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JAL-3383 JAL-3253-applet Allows for possibility of a sequence caching
[jalview.git]
/
src
/
jalview
/
renderer
/
OverviewResColourFinder.java
diff --git
a/src/jalview/renderer/OverviewResColourFinder.java
b/src/jalview/renderer/OverviewResColourFinder.java
index
a497d92
..
ff52f1d
100644
(file)
--- a/
src/jalview/renderer/OverviewResColourFinder.java
+++ b/
src/jalview/renderer/OverviewResColourFinder.java
@@
-81,30
+81,24
@@
public class OverviewResColourFinder extends ResidueColourFinder
@Override
public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
@Override
public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
- Color resBoxColour = RESIDUE_COLOUR;
+ seq.resetColors();
+ Color c = seq.getColor(i);
+ if (c != null)
+ {
+ return c;
+ }
char currentChar = seq.getCharAt(i);
char currentChar = seq.getCharAt(i);
-
// In the overview window, gaps are coloured grey, unless the colour scheme
// specifies a gap colour, in which case gaps honour the colour scheme
// settings
// In the overview window, gaps are coloured grey, unless the colour scheme
// specifies a gap colour, in which case gaps honour the colour scheme
// settings
- if (shader.getColourScheme() != null)
+ boolean isGap = Comparison.isGap(currentChar);
+ if (shader.getColourScheme() == null)
{
{
- if (Comparison.isGap(currentChar)
- && (!shader.getColourScheme().hasGapColour()))
- {
- resBoxColour = GAP_COLOUR;
- }
- else
- {
- resBoxColour = shader.findColour(currentChar, i, seq);
- }
+ return seq.setColor(i, isGap ? GAP_COLOUR : RESIDUE_COLOUR);
}
}
- else if (Comparison.isGap(currentChar))
- {
- resBoxColour = GAP_COLOUR;
- }
-
- return resBoxColour;
+ return seq.setColor(i,
+ isGap && !shader.getColourScheme().hasGapColour() ? GAP_COLOUR
+ : shader.findColour(currentChar, i, seq));
}
/**
}
/**
@@
-113,21
+107,13
@@
public class OverviewResColourFinder extends ResidueColourFinder
*/
@Override
protected Color getResidueBoxColour(boolean showBoxes,
*/
@Override
protected Color getResidueBoxColour(boolean showBoxes,
- ResidueShaderI shader,
- SequenceGroup[] allGroups, SequenceI seq, int i)
+ ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
+ int i)
{
{
- ResidueShaderI currentShader;
SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
i);
SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
i);
- if (currentSequenceGroup != null)
- {
- currentShader = currentSequenceGroup.getGroupColourScheme();
- }
- else
- {
- currentShader = shader;
- }
-
+ ResidueShaderI currentShader = (currentSequenceGroup == null ? shader
+ : currentSequenceGroup.getGroupColourScheme());
return getBoxColour(currentShader, seq, i);
}
return getBoxColour(currentShader, seq, i);
}