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.visibleToAbsoluteColumn(column);
59 if (aa_annotations[column] == null)
64 if (_aa.sequenceRef != null)
66 // get the sequence position for the column
67 column = _aa.sequenceRef.findPosition(column) - 1;
69 ContactListI contacts = viewport.getContactList(_aa, column);
74 int contact_height = contacts.getContactHeight();
75 // fractional number of contacts covering each pixel
76 double contacts_per_pixel = ((double) contact_height)
77 / ((double) _aa.graphHeight);
81 if (contacts_per_pixel >= 1)
83 // many contacts rendered per pixel
88 // pixel height for each contact
89 pixels_step = (int) Math
90 .ceil(((double) _aa.graphHeight) / (double) contact_height);
96 eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step)
98 cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
99 cend = (int) Math.min(contact_height,
100 Math.ceil(cstart + contacts_per_pixel * pixels_step));
102 // TODO show maximum colour for range - sort of done
103 // also need a 'getMaxPosForRange(start,end)' to accurately render
104 Color col = getColorForRange(min, max, contacts, cstart, cend);
111 g.fillRect(x * charWidth, ht, charWidth, 1 + pixels_step);
115 g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
123 Color minColor = Color.white, maxColor = Color.magenta;
125 Color shadeFor(float min, float max, float value)
127 return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor,
131 public Color getColorForRange(float min, float max, ContactListI cl,
134 ContactRange cr = cl.getRangeFor(i, j);
135 // average for moment - probably more interested in maxIntProj though
136 return shadeFor(min, max, (float) cr.getMean());