &dim_mapper) override
Moves the item on the drawing canvas; behavior depends on item type and is implemented in the subclas...
Definition: Annotation1DPeakItem.h:171
DataPoint position_
The position of the label (e.g. the Peak1D)
Definition: Annotation1DPeakItem.h:301
DPosition & abs() noexcept
Make all dimension values positive.
Definition: DPosition.h:111
void fromXY(const DRange< N_DIM > &in, RangeManager< Ranges... > &output) const
Definition: DimMapper.h:752
Point map(const T &data) const
convert an OpenMS datatype (such as Feature) to an N_DIM-dimensional point
Definition: DimMapper.h:716
Manipulates X or Y component of points in the X-Y plane, by assuming one axis (either X or Y axis) ha...
Definition: Plot1DCanvas.h:42
QPoint gravitateZero(QPoint p) const
Definition: Plot1DCanvas.h:204
Gravitator swap() const
Swap gravity axis (from X to Y, or vice versa)
Definition: Plot1DCanvas.h:108
Canvas for visualization of one or several spectra.
Definition: Plot1DCanvas.h:295
void dataToWidget(const DPosition< 2 > &peak, QPoint &point, bool flipped=false)
For convenience - calls dataToWidget.
const Gravitator & getGravitator() const
Get gravity manipulation object to apply gravity to points.
Definition: Plot1DCanvas.h:504
void pushIntoDataRange(T &data_point, const int layer_index)
Pushes a data point back into the valid data range of the current layer area. Useful for annotation i...
Definition: Plot1DCanvas.h:434
PointXYType widgetToDataDistance(double x, double y)
compute distance in data coordinates (unit axis as shown) when moving x/y pixel in chart/widget coord...
Definition: Plot1DCanvas.h:412
const DimMapper< 2 > & getMapper() const
Get Mapper to translate between values for axis (X/Y) and units (m/z, RT, intensity,...
const double h
Definition: Constants.h:141
QPointF intersectionPoint(const QRectF &rect, const QPointF &p)
Find the point on a rectangle where a ray/line from a point p to its center would intersect at.
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Contains annotations of a peak.
Definition: PeptideHit.h:76
double intensity
Definition: PeptideHit.h:80
double mz
Definition: PeptideHit.h:79
String annotation
Definition: PeptideHit.h:77
int charge
Definition: PeptideHit.h:78