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Coverage Report

  1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.renderer

File ContactMapRenderer.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
21% of files have more coverage

Code metrics

32
66
8
2
293
177
28
0.42
8.25
4
3.5

Classes

Class Line # Actions
ContactMapRenderer 40 59 27
0.693877669.4%
ContactMapRenderer.Shading 48 7 1
1.0100%
 

Contributing tests

This file is covered by 9 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.renderer;
22   
23    import java.awt.Color;
24    import java.awt.Graphics;
25   
26    import jalview.api.AlignViewportI;
27    import jalview.datamodel.AlignmentAnnotation;
28    import jalview.datamodel.Annotation;
29    import jalview.datamodel.ColumnSelection;
30    import jalview.datamodel.ContactListI;
31    import jalview.datamodel.ContactMatrixI;
32    import jalview.datamodel.ContactRange;
33    import jalview.datamodel.HiddenColumns;
34    import jalview.renderer.api.AnnotationRowRendererI;
35   
36    /**
37    * @author jprocter
38    *
39    */
 
40    public abstract class ContactMapRenderer implements AnnotationRowRendererI
41    {
42    /**
43    * bean holding colours for shading
44    *
45    * @author jprocter
46    *
47    */
 
48    public class Shading
49    {
50    /**
51    * shown when no data available from map
52    */
53    Color no_data;
54   
55    /**
56    * shown for region not currently visible - should normally not see this
57    */
58    Color hidden;
59   
60    /**
61    * linear shading scheme min/max
62    */
63    Color maxColor, minColor;
64   
65    /**
66    * linear shading scheme min/max for selected region
67    */
68    Color selMinColor, selMaxColor;
69   
70    /**
71    *
72    * @param no_data
73    * - colour when no data available
74    * @param hidden
75    * - colour if this row is hidden
76    * @param maxColor
77    * - colour for maximum value of contact
78    * @param minColor
79    * - colour for minimum value of contact
80    * @param selMinColor
81    * - min colour if the contact has been selected
82    * @param selMaxColor
83    * - max colour if contact is selected
84    */
 
85  139 toggle public Shading(Color no_data, Color hidden, Color maxColor,
86    Color minColor, Color selMinColor, Color selMaxColor)
87    {
88  139 super();
89  139 this.no_data = no_data;
90  139 this.hidden = hidden;
91  139 this.maxColor = maxColor;
92  139 this.minColor = minColor;
93  139 this.selMinColor = selMinColor;
94  139 this.selMaxColor = selMaxColor;
95    }
96   
97    }
98   
99    final Shading shade;
100   
101    /**
102    * build an EBI-AlphaFold style renderer of PAE matrices
103    *
104    * @return
105    */
 
106  139 toggle public static ContactMapRenderer newPAERenderer()
107    {
108  139 return new ContactMapRenderer()
109    {
 
110  139 toggle @Override
111    public Shading getShade()
112    {
113  139 return new Shading(Color.pink, Color.red,
114   
115    new Color(247, 252, 245), new Color(0, 68, 28),
116    new Color(28, 0, 68), new Color(245, 247, 252));
117    }
118    };
119    }
120   
121    /**
122    *
123    * @return instance of Shading used to initialise the renderer
124    */
125    public abstract Shading getShade();
126   
 
127  139 toggle public ContactMapRenderer()
128    {
129  139 this.shade = getShade();
130    }
131   
 
132  139 toggle @Override
133    public void renderRow(Graphics g, int charWidth, int charHeight,
134    boolean hasHiddenColumns, AlignViewportI viewport,
135    HiddenColumns hiddenColumns, ColumnSelection columnSelection,
136    AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
137    int eRes, float min, float max, int y)
138    {
139  139 if (sRes > aa_annotations.length)
140    {
141  0 return;
142    }
143  139 eRes = Math.min(eRes, aa_annotations.length);
144   
145  139 int x = 0, topY = y;
146   
147    // uncomment below to render whole area of matrix as pink
148    // g.setColor(shade.no_data);
149    // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth,
150    // _aa.graphHeight);
151   
152  139 boolean showGroups = _aa.isShowGroupsForContactMatrix();
153  139 int column;
154  139 int aaMax = aa_annotations.length - 1;
155  139 ContactMatrixI cm = viewport.getContactMatrix(_aa);
156  139 if (cm == null)
157    {
158  0 return;
159    }
160  8223 while (x < eRes - sRes)
161    {
162  8084 column = sRes + x;
163  8084 if (hasHiddenColumns)
164    {
165  0 column = hiddenColumns.visibleToAbsoluteColumn(column);
166    }
167    // TODO: highlight columns selected
168  8084 boolean colsel = false;
169  8084 if (columnSelection != null)
170    {
171  8084 colsel = columnSelection.contains(column);
172    }
173   
174  8084 if (column > aaMax)
175    {
176  0 break;
177    }
178   
179  8084 if (aa_annotations[column] == null)
180    {
181  4532 x++;
182  4532 continue;
183    }
184  3552 ContactListI contacts = viewport.getContactList(_aa, column);
185  3552 if (contacts == null)
186    {
187  0 x++;
188  0 continue;
189    }
190    // ContactListI from viewport can map column -> group
191  3552 Color gpcol = (cm == null) ? Color.white
192    : contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
193    // feature still in development - highlight or omit regions hidden in
194    // the alignment - currently marks them as red rows
195  3552 boolean maskHiddenCols = false;
196    // TODO: optionally pass visible column mask to the ContactGeometry object
197    // so it maps
198    // only visible contacts to geometry
199    // Bean holding mapping from contact list to pixels
200    // TODO: allow bracketing/limiting of range on contacts to render (like
201    // visible column mask but more flexible?)
202   
203    // COntactListI provides mapping for column -> cm-groupmapping
204  3552 final ContactGeometry cgeom = new ContactGeometry(contacts,
205    _aa.graphHeight);
206   
207  3552 for (int ht = 0, botY = topY
208  145628 - _aa.height; ht < _aa.graphHeight; ht += cgeom.pixels_step)
209    {
210  142079 ContactGeometry.contactInterval ci = cgeom.mapFor(ht);
211    // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
212    // cend = (int) Math.min(contact_height,
213    // Math.ceil(cstart + contacts_per_pixel * pixels_step));
214   
215  142069 Color col;
216  142071 boolean rowsel = false;
217  142077 boolean containsHidden = false;
218  142078 if (columnSelection != null)
219    {
220  142080 rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
221    maskHiddenCols);
222    }
223    // TODO: show selected region
224  142080 if (colsel || rowsel)
225    {
226   
227  0 col = getSelectedColorForRange(min, max, contacts, ci.cStart,
228    ci.cEnd);
229  0 if (colsel && rowsel)
230    {
231  0 col = new Color(col.getBlue(), col.getGreen(), col.getRed());
232    }
233    else
234    {
235  0 col = new Color(col.getBlue(), col.getBlue(), col.getBlue());
236    }
237    }
238    else
239    {
240  142080 col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd);
241    }
242  142079 if (containsHidden)
243    {
244  0 col = shade.hidden;
245    }
246  142079 if (showGroups && gpcol != null && gpcol != Color.white)
247    {
248    // todo - could overlay group as a transparent rectangle ?
249  0 col = new Color((int) ((col.getRed() + gpcol.getRed()) / 2f),
250    (int) ((col.getGreen() + gpcol.getGreen()) / 2f),
251    (int) ((col.getBlue() + gpcol.getBlue()) / 2f));
252    }
253  142080 g.setColor(col);
254  142080 if (cgeom.pixels_step > 1)
255    {
256  0 g.fillRect(x * charWidth, botY + ht, charWidth,
257    cgeom.pixels_step);
258    }
259    else
260    {
261  142078 g.drawLine(x * charWidth, botY + ht, (x + 1) * charWidth,
262    botY + ht);
263    }
264    }
265  3552 x++;
266    }
267   
268    }
269   
 
270  142076 toggle Color shadeFor(float min, float max, float value)
271    {
272  142076 return jalview.util.ColorUtils.getGraduatedColour(value, 0,
273    shade.minColor, max, shade.maxColor);
274    }
275   
 
276  142079 toggle public Color getColorForRange(float min, float max, ContactListI cl,
277    int i, int j)
278    {
279  142079 ContactRange cr = cl.getRangeFor(i, j);
280    // average for moment - probably more interested in maxIntProj though
281  142076 return shadeFor(min, max, (float) cr.getMean());
282    }
283   
 
284  0 toggle public Color getSelectedColorForRange(float min, float max,
285    ContactListI cl, int i, int j)
286    {
287  0 ContactRange cr = cl.getRangeFor(i, j);
288    // average for moment - probably more interested in maxIntProj though
289  0 return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMin(),
290    0, shade.selMinColor, max, shade.selMaxColor);
291    }
292   
293    }
  • Report generated by OpenClover v 4.4.1 on Fri Dec 6 2024 13:54:25 GMT using coverage data from Fri Dec 6 2024 13:54:13 GMT.
  • OpenClover is free and open-source software.