X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAbstractJabaCalcWorker.java;h=26fe0a20ce215c830d6559ce064abc5036202fba;hb=7e441a4a9594821ec56539b29cb3b8a13bfa3c65;hp=8dc4bc5c3a6f7055f49447271dad7f833207c843;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git
diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index 8dc4bc5..26fe0a2 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 2.9.0b2)
- * 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 +30,7 @@ import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.IProgressIndicator;
+import jalview.schemes.ResidueProperties;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
@@ -63,6 +64,11 @@ 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 +78,10 @@ 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 +121,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
public List