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(JAL-893) update to VARNAv3.9-dev version
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
e94fba4
..
ad704c3
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-80,7
+80,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
public Color getResidueBoxColour(SequenceI seq, int i)
{
public Color getResidueBoxColour(SequenceI seq, int i)
{
- allGroups = av.alignment.findAllGroups(seq);
+ allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
{
if (inCurrentSequenceGroup(i))
{
@@
-91,7
+91,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
return resBoxColour;
}
return resBoxColour;
@@
-205,7
+205,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
}
}
}
@@
-328,7
+328,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (currentSequenceGroup.getShowNonconserved()) // todo optimize
{
// todo - use sequence group consensus
if (currentSequenceGroup.getShowNonconserved()) // todo optimize
{
// todo - use sequence group consensus
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
}
}
@@
-343,7
+343,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.getColourText())
{
getboxColour = true;
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
if (av.getShowBoxes())
{
if (av.getShowBoxes())
{
@@
-359,7
+359,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (!getboxColour)
{
{
if (!getboxColour)
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
@@
-368,9
+368,9
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
graphics.setColor(av.textColour2);
}
}
graphics.setColor(av.textColour2);
}
}
- if (av.showUnconserved)
+ if (av.getShowUnconserved())
{
{
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
}
}