off by one for sequence associated annotation

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

diff --git a/src/jalview/ws/jws2/AAConsClient.java b/src/jalview/ws/jws2/AAConsClient.java
index c90f5c4..c565915 100644 (file)
--- a/src/jalview/ws/jws2/AAConsClient.java
+++ b/src/jalview/ws/jws2/AAConsClient.java
@@ -2,7 +2,6 @@ package jalview.ws.jws2;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
 import jalview.ws.jws2.dm.AAConsSettings;
@@ -10,9 +9,9 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.TreeSet;
 
 import compbio.data.sequence.Score;
@@ -29,19 +28,27 @@ public class AAConsClient extends JabawsAlignCalcWorker
     alignedSeqs = true;
     nucleotidesAllowed = false;
     proteinAllowed = true;
-    gapMap=new boolean[0];
+    gapMap = new boolean[0];
     initViewportParams();
   }
 
   protected void initViewportParams()
   {
-    ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(getCalcId(), new AAConsSettings(true, service, this.preset, (arguments!=null) ?  JabaParamStore.getJwsArgsfromJaba(arguments) : null), true);
+    ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+            getCalcId(),
+            new AAConsSettings(true, service, this.preset,
+                    (arguments != null) ? JabaParamStore
+                            .getJwsArgsfromJaba(arguments) : null), true);
   }
+
   @Override
-  public void updateParameters(WsParamSetI newpreset, java.util.List<Argument> newarguments) {
+  public void updateParameters(WsParamSetI newpreset,
+          java.util.List<Argument> newarguments)
+  {
     super.updateParameters(newpreset, newarguments);
     initViewportParams();
   };
+
   public String getServiceActionText()
   {
     return "calculating Amino acid consensus using AACons service";
@@ -56,16 +63,12 @@ public class AAConsClient extends JabawsAlignCalcWorker
   {
     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
     {
-      AlignmentAnnotation annotation;
       Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
       int alWidth = alignViewport.getAlignment().getWidth();
-      AlignmentI alignment;
-      int ann = (alignment = alignViewport.getAlignment())
-              .getAlignmentAnnotation().length;
       ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
       for (String score : scoremap.keySet())
       {
-        TreeSet<Score> scores = scoremap.get(score);
+        Set<Score> scores = scoremap.get(score);
         for (Score scr : scores)
         {
           if (scr.getRanges() != null && scr.getRanges().size() > 0)
@@ -82,98 +85,30 @@ public class AAConsClient extends JabawsAlignCalcWorker
           }
           else
           {
-            // simple annotation row
-            annotation = alignViewport.getAlignment()
-                    .findOrCreateAnnotation(scr.getMethod(), getCalcId(), true,
-                            null, null);
-
-            Annotation[] elm = new Annotation[alWidth];
-            if (alWidth == gapMap.length) // scr.getScores().size())
-            {
-              Iterator<Float> vals = scr.getScores().iterator();
-              float m = 0f, x = 0f;
-              for (int i = 0; vals.hasNext(); i++)
-              {
-                float val = vals.next().floatValue();
-                if (i == 0)
-                {
-                  m = val;
-                  x = val;
-                }
-                else
-                {
-                  if (m > val)
-                  {
-                    m = val;
-                  }
-                  ;
-                  if (x < val)
-                  {
-                    x = val;
-                  }
-                }
-                // if we're at a gapped column then skip to next ungapped position
-                if (gapMap != null && gapMap.length > 0)
-                {
-                  while (!gapMap[i])
-                  {
-                    elm[i++]=new Annotation("", "" , ' ', Float.NaN);
-                  }
-                }
-                elm[i] = new Annotation("", "" + val, ' ', val);
-              }
-
-              annotation.annotations = elm;
-              annotation.belowAlignment = true;
-              if (x < 0)
-              {
-                x = 0;
-              }
-              x += (x - m) * 0.1;
-              annotation.graphMax = x;
-              annotation.graphMin = m;
-              annotation.validateRangeAndDisplay();
-              ourAnnot.add(annotation);
-            }
+            createAnnotationRowsForScores(ourAnnot, getCalcId(), alWidth,
+                    scr);
           }
         }
       }
+
       if (ourAnnot.size() > 0)
       {
-        List<AlignmentAnnotation> our = ourAnnots;
-        ourAnnots = ourAnnot;
-        if (our != null)
-        {
-          if (our.size() > 0)
-          {
-            for (AlignmentAnnotation an : our)
-            {
-              if (!ourAnnots.contains(an))
-              {
-                // remove the old annotation
-                alignment.deleteAnnotation(an);
-              }
-            }
-          }
-          our.clear();
-        }
-      }
-      // if (ann !=
-      // alignViewport.getAlignment().getAlignmentAnnotation().length)
-      {
-        ap.adjustAnnotationHeight();
+        updateOurAnnots(ourAnnot);
       }
-      /*
-       * else { ap.paintAlignment(true); }
-       */
     }
   }
 
-  public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
+  public String getCalcId()
   {
-    // List<AlignmentAnnotation>
-    // ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
-    // TODO Auto-generated method stub
+    return SequenceAnnotationWSClient.AAConsCalcId;
+  }
 
+  public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
+  {
+    for (AlignmentAnnotation aa : alignPanel.getAlignment().findAnnotation(
+            SequenceAnnotationWSClient.AAConsCalcId))
+    {
+      alignPanel.getAlignment().deleteAnnotation(aa);
+    }
   }
 }