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JAL-966 SearchResultsI now on viewmodels.AlignmentViewport rather than on SeqCanvas
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
22c537a
..
9a408e3
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-23,7
+23,6
@@
package jalview.datamodel;
import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.schemes.ColourSchemeI;
import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
import java.awt.Color;
import java.util.ArrayList;
import java.awt.Color;
import java.util.ArrayList;
@@
-529,6
+528,7
@@
public class SequenceGroup implements AnnotatedCollectionI
}
// TODO: try harder to detect changes in state in order to minimise
// recalculation effort
}
// TODO: try harder to detect changes in state in order to minimise
// recalculation effort
+ boolean upd = false;
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
try
{
Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
@@
-536,18
+536,19
@@
public class SequenceGroup implements AnnotatedCollectionI
if (consensus != null)
{
_updateConsensusRow(cnsns, sequences.size());
if (consensus != null)
{
_updateConsensusRow(cnsns, sequences.size());
+ upd = true;
}
if (cs != null)
{
cs.setConsensus(cnsns);
}
if (cs != null)
{
cs.setConsensus(cnsns);
+ upd = true;
}
if ((conservation != null)
|| (cs != null && cs.conservationApplied()))
{
}
if ((conservation != null)
|| (cs != null && cs.conservationApplied()))
{
- Conservation c = new Conservation(groupName,
- ResidueProperties.propHash, 3, sequences, startRes,
- endRes + 1);
+ Conservation c = new Conservation(groupName, 3, sequences,
+ startRes, endRes + 1);
c.calculate();
c.verdict(false, consPercGaps);
if (conservation != null)
c.calculate();
c.verdict(false, consPercGaps);
if (conservation != null)
@@
-561,6
+562,8
@@
public class SequenceGroup implements AnnotatedCollectionI
cs.setConservation(c);
}
}
cs.setConservation(c);
}
}
+ // eager update - will cause a refresh of overview regardless
+ upd = true;
}
if (cs != null && !defer)
{
}
if (cs != null && !defer)
{
@@
-570,14
+573,14
@@
public class SequenceGroup implements AnnotatedCollectionI
}
else
{
}
else
{
- return false;
+ return upd;
}
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
System.out.println("Out of memory loading groups: " + err);
}
}
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
System.out.println("Out of memory loading groups: " + err);
}
- return false;
+ return upd;
}
private void _updateConservationRow(Conservation c)
}
private void _updateConservationRow(Conservation c)