import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.renderer.ResidueShaderI;
+import jalview.renderer.ResidueColourFinder;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import java.awt.Color;
SequenceGroup[] allGroups = null;
- Color resBoxColour;
+ // Color resBoxColour;
Graphics graphics;
boolean monospacedFont;
+ ResidueColourFinder resColourFinder;
+
/**
* Creates a new SequenceRenderer object
*
public SequenceRenderer(AlignViewportI viewport)
{
this.av = viewport;
+ resColourFinder = new ResidueColourFinder();
}
/**
this.renderGaps = renderGaps;
}
- protected Color getResidueBoxColour(SequenceI seq, int i)
- {
- // rate limiting step when rendering overview for lots of groups
- allGroups = av.getAlignment().findAllGroups(seq);
-
- SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i);
- if (currentSequenceGroup != null)
- {
- if (currentSequenceGroup.getDisplayBoxes())
- {
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
- }
- }
- else if (av.getShowBoxes())
- {
- getBoxColour(av.getResidueShading(), seq, i);
- }
-
- return resBoxColour;
- }
-
/**
* Get the residue colour at the given sequence position - as determined by
* the sequence group colour (if any), else the colour scheme, possibly
public Color getResidueColour(final SequenceI seq, int position,
FeatureColourFinder finder)
{
- Color col = getResidueBoxColour(seq, position);
-
- if (finder != null)
- {
- col = finder.findFeatureColour(col, seq, position);
- }
- return col;
+ return resColourFinder.getResidueColour(av.getResidueShading(),
+ allGroups, seq, position,
+ finder);
}
- /**
- * DOCUMENT ME!
- *
- * @param shader
- * DOCUMENT ME!
- * @param seq
- * DOCUMENT ME!
- * @param i
- * DOCUMENT ME!
- */
- void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
- {
- if (shader.getColourScheme() != null)
- {
- resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
- }
- else
- {
- resBoxColour = Color.white;
- }
- }
+
/**
* DOCUMENT ME!
public synchronized void drawBoxes(SequenceI seq, int start, int end,
int y1)
{
+ Color resBoxColour = Color.white;
+
if (seq == null)
{
return; // fix for racecondition
if (i < length)
{
- SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i);
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(
+ allGroups, i);
if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq,
i);
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
}
boolean srep = av.isDisplayReferenceSeq();
boolean getboxColour = false;
boolean isarep = av.getAlignment().getSeqrep() == seq;
+ Color resBoxColour = Color.white;
for (int i = start; i <= end; i++)
{
continue;
}
- SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i);
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(
+ allGroups, i);
if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
|| currentSequenceGroup.getColourText())
{
getboxColour = true;
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq,
i);
if (currentSequenceGroup.getColourText())
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
{
if (!getboxColour)
{
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
/**
* DOCUMENT ME!
*
- * @param res
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- SequenceGroup inCurrentSequenceGroup(int res)
- {
- if (allGroups == null)
- {
- return null;
- }
-
- for (int i = 0; i < allGroups.length; i++)
- {
- if ((allGroups[i].getStartRes() <= res)
- && (allGroups[i].getEndRes() >= res))
- {
- return (allGroups[i]);
- }
- }
-
- return null;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param seq
* DOCUMENT ME!
* @param start