X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2Fjabaws2%2FAAConClient.java;fp=src%2Fjalview%2Fws%2Fjws2%2Fjabaws2%2FAAConClient.java;h=f0a4b67248981b81e4779a924e62de653ba2bf20;hb=47ecacc91ed5d80b59b42d255ef5c13e79d3dfa0;hp=0000000000000000000000000000000000000000;hpb=128f413cad94e4675d241f8079dd275a4199b6d8;p=jalview.git

diff --git a/src/jalview/ws/jws2/jabaws2/AAConClient.java b/src/jalview/ws/jws2/jabaws2/AAConClient.java
new file mode 100644
index 0000000..f0a4b67
--- /dev/null
+++ b/src/jalview/ws/jws2/jabaws2/AAConClient.java
@@ -0,0 +1,102 @@
+/*
+ * 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.
+ *  
+ * 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.jabaws2;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.util.MessageManager;
+import jalview.ws.gui.AnnotationWsJob;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import compbio.data.sequence.Score;
+
+public class AAConClient extends JabawsAnnotationInstance
+{
+  // configuration for factory
+  public static String getServiceActionText()
+  {
+    return "calculating Amino acid consensus using AACon service";
+  }
+
+
+
+  private static String CALC_ID = "jabaws2.AACon";
+
+  public static AlignAnalysisUIText getAlignAnalysisUIText()
+  {
+    return new AlignAnalysisUIText(
+            compbio.ws.client.Services.AAConWS.toString(),
+            AAConClient.class, CALC_ID, false, true, true, true,
+            true, 2, MessageManager.getString("label.aacon_calculations"),
+            MessageManager.getString("tooltip.aacon_calculations"),
+            MessageManager.getString("label.aacon_settings"),
+            MessageManager.getString("tooltip.aacon_settings"));
+  }
+
+  // instance
+  public AAConClient(Jws2Instance handle)
+  {
+    super(handle);
+  }
+
+  @Override
+  List<AlignmentAnnotation> annotationFromScoreManager(
+          AnnotationWsJob running, AlignViewportI alignViewport,
+          boolean[] gapMap)
+  {
+
+    Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
+    int alWidth = alignViewport.getAlignment().getWidth();
+    ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
+    for (String score : scoremap.keySet())
+    {
+      Set<Score> scores = scoremap.get(score);
+      for (Score scr : scores)
+      {
+        if (scr.getRanges() != null && scr.getRanges().size() > 0)
+        {
+          /**
+           * annotation in range annotation = findOrCreate(scr.getMethod(),
+           * true, null, null); Annotation[] elm = new Annotation[alWidth];
+           * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng :
+           * scr.getRanges()) { float val = vals.next().floatValue(); for (int i
+           * = rng.from; i <= rng.to; i++) { elm[i] = new Annotation("", "", '
+           * ', val); } } annotation.annotations = elm;
+           * annotation.validateRangeAndDisplay();
+           */
+        }
+        else
+        {
+          createAnnotationRowsForScores(alignViewport, gapMap, ourAnnot,
+                  getCalcId(), alWidth, scr);
+        }
+      }
+    }
+    return ourAnnot;
+  }
+
+}