/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;
import compbio.metadata.Argument;
-public class AAConClient extends JabawsAlignCalcWorker
+public class AAConClient extends JabawsCalcWorker
{
public AAConClient(Jws2Instance service, AlignFrame alignFrame,
initViewportParams();
}
- protected void initViewportParams()
- {
- ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
- getCalcId(),
- new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
- }
-
- @Override
- public void updateParameters(WsParamSetI newpreset,
- java.util.List<Argument> newarguments)
- {
- super.updateParameters(newpreset, newarguments);
- initViewportParams();
- };
-
public String getServiceActionText()
{
return "calculating Amino acid consensus using AACon service";
}
}
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ @Override
public String getCalcId()
{
- return SequenceAnnotationWSClient.AAConCalcId;
+ return CALC_ID;
}
- public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
+ private static String CALC_ID = "jabaws2.AACon";
+
+ public static AlignAnalysisUIText getAlignAnalysisUITest()
{
- for (AlignmentAnnotation aa : alignPanel.getAlignment().findAnnotation(
- SequenceAnnotationWSClient.AAConCalcId))
- {
- alignPanel.getAlignment().deleteAnnotation(aa);
- }
+ return new AlignAnalysisUIText(
+ compbio.ws.client.Services.AAConWS.toString(),
+ jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true,
+ "AACon Calculations",
+ "When checked, AACon calculations are updated automatically.",
+ "Change AACon Settings...",
+ "Modify settings for AACon calculations.");
}
}