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JAL-98 ProfileI interface for Profile
[jalview.git]
/
src
/
jalview
/
workers
/
ConsensusThread.java
diff --git
a/src/jalview/workers/ConsensusThread.java
b/src/jalview/workers/ConsensusThread.java
index
4bd8c48
..
2b11477
100644
(file)
--- a/
src/jalview/workers/ConsensusThread.java
+++ b/
src/jalview/workers/ConsensusThread.java
@@
-26,7
+26,7
@@
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.Profile;
+import jalview.datamodel.ProfileI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
@@
-124,7
+124,7
@@
public class ConsensusThread extends AlignCalcWorker
*/
protected void computeConsensus(AlignmentI alignment)
{
*/
protected void computeConsensus(AlignmentI alignment)
{
- Profile[] hconsensus = new Profile[alignment.getWidth()];
+ ProfileI[] hconsensus = new ProfileI[alignment.getWidth()];
SequenceI[] aseqs = getSequences();
AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
SequenceI[] aseqs = getSequences();
AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
@@
-144,7
+144,7
@@
public class ConsensusThread extends AlignCalcWorker
/**
* @param hconsensus
*/
/**
* @param hconsensus
*/
- protected void setColourSchemeConsensus(Profile[] hconsensus)
+ protected void setColourSchemeConsensus(ProfileI[] hconsensus)
{
ColourSchemeI globalColourScheme = alignViewport
.getGlobalColourScheme();
{
ColourSchemeI globalColourScheme = alignViewport
.getGlobalColourScheme();
@@
-177,7
+177,7
@@
public class ConsensusThread extends AlignCalcWorker
public void updateResultAnnotation(boolean immediate)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
public void updateResultAnnotation(boolean immediate)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- Profile[] hconsensus = (Profile[]) getViewportConsensus();
+ ProfileI[] hconsensus = (ProfileI[]) getViewportConsensus();
if (immediate || !calcMan.isWorking(this) && consensus != null
&& hconsensus != null)
{
if (immediate || !calcMan.isWorking(this) && consensus != null
&& hconsensus != null)
{
@@
-195,7
+195,7
@@
public class ConsensusThread extends AlignCalcWorker
* the computed consensus data
*/
protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
* the computed consensus data
*/
protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
- Profile[] hconsensus)
+ ProfileI[] hconsensus)
{
long nseq = getSequences().length;
AAFrequency.completeConsensus(consensusAnnotation, hconsensus, 0,
{
long nseq = getSequences().length;
AAFrequency.completeConsensus(consensusAnnotation, hconsensus, 0,