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JAL-2388 Comment typo
[jalview.git]
/
src
/
jalview
/
appletgui
/
SequenceRenderer.java
diff --git
a/src/jalview/appletgui/SequenceRenderer.java
b/src/jalview/appletgui/SequenceRenderer.java
index
970d20e
..
86d1f98
100755
(executable)
--- a/
src/jalview/appletgui/SequenceRenderer.java
+++ b/
src/jalview/appletgui/SequenceRenderer.java
@@
-23,7
+23,7
@@
package jalview.appletgui;
import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
import java.awt.Color;
import java.awt.Font;
import java.awt.Color;
import java.awt.Font;
@@
-78,12
+78,12
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (currentSequenceGroup.getDisplayBoxes())
{
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
{
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
return resBoxColour;
}
return resBoxColour;
@@
-114,11
+114,11
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
return col;
}
return col;
}
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+ void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
{
- if (cs != null)
+ if (shader != null)
{
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
+ resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@
-176,12
+176,13
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (currentSequenceGroup.getDisplayBoxes())
{
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ i);
}
}
else if (av.getShowBoxes())
{
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
}
}
}
@@
-254,7
+255,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (currentSequenceGroup.getColourText())
{
if (currentSequenceGroup.getColourText())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
graphics.setColor(resBoxColour.darker());
}
if (currentSequenceGroup.getShowNonconserved())
graphics.setColor(resBoxColour.darker());
}
if (currentSequenceGroup.getShowNonconserved())
@@
-271,7
+272,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.getColourText())
{
if (av.getColourText())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
graphics.setColor(resBoxColour.darker());
if (av.getShowBoxes())
{
graphics.setColor(resBoxColour.darker());