X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=c98c27d155f0585d33cb996219cd32634e981158;hb=17de9804e86a60c532039b6630d77480f903e9e0;hp=1cce3fff9d0eade7f5e0daa41a1ef460e57dd2b1;hpb=679e63aab1a22d128bf429a07514eb15f8b288e1;p=jalview.git diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java index 1cce3ff..c98c27d 100644 --- a/src/jalview/workers/ConsensusThread.java +++ b/src/jalview/workers/ConsensusThread.java @@ -28,7 +28,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.ProfilesI; import jalview.datamodel.SequenceI; -import jalview.schemes.ColourSchemeI; +import jalview.renderer.ResidueShaderI; public class ConsensusThread extends AlignCalcWorker { @@ -58,12 +58,13 @@ public class ConsensusThread extends AlignCalcWorker } while (!calcMan.notifyWorking(this)) { - // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around."); + // System.err.println("Thread + // (Consensus"+Thread.currentThread().getName()+") Waiting around."); try { if (ap != null) { - ap.paintAlignment(false); + ap.paintAlignment(false, false); } Thread.sleep(200); } catch (Exception ex) @@ -92,7 +93,7 @@ public class ConsensusThread extends AlignCalcWorker if (ap != null) { - ap.paintAlignment(true); + ap.paintAlignment(true, true); } } catch (OutOfMemoryError error) { @@ -117,7 +118,10 @@ public class ConsensusThread extends AlignCalcWorker protected void eraseConsensus(int aWidth) { AlignmentAnnotation consensus = getConsensusAnnotation(); - consensus.annotations = new Annotation[aWidth]; + if (consensus != null) + { + consensus.annotations = new Annotation[aWidth]; + } AlignmentAnnotation gap = getGapAnnotation(); if (gap != null) { @@ -153,11 +157,10 @@ public class ConsensusThread extends AlignCalcWorker */ protected void setColourSchemeConsensus(ProfilesI hconsensus) { - ColourSchemeI globalColourScheme = alignViewport - .getGlobalColourScheme(); - if (globalColourScheme != null) + ResidueShaderI cs = alignViewport.getResidueShading(); + if (cs != null) { - globalColourScheme.setConsensus(hconsensus); + cs.setConsensus(hconsensus); } } @@ -219,7 +222,6 @@ public class ConsensusThread extends AlignCalcWorker protected void deriveConsensus(AlignmentAnnotation consensusAnnotation, ProfilesI hconsensus) { - long nseq = getSequences().length; AAFrequency.completeConsensus(consensusAnnotation, hconsensus, hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,