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JAL-3933 configure root logger console appender to stderr
[jalview.git]
/
src
/
jalview
/
renderer
/
OverviewRenderer.java
diff --git
a/src/jalview/renderer/OverviewRenderer.java
b/src/jalview/renderer/OverviewRenderer.java
index
1c50aab
..
e9b4de4
100644
(file)
--- a/
src/jalview/renderer/OverviewRenderer.java
+++ b/
src/jalview/renderer/OverviewRenderer.java
@@
-44,8
+44,6
@@
public class OverviewRenderer
// transparency of hidden cols/seqs overlay
private final float TRANSPARENCY = 0.5f;
// transparency of hidden cols/seqs overlay
private final float TRANSPARENCY = 0.5f;
- private final Color HIDDEN_COLOUR = Color.DARK_GRAY.darker();
-
public static final String UPDATE = "OverviewUpdate";
private static final int MAX_PROGRESS = 100;
public static final String UPDATE = "OverviewUpdate";
private static final int MAX_PROGRESS = 100;
@@
-152,7
+150,7
@@
public class OverviewRenderer
if (pixelCol <= endCol)
{
rgbcolor = getColumnColourFromSequence(allGroups, seq,
if (pixelCol <= endCol)
{
rgbcolor = getColumnColourFromSequence(allGroups, seq,
- alignmentCol, finder);
+ alignmentCol);
// fill in the appropriate number of pixels
for (int row = pixelRow; row <= endRow; ++row)
// fill in the appropriate number of pixels
for (int row = pixelRow; row <= endRow; ++row)
@@
-216,27
+214,23
@@
public class OverviewRenderer
}
/*
}
/*
- * Find the colour of a sequence at a specified column position
+ * Find the RGB value of the colour of a sequence at a specified column position
*
* @param seq
* sequence to get colour for
* @param lastcol
* column position to get colour for
*
* @param seq
* sequence to get colour for
* @param lastcol
* column position to get colour for
- * @param fcfinder
- * FeatureColourFinder to use
* @return colour of sequence at this position, as RGB
*/
* @return colour of sequence at this position, as RGB
*/
- private int getColumnColourFromSequence(SequenceGroup[] allGroups,
- jalview.datamodel.SequenceI seq,
- int lastcol, FeatureColourFinder fcfinder)
+ int getColumnColourFromSequence(SequenceGroup[] allGroups,
+ SequenceI seq, int lastcol)
{
{
- Color color = Color.white;
+ Color color = resColFinder.GAP_COLOUR;
if ((seq != null) && (seq.getLength() > lastcol))
{
color = resColFinder.getResidueColour(true, shader, allGroups, seq,
if ((seq != null) && (seq.getLength() > lastcol))
{
color = resColFinder.getResidueColour(true, shader, allGroups, seq,
- lastcol,
- fcfinder);
+ lastcol, finder);
}
return color.getRGB();
}
return color.getRGB();
@@
-359,15
+353,13
@@
public class OverviewRenderer
* the graphics object to draw on
* @param anno
* alignment annotation information
* the graphics object to draw on
* @param anno
* alignment annotation information
- * @param charWidth
- * alignment character width value
* @param y
* y-position for the annotation graph
* @param cols
* the collection of columns used in the overview panel
*/
* @param y
* y-position for the annotation graph
* @param cols
* the collection of columns used in the overview panel
*/
- public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
- int y, AlignmentColsCollectionI cols)
+ public void drawGraph(Graphics g, AlignmentAnnotation anno, int y,
+ AlignmentColsCollectionI cols)
{
Annotation[] annotations = anno.annotations;
g.setColor(Color.white);
{
Annotation[] annotations = anno.annotations;
g.setColor(Color.white);