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conservation & consensus recalc if group changed
author
amwaterhouse
<Andrew Waterhouse>
Fri, 15 Apr 2005 14:56:12 +0000
(14:56 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 15 Apr 2005 14:56:12 +0000
(14:56 +0000)
src/jalview/datamodel/SequenceGroup.java
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diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
0cf954b
..
7aae434
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-14,7
+14,6
@@
public class SequenceGroup
boolean displayBoxes;
\r
boolean displayText;
\r
boolean colourText;
\r
boolean displayBoxes;
\r
boolean displayText;
\r
boolean colourText;
\r
- boolean aaFrequencyValid = false;
\r
public Vector sequences = new Vector();
\r
int width = -1;
\r
public ColourSchemeI cs;
\r
public Vector sequences = new Vector();
\r
int width = -1;
\r
public ColourSchemeI cs;
\r
@@
-79,7
+78,6
@@
public class SequenceGroup
if(endRes>=col)
\r
endRes = col;
\r
\r
if(endRes>=col)
\r
endRes = col;
\r
\r
-
\r
return true;
\r
}
\r
\r
return true;
\r
}
\r
\r
@@
-108,6
+106,24
@@
public class SequenceGroup
{
\r
if(!sequences.contains(s))
\r
sequences.addElement(s);
\r
{
\r
if(!sequences.contains(s))
\r
sequences.addElement(s);
\r
+
\r
+
\r
+ if(cs!=null)
\r
+ cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );
\r
+
\r
+ if(cs instanceof ConservationColourScheme)
\r
+ recalcConservation();
\r
+ }
\r
+
\r
+ void recalcConservation()
\r
+ {
\r
+ Conservation c = new Conservation(groupName,
\r
+ ResidueProperties.propHash, 3,
\r
+ sequences, 0, getWidth());
\r
+ c.calculate();
\r
+ c.verdict(false, 25);
\r
+ ConservationColourScheme ccs = (ConservationColourScheme)cs;
\r
+ ccs.conserve = c;
\r
}
\r
\r
public void addOrRemove(SequenceI s)
\r
}
\r
\r
public void addOrRemove(SequenceI s)
\r
@@
-121,6
+137,12
@@
public class SequenceGroup
public void deleteSequence(SequenceI s)
\r
{
\r
sequences.removeElement(s);
\r
public void deleteSequence(SequenceI s)
\r
{
\r
sequences.removeElement(s);
\r
+
\r
+ if(cs!=null)
\r
+ cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );
\r
+
\r
+ if(cs instanceof ConservationColourScheme)
\r
+ recalcConservation();
\r
}
\r
\r
\r
}
\r
\r
\r
@@
-184,19
+206,8
@@
public class SequenceGroup
return displayBoxes;
\r
}
\r
\r
return displayBoxes;
\r
}
\r
\r
- public Vector getAAFrequency()
\r
- {
\r
- if (aaFrequency == null || aaFrequencyValid == false)
\r
- {
\r
- aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());
\r
- aaFrequencyValid = true;
\r
- }
\r
- return aaFrequency;
\r
- }
\r
-
\r
public int getWidth()
\r
{
\r
public int getWidth()
\r
{
\r
- System.out.println("it is called");
\r
// MC This needs to get reset when characters are inserted and deleted
\r
for (int i = 0; i < sequences.size(); i++)
\r
{
\r
// MC This needs to get reset when characters are inserted and deleted
\r
for (int i = 0; i < sequences.size(); i++)
\r
{
\r