X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAbstractJabaCalcWorker.java;h=dd64e778c3f40ed801bd70fe6bc789226adcc087;hb=4687e1243f51bd09334792b8a7ce518a5aa07de7;hp=897aa1eae1831c297a4729c43468a89ecb8e40cb;hpb=db4eacee27b836db4126dca551887bfc6652d72a;p=jalview.git diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java index 897aa1e..dd64e77 100644 --- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java +++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java @@ -30,6 +30,8 @@ import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.IProgressIndicator; +import jalview.gui.IProgressIndicatorHandler; +import jalview.schemes.ResidueProperties; import jalview.workers.AlignCalcWorker; import jalview.ws.jws2.dm.AAConSettings; import jalview.ws.jws2.dm.JabaWsParamSet; @@ -63,6 +65,11 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker protected boolean submitGaps = true; /** + * by default, we filter out non-standard residues before submission + */ + protected boolean filterNonStandardResidues = true; + + /** * Recover any existing parameters for this service */ protected void initViewportParams() @@ -72,8 +79,10 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor( getCalcId(), new AAConSettings(true, service, this.preset, - (arguments != null) ? JabaParamStore - .getJwsArgsfromJaba(arguments) : null), true); + (arguments != null) + ? JabaParamStore.getJwsArgsfromJaba(arguments) + : null), + true); } } @@ -113,7 +122,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker public List