4 package jalview.renderer;
6 import jalview.api.AlignViewportI;
7 import jalview.datamodel.AlignmentAnnotation;
8 import jalview.datamodel.Annotation;
9 import jalview.datamodel.ColumnSelection;
10 import jalview.datamodel.ContactListI;
11 import jalview.datamodel.ContactRange;
12 import jalview.datamodel.HiddenColumns;
13 import jalview.renderer.api.AnnotationRowRendererI;
15 import java.awt.Color;
16 import java.awt.Graphics;
22 public class ContactMapRenderer implements AnnotationRowRendererI
26 public void renderRow(Graphics g, int charWidth, int charHeight,
27 boolean hasHiddenColumns, AlignViewportI viewport, HiddenColumns hiddenColumns,
28 ColumnSelection columnSelection, AlignmentAnnotation _aa,
29 Annotation[] aa_annotations, int sRes, int eRes, float min,
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.adjustForHiddenColumns(column);
59 if (aa_annotations[column] == null)
65 * {profile type, #values, total count, char1, pct1, char2, pct2...}
67 ContactListI contacts = viewport.getContactList(_aa, column);
73 // cell height to render
74 double scale = (_aa.graphHeight < contacts.getContactHeight()) ? 1
75 : ((double) _aa.graphHeight)
76 / (double) contacts.getContactHeight();
77 int cstart, cend = -1;
78 for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= scale)
81 cend = Math.max(cstart + 1, contacts.getContactHeight()
82 * ((ht - y2) / _aa.graphHeight));
83 // TODO show maximum colour for range - sort of done
84 // also need a 'getMaxPosForRange(start,end)'
85 g.setColor(getColorForRange(min, max, contacts, cstart, cend));
89 g.fillRect(x * charWidth, ht, charWidth, 1 + (int) scale);
93 g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
101 Color minColor = Color.white, maxColor = Color.magenta;
104 Color shadeFor(float min, float max, float value)
106 return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
110 public Color getColorForRange(float min, float max, ContactListI cl,
113 ContactRange cr = cl.getRangeFor(i, j);
114 // average for moment - probably more interested in maxIntProj though
115 return shadeFor(min, max, (float) cr.getMean());