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JAL-4390 don't output alignment to text panel and stdout when lots of sequences proce...
[jalview.git]
/
src
/
jalview
/
renderer
/
OverviewRenderer.java
diff --git
a/src/jalview/renderer/OverviewRenderer.java
b/src/jalview/renderer/OverviewRenderer.java
index
b126465
..
1ff032b
100644
(file)
--- a/
src/jalview/renderer/OverviewRenderer.java
+++ b/
src/jalview/renderer/OverviewRenderer.java
@@
-76,8
+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;
@@
-120,7
+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);
@@
-130,7
+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)
@@
-139,11
+139,11
@@
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
// 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
@@
-151,7
+151,7
@@
public class OverviewRenderer
{
rgbcolor = getColumnColourFromSequence(allGroups, seq,
alignmentCol);
{
rgbcolor = getColumnColourFromSequence(allGroups, seq,
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)
{
@@
-222,8
+222,8
@@
public class OverviewRenderer
* column position to get colour for
* @return colour of sequence at this position, as RGB
*/
* column position to get colour for
* @return colour of sequence at this position, as RGB
*/
- int getColumnColourFromSequence(SequenceGroup[] allGroups,
- SequenceI seq, int lastcol)
+ int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq,
+ int lastcol)
{
Color color = resColFinder.gapColour;
{
Color color = resColFinder.gapColour;