import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ProfilesI;
+import jalview.renderer.api.AnnotationRendererFactoryI;
+import jalview.renderer.api.AnnotationRowRendererI;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.ResidueProperties;
+import jalview.schemes.ZappoColourScheme;
import jalview.util.Platform;
import java.awt.BasicStroke;
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
- ColourSchemeI profcolour = null;
+ ResidueShaderI profcolour = null;
private ColumnSelection columnSelection;
hStrucConsensus = null;
fadedImage = null;
annotationPanel = null;
+ rendererFactoryI = null;
}
void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
useClip = false;
}
+ rendererFactoryI = AnnotationRendererFactory.getRendererFactory();
updateFromAlignViewport(av);
}
av_renderHistogram = av.isShowConsensusHistogram();
av_renderProfile = av.isShowSequenceLogo();
av_normaliseProfile = av.isNormaliseSequenceLogo();
- profcolour = av.getGlobalColourScheme();
- if (profcolour == null)
+ profcolour = av.getResidueShading();
+ if (profcolour == null || profcolour.getColourScheme() == null)
{
- // Set the default colour for sequence logo if the alignnent has no
- // colourscheme set
- profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
- : new jalview.schemes.ZappoColourScheme();
+ /*
+ * Use default colour for sequence logo if
+ * the alignment has no colourscheme set
+ * (would like to use user preference but n/a for applet)
+ */
+ ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
+ : new ZappoColourScheme();
+ profcolour = new ResidueShader(col);
}
columnSelection = av.getColumnSelection();
hconsensus = av.getSequenceConsensusHash();
boolean rna = false;
+ private AnnotationRendererFactoryI rendererFactoryI;
+
/**
* Render the annotation rows associated with an alignment.
*
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
- if (row.autoCalculated && row.label != null
- && row.label.startsWith("Consen"))
- {
- drawProfileDensity(g, row, row_annotations, startRes, endRes,
- row.graphMin, row.graphMax, y);
- }
- else
- {
drawBarGraph(g, row, row_annotations, startRes, endRes,
row.graphMin, row.graphMax, y, renderHistogram,
renderProfile, normaliseProfile);
+ }
+ else
+ {
+ AnnotationRowRendererI renderer = rendererFactoryI
+ .getRendererFor(row);
+ if (renderer != null)
+ {
+ renderer.renderRow(g, charWidth, charHeight,
+ hasHiddenColumns, av, columnSelection, row,
+ row_annotations, startRes, endRes, row.graphMin,
+ row.graphMax, y);
+ }
+ if (debugRedraw)
+ {
+ if (renderer == null)
+ {
+ System.err.println("No renderer found for "
+ + row.toString());
+ }
+ else
+ {
+ System.err.println("rendered with "
+ + renderer.getClass().toString());
+ }
}
+
}
}
}
}
}
-
- void drawProfileDensity(Graphics g, AlignmentAnnotation _aa,
- Annotation[] aa_annotations, int sRes, int eRes, float min,
- float max, int y)
- {
- if (sRes > aa_annotations.length)
- {
- return;
- }
- Font ofont = g.getFont();
- eRes = Math.min(eRes, aa_annotations.length);
-
- int x = 0, y2 = y;
-
-
-
- g.setColor(Color.pink);
-
- g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
-
- int column;
- int aaMax = aa_annotations.length - 1;
- while (x < eRes - sRes)
- {
- column = sRes + x;
- if (hasHiddenColumns)
- {
- column = columnSelection.adjustForHiddenColumns(column);
- }
-
- if (column > aaMax)
- {
- break;
- }
-
- if (aa_annotations[column] == null)
- {
- x++;
- continue;
- }
- if (aa_annotations[column].colour == null)
- {
- g.setColor(Color.black);
- }
- else
- {
- g.setColor(aa_annotations[column].colour);
- }
-
-
- /*
- * {profile type, #values, total count, char1, pct1, char2, pct2...}
- */
- int profl[] = getProfileFor(_aa, column);
-
- // just try to draw the logo if profl is not null
- if (profl != null && profl[2] != 0)
- {
- boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
- boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
- float ht = y2; // - _aa.graphHeight;
- char[] dc;
-
- /**
- * Render a single base for a sequence profile, a base pair for
- * structure profile, and a triplet for a cdna profile
- */
- dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
-
- double scale = _aa.graphHeight / (profl[1]);
-
- /*
- * Traverse the character(s)/percentage data in the array
- */
- int c = 3;
- int valuesProcessed = 0;
- // profl[1] is the number of values in the profile
-
- while (valuesProcessed < profl[1])
- {
- if (isStructureProfile)
- {
- // todo can we encode a structure pair as an int, like codons?
- dc[0] = (char) profl[c++];
- dc[1] = (char) profl[c++];
- }
- else if (isCdnaProfile)
- {
- dc = CodingUtils.decodeCodon(profl[c++]);
- }
- else
- {
- dc[0] = (char) profl[c++];
- }
-
- ht -= scale;
- // next profl[] position is profile % for the character(s)
- // render boxes
- g.setColor(jalview.util.ColorUtils.getGraduatedColour(profl[c++],
- 0f, Color.gray, 100, Color.blue));
- // g.setColor(profcolour.findColour(dc[0]).darker());
-
- g.fillRect(x * charWidth, (int) ht, charWidth, (int) scale);
- valuesProcessed++;
- }
- g.setFont(ofont);
- }
- x++;
-
- }
-
- // if (_aa.threshold != null)
- // {
- // g.setColor(_aa.threshold.colour);
- // Graphics2D g2 = (Graphics2D) g;
- // g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
- // BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
- //
- // y2 = (int) (y - ((_aa.threshold.value - min) / range)
- // * _aa.graphHeight);
- // g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
- // g2.setStroke(new BasicStroke());
- // }
- }
-
}
git://source.jalview.org / jalview.git / blobdiff