4 package jalview.renderer;
7 import java.awt.Graphics;
9 import jalview.api.AlignViewportI;
10 import jalview.datamodel.AlignmentAnnotation;
11 import jalview.datamodel.Annotation;
12 import jalview.datamodel.ColumnSelection;
13 import jalview.datamodel.ContactListI;
14 import jalview.datamodel.ContactRange;
15 import jalview.datamodel.HiddenColumns;
16 import jalview.renderer.api.AnnotationRowRendererI;
22 public class ContactMapRenderer implements AnnotationRowRendererI
26 public void renderRow(Graphics g, int charWidth, int charHeight,
27 boolean hasHiddenColumns, AlignViewportI viewport,
28 HiddenColumns hiddenColumns, ColumnSelection columnSelection,
29 AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
30 int eRes, float min, float max, int y)
32 if (sRes > aa_annotations.length)
36 eRes = Math.min(eRes, aa_annotations.length);
40 g.setColor(Color.pink);
42 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
45 int aaMax = aa_annotations.length - 1;
46 while (x < eRes - sRes)
51 column = hiddenColumns.visibleToAbsoluteColumn(column);
53 // TODO: highlight columns selected
54 boolean colsel = false;
55 if (columnSelection != null)
57 colsel = columnSelection.contains(column);
65 if (aa_annotations[column] == null)
70 ContactListI contacts = viewport.getContactList(_aa, column);
75 // Bean holding mapping from contact list to pixels
76 final ContactGeometry cgeom = new ContactGeometry(contacts,
79 for (int ht = y2, eht = y2
80 - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
82 ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
83 y2 - ht + cgeom.pixels_step);
84 // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
85 // cend = (int) Math.min(contact_height,
86 // Math.ceil(cstart + contacts_per_pixel * pixels_step));
88 // TODO show maximum colour for range - sort of done
89 // also need a 'getMaxPosForRange(start,end)' to accurately render
91 boolean rowsel = false;
92 if (columnSelection != null)
94 if (_aa.sequenceRef == null)
96 rowsel = columnSelection.intersects(ci.cStart, ci.cEnd);
100 // TODO check we have correctly mapped cstart to local sequence
102 int s = _aa.sequenceRef.findIndex(ci.cStart);
103 int e = _aa.sequenceRef.findIndex(ci.cEnd);
104 if (s > 0 && s < _aa.sequenceRef.getLength())
106 rowsel = columnSelection.intersects(s, e);
110 // TODO: show selected region
111 if (colsel || rowsel)
114 col = getSelectedColorForRange(min, max, contacts, ci.cStart,
116 if (colsel && rowsel)
118 col = new Color(col.getBlue(), col.getGreen(), col.getRed());
122 col = new Color(col.getBlue(), col.getBlue(), col.getBlue());
128 col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd);
131 if (cgeom.pixels_step > 1)
133 g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
137 g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
145 // Shading parameters
146 // currently hardwired for alphafold
147 Color maxColor = new Color(246, 252, 243),
148 minColor = new Color(0, 60, 26),
149 selMinColor = new Color(26, 0, 60),
150 selMaxColor = new Color(243, 246, 252);
152 Color shadeFor(float min, float max, float value)
154 return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
158 public Color getColorForRange(float min, float max, ContactListI cl,
161 ContactRange cr = cl.getRangeFor(i, j);
162 // average for moment - probably more interested in maxIntProj though
163 return shadeFor(min, max, (float) cr.getMean());
166 public Color getSelectedColorForRange(float min, float max,
167 ContactListI cl, int i, int j)
169 ContactRange cr = cl.getRangeFor(i, j);
170 // average for moment - probably more interested in maxIntProj though
171 return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
172 0, selMinColor, max, selMaxColor);