JAL-1925 update source version in license

[jalview.git] / src / jalview / ws / jws2 / AAConClient.java

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index a88a221..b025a80 100644 (file)
--- a/src/jalview/ws/jws2/AAConClient.java
+++ b/src/jalview/ws/jws2/AAConClient.java
@@ -1,12 +1,31 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.
+ *  
+ * 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/>.
+ * 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;
@@ -14,10 +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,
@@ -32,23 +52,6 @@ public class AAConClient extends JabawsAlignCalcWorker
     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";
@@ -98,17 +101,28 @@ public class AAConClient extends JabawsAlignCalcWorker
     }
   }
 
+  @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,
+            MessageManager.getString("label.aacon_calculations"),
+            MessageManager.getString("tooltip.aacon_calculations"),
+            MessageManager.getString("label.aacon_settings"),
+            MessageManager.getString("tooltip.aacon_settings"));
   }
 }