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Merge branch 'doc/JAL-4090_Release_2_11_3_0' into develop
[jalview.git]
/
src
/
jalview
/
renderer
/
OverviewRenderer.java
diff --git
a/src/jalview/renderer/OverviewRenderer.java
b/src/jalview/renderer/OverviewRenderer.java
index
1c50aab
..
1ff032b
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;
@@
-78,8
+76,8
@@
public class OverviewRenderer
private OverviewResColourFinder resColFinder;
public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,
private OverviewResColourFinder resColFinder;
public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,
- AlignmentI alignment,
- ResidueShaderI resshader, OverviewResColourFinder colFinder)
+ AlignmentI alignment, ResidueShaderI resshader,
+ OverviewResColourFinder colFinder)
{
finder = new FeatureColourFinder(fr);
resColFinder = colFinder;
{
finder = new FeatureColourFinder(fr);
resColFinder = colFinder;
@@
-122,7
+120,7
@@
public class OverviewRenderer
{
break;
}
{
break;
}
-
+
// get details of this alignment row
SequenceI seq = rows.getSequence(alignmentRow);
// get details of this alignment row
SequenceI seq = rows.getSequence(alignmentRow);
@@
-132,7
+130,7
@@
public class OverviewRenderer
// calculate where this row extends to in pixels
int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
miniMe.getHeight() - 1);
// calculate where this row extends to in pixels
int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
miniMe.getHeight() - 1);
-
+
int colIndex = 0;
int pixelCol = 0;
for (int alignmentCol : cols)
int colIndex = 0;
int pixelCol = 0;
for (int alignmentCol : cols)
@@
-141,19
+139,19
@@
public class OverviewRenderer
{
break;
}
{
break;
}
-
+
// calculate where this column extends to in pixels
int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
miniMe.getWidth() - 1);
// calculate where this column extends to in pixels
int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
miniMe.getWidth() - 1);
-
+
// don't do expensive colour determination if we're not going to use it
// NB this is important to avoid performance issues in the overview
// panel
if (pixelCol <= endCol)
{
rgbcolor = getColumnColourFromSequence(allGroups, seq,
// don't do expensive colour determination if we're not going to use it
// NB this is important to avoid performance issues in the overview
// panel
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.gapColour;
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();
@@
-294,8
+288,8
@@
public class OverviewRenderer
Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
// set background to transparent
Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
// set background to transparent
- g2d.setComposite(AlphaComposite.Clear);
- g2d.fillRect(0, 0, width, height);
+ // g2d.setComposite(AlphaComposite.Clear);
+ // g2d.fillRect(0, 0, width, height);
// set next colour to opaque
g2d.setComposite(AlphaComposite.Src);
// set next colour to opaque
g2d.setComposite(AlphaComposite.Src);
@@
-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);