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Discover user colours
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignFrame.java
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
0bdcb55
..
db1f9c9
100755
(executable)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-808,14
+808,14
@@
public class AlignFrame
\r
if (cs instanceof ResidueColourScheme)
\r
{
\r
\r
if (cs instanceof ResidueColourScheme)
\r
{
\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);
\r
+ ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
}
\r
\r
viewport.setGlobalColourScheme(cs);
\r
}
\r
else if (cs instanceof ResidueColourScheme)
\r
{
\r
}
\r
\r
viewport.setGlobalColourScheme(cs);
\r
}
\r
else if (cs instanceof ResidueColourScheme)
\r
{
\r
- ( (ResidueColourScheme) cs).setThreshold(0);
\r
+ ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
}
\r
\r
if (viewport.getConservationSelected())
\r
}
\r
\r
if (viewport.getConservationSelected())
\r
@@
-885,7
+885,7
@@
public class AlignFrame
{
\r
if (sg.cs instanceof ResidueColourScheme)
\r
{
\r
{
\r
if (sg.cs instanceof ResidueColourScheme)
\r
{
\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
}
\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
}
\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
@@
-914,6
+914,8
@@
public class AlignFrame
}
\r
}
\r
\r
}
\r
}
\r
\r
+ updateCSConsensus();
\r
+
\r
if (alignPanel.getOverviewPanel() != null)
\r
{
\r
alignPanel.getOverviewPanel().updateOverviewImage();
\r
if (alignPanel.getOverviewPanel() != null)
\r
{
\r
alignPanel.getOverviewPanel().updateOverviewImage();
\r
@@
-922,6
+924,12
@@
public class AlignFrame
alignPanel.repaint();
\r
}
\r
\r
alignPanel.repaint();
\r
}
\r
\r
+ public void updateCSConsensus()
\r
+ {
\r
+ //Colour schemes must have their consensus updated
\r
+
\r
+ }
\r
+
\r
protected void modifyPID_actionPerformed(ActionEvent e)
\r
{
\r
if (viewport.getAbovePIDThreshold())
\r
protected void modifyPID_actionPerformed(ActionEvent e)
\r
{
\r
if (viewport.getAbovePIDThreshold())
\r