X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FAAConClient.java;h=327864adb9a1d562c4029f764c985331244a8c50;hb=06de78be50c3934158fa1d35ec92ad86b54e959f;hp=b6f67d92b6e7418c77ecc02cda63af1ee55dba96;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index b6f67d9..327864a 100644
--- a/src/jalview/ws/jws2/AAConClient.java
+++ b/src/jalview/ws/jws2/AAConClient.java
@@ -1,29 +1,31 @@
/*
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignmentPanel;
-import jalview.ws.jws2.dm.AAConSettings;
+import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
import java.util.ArrayList;
import java.util.List;
@@ -31,10 +33,11 @@ import java.util.Map;
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,
@@ -45,27 +48,12 @@ public class AAConClient extends JabawsAlignCalcWorker
alignedSeqs = true;
nucleotidesAllowed = false;
proteinAllowed = true;
+ filterNonStandardResidues = true;
gapMap = new boolean[0];
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 newarguments)
- {
- super.updateParameters(newpreset, newarguments);
- initViewportParams();
- };
-
public String getServiceActionText()
{
return "calculating Amino acid consensus using AACon service";
@@ -76,13 +64,14 @@ public class AAConClient extends JabawsAlignCalcWorker
* current visualization settings.
*/
+ @Override
public void updateResultAnnotation(boolean immediate)
{
if (immediate || !calcMan.isWorking(this) && scoremanager != null)
{
Map> scoremap = scoremanager.asMap();
int alWidth = alignViewport.getAlignment().getWidth();
- ArrayList ourAnnot = new ArrayList();
+ ArrayList ourAnnot = new ArrayList<>();
for (String score : scoremap.keySet())
{
Set scores = scoremap.get(score);
@@ -115,17 +104,28 @@ public class AAConClient extends JabawsAlignCalcWorker
}
}
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List 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,
+ MessageManager.getString("label.aacon_calculations"),
+ MessageManager.getString("tooltip.aacon_calculations"),
+ MessageManager.getString("label.aacon_settings"),
+ MessageManager.getString("tooltip.aacon_settings"));
}
}