X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FStrucConsensusThread.java;h=9694b3759eea8b5d013fd7f07bb0b7bec8e7cad6;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=72d26ffa429bfdf6628fdcd96a3b639298247939;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java index 72d26ff..9694b37 100644 --- a/src/jalview/workers/StrucConsensusThread.java +++ b/src/jalview/workers/StrucConsensusThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,8 +20,6 @@ */ package jalview.workers; -import java.util.Hashtable; - import jalview.analysis.StructureFrequency; import jalview.api.AlignCalcWorkerI; import jalview.api.AlignViewportI; @@ -31,6 +29,8 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.SequenceI; +import java.util.Hashtable; + public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI { @@ -74,6 +74,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements if (alignViewport.isClosed()) { abortAndDestroy(); + return; } AlignmentI alignment = alignViewport.getAlignment(); @@ -97,7 +98,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements // select rna struct to use for calculation for (int i = 0; i < aa.length; i++) { - if (aa[i].getRNAStruc() != null && aa[i].isValidStruc()) + if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc()) { rnaStruc = aa[i]; break; @@ -125,11 +126,6 @@ public class StrucConsensusThread extends AlignCalcWorker implements alignViewport.setRnaStructureConsensusHash(hStrucConsensus); // TODO AlignmentAnnotation rnaStruc!!! updateResultAnnotation(true); - if (alignViewport.getGlobalColourScheme() != null) - { - alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus); - } - } catch (OutOfMemoryError error) { calcMan.workerCannotRun(this); @@ -165,7 +161,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements { StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus, 0, hStrucConsensus.length, - alignViewport.getIgnoreGapsConsensus(), + alignViewport.isIgnoreGapsConsensus(), alignViewport.isShowSequenceLogo(), nseq); } }