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set icon false if raising windows
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
dc22704
..
f640ebb
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-49,6
+49,10
@@
public class SequenceGroup
int startRes = 0;
\r
int endRes = 0;
\r
Color outlineColour = Color.black;
\r
int startRes = 0;
\r
int endRes = 0;
\r
Color outlineColour = Color.black;
\r
+ public int thresholdTextColour = 0;
\r
+ public Color textColour = Color.black;
\r
+ public Color textColour2 = Color.white;
\r
+
\r
\r
/**
\r
* Creates a new SequenceGroup object.
\r
\r
/**
\r
* Creates a new SequenceGroup object.
\r
@@
-338,7
+342,7
@@
public class SequenceGroup
\r
try
\r
{
\r
\r
try
\r
{
\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
\r
+ cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));
\r
\r
if (cs instanceof ClustalxColourScheme)
\r
{
\r
\r
if (cs instanceof ClustalxColourScheme)
\r
{
\r
@@
-349,7
+353,7
@@
public class SequenceGroup
{
\r
Conservation c = new Conservation(groupName,
\r
ResidueProperties.propHash, 3, sequences,
\r
{
\r
Conservation c = new Conservation(groupName,
\r
ResidueProperties.propHash, 3, sequences,
\r
- 0, getWidth());
\r
+ startRes, endRes+1);
\r
c.calculate();
\r
c.verdict(false, 25);
\r
\r
c.calculate();
\r
c.verdict(false, 25);
\r
\r