Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalv...

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

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
deleted file mode 100644 (file)
index ddd69a7..0000000
--- a/src/jalview/ws/jws2/AAConClient.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * 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;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.gui.AlignFrame;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.WsParamSetI;
-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.FastaSequence;
-import compbio.data.sequence.Score;
-
-public class AAConClient extends JabawsCalcWorker
-{
-
-  public AAConClient(Jws2Instance service, AlignFrame alignFrame,
-          WsParamSetI preset, List<ArgumentI> paramset)
-  {
-    super(service, alignFrame, preset, paramset);
-    submitGaps = true;
-    alignedSeqs = true;
-    nucleotidesAllowed = false;
-    proteinAllowed = true;
-    filterNonStandardResidues = true;
-    gapMap = new boolean[0];
-    initViewportParams();
-  }
-
-  @Override
-  public String getServiceActionText()
-  {
-    return "calculating Amino acid consensus using AACon service";
-  }
-
-  /**
-   * update the consensus annotation from the sequence profile data using
-   * current visualization settings.
-   */
-
-  @Override
-  public void updateResultAnnotation(boolean immediate)
-  {
-    if (immediate || !calcMan.isWorking(this) && scoremanager != null)
-    {
-      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(ourAnnot, getCalcId(), alWidth,
-                    scr);
-          }
-        }
-      }
-
-      if (ourAnnot.size() > 0)
-      {
-        updateOurAnnots(ourAnnot);
-      }
-    }
-  }
-
-  @Override
-  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
-  {
-    return (seqs.size() > 1);
-  }
-
-  @Override
-  public String getCalcId()
-  {
-    return CALC_ID;
-  }
-
-  private static String CALC_ID = "jabaws2.AACon";
-
-  public static AlignAnalysisUIText getAlignAnalysisUITest()
-  {
-    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"));
-  }
-}