X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FAbstractJabaCalcWorker.java;h=dd64e778c3f40ed801bd70fe6bc789226adcc087;hb=efb5cfa00ee832a62dfdf59f5fb847a0e16424d9;hp=fa1e3d14ec996bcd24ead27edab4307a0d91e865;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git
diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index fa1e3d1..dd64e77 100644
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
@@ -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