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JAL-4046 JAL-3993 patch for 2.11.2.4 release
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
fb967ed
..
43fef15
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-100,9
+100,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
allGroups = av.getAlignment().findAllGroups(seq);
return resColourFinder.getResidueColour(av.getShowBoxes(),
{
allGroups = av.getAlignment().findAllGroups(seq);
return resColourFinder.getResidueColour(av.getShowBoxes(),
- av.getResidueShading(),
- allGroups, seq, position,
- finder);
+ av.getResidueShading(), allGroups, seq, position, finder);
}
/**
}
/**
@@
-183,15
+181,13
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (i < length)
{
SequenceGroup currentSequenceGroup = resColourFinder
if (i < length)
{
SequenceGroup currentSequenceGroup = resColourFinder
- .getCurrentSequenceGroup(
- allGroups, i);
+ .getCurrentSequenceGroup(allGroups, i);
if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
resBoxColour = resColourFinder.getBoxColour(
if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
resBoxColour = resColourFinder.getBoxColour(
- currentSequenceGroup.getGroupColourScheme(), seq,
- i);
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
}
}
else if (av.getShowBoxes())
@@
-257,8
+253,9
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
graphics.setColor(av.getTextColour());
}
graphics.setColor(av.getTextColour());
- boolean drawAllText = monospacedFont && av.getShowText() && allGroups.length == 0
- && !av.getColourText() && av.getThresholdTextColour() == 0;
+ boolean drawAllText = monospacedFont && av.getShowText()
+ && allGroups.length == 0 && !av.getColourText()
+ && av.getThresholdTextColour() == 0;
/*
* EPS or SVG misaligns monospaced strings (JAL-3239)
/*
* EPS or SVG misaligns monospaced strings (JAL-3239)
@@
-303,8
+300,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
SequenceGroup currentSequenceGroup = resColourFinder
}
SequenceGroup currentSequenceGroup = resColourFinder
- .getCurrentSequenceGroup(
- allGroups, i);
+ .getCurrentSequenceGroup(allGroups, i);
if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
@@
-317,8
+313,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
getboxColour = true;
resBoxColour = resColourFinder.getBoxColour(
{
getboxColour = true;
resBoxColour = resColourFinder.getBoxColour(
- currentSequenceGroup.getGroupColourScheme(), seq,
- i);
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
if (currentSequenceGroup.getColourText())
{
if (currentSequenceGroup.getColourText())
{
@@
-340,7
+335,8
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
graphics.setColor(currentSequenceGroup.textColour);
}
boolean isgrep = currentSequenceGroup != null
graphics.setColor(currentSequenceGroup.textColour);
}
boolean isgrep = currentSequenceGroup != null
- ? currentSequenceGroup.getSeqrep() == seq : false;
+ ? currentSequenceGroup.getSeqrep() == seq
+ : false;
if (!isarep && !isgrep
&& currentSequenceGroup.getShowNonconserved()) // todo
// optimize
if (!isarep && !isgrep
&& currentSequenceGroup.getShowNonconserved()) // todo
// optimize