X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencefeature.java;h=f8d86d55fef62123725f3d29cb75c9f36439dbaa;hb=3027bfb4b1b13af8686abcd419888e03141bd672;hp=f02fe3ef7ab000fdb582deb3c08301d97b9c4416;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index f02fe3e..f8d86d5 100644
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -1,26 +1,35 @@
 /*
- * 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 <http://www.gnu.org/licenses/>.
+ * 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.io.vamsas;
 
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.UrlLink;
+
 import java.util.Enumeration;
+import java.util.Iterator;
 import java.util.Vector;
 
-import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DataSetAnnotations;
 import uk.ac.vamsas.objects.core.Link;
 import uk.ac.vamsas.objects.core.Property;
@@ -28,13 +37,7 @@ import uk.ac.vamsas.objects.core.Provenance;
 import uk.ac.vamsas.objects.core.RangeAnnotation;
 import uk.ac.vamsas.objects.core.Score;
 import uk.ac.vamsas.objects.core.Seg;
-import uk.ac.vamsas.objects.core.Sequence;
 import uk.ac.vamsas.objects.utils.Properties;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.UrlLink;
 
 /**
  * @author JimP
@@ -69,6 +72,7 @@ public class Sequencefeature extends Rangetype
     doJvUpdate();
   }
 
+  @Override
   public void addToDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -87,15 +91,14 @@ public class Sequencefeature extends Rangetype
     dataset.addDataSetAnnotations(dsa);
   }
 
+  @Override
   public void addFromDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
     if (dsa.getSeqRefCount() != 1)
     {
-      Cache.log
-              .warn("Not binding "
-                      + dsa.getVorbaId()
-                      + " to Sequence Feature - has multiple dataset sequence references.");
+      Cache.log.warn("Not binding " + dsa.getVorbaId()
+              + " to Sequence Feature - has multiple dataset sequence references.");
       return;
     }
     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
@@ -104,6 +107,7 @@ public class Sequencefeature extends Rangetype
     bindjvvobj(sf, dsa);
   }
 
+  @Override
   public void conflict()
   {
     log.warn("Untested sequencefeature conflict code");
@@ -116,6 +120,7 @@ public class Sequencefeature extends Rangetype
     addToDocument(); // and create a new feature in the document
   }
 
+  @Override
   public void updateToDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -123,8 +128,8 @@ public class Sequencefeature extends Rangetype
     if (dsa.getSeqRefCount() != 1)
     {
       replaceJvObjMapping(feature, null);
-      Cache.log
-              .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
+      Cache.log.warn(
+              "Binding of annotation to jalview feature has changed. Removing binding and recreating.");
       doSync(); // re-verify bindings.
     }
     else
@@ -142,6 +147,7 @@ public class Sequencefeature extends Rangetype
 
   }
 
+  @Override
   public void updateFromDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -150,10 +156,8 @@ public class Sequencefeature extends Rangetype
     {
       // conflicting update from document - we cannot map this feature anymore.
       replaceJvObjMapping(feature, null);
-      Cache.log
-              .warn("annotation ("
-                      + dsa.getVorbaId()
-                      + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
+      Cache.log.warn("annotation (" + dsa.getVorbaId()
+              + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
       // - consider deleting the feature ?
       dsSeq.deleteFeature(feature);
       // doSync();
@@ -194,19 +198,18 @@ public class Sequencefeature extends Rangetype
     vSeg.setInclusive(true);
     if (dsa.getSegCount() > 1)
     {
-      Cache.log
-              .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+      Cache.log.debug(
+              "About to destroy complex annotation in vamsas document mapped to sequence feature ("
                       + dsa.getVorbaId() + ")");
     }
-    dsa.setSeg(new Seg[]
-    { vSeg });
+    dsa.setSeg(new Seg[] { vSeg });
     dsa.setDescription(feature.getDescription());
     dsa.setStatus(feature.getStatus());
     if (feature.links != null && feature.links.size() > 0)
     {
       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
       {
-        String link = (String) feature.links.elementAt(i);
+        String link = feature.links.elementAt(i);
         UrlLink ulink = new UrlLink(link);
         if (ulink.isValid())
         {
@@ -219,21 +222,20 @@ public class Sequencefeature extends Rangetype
       }
     }
     dsa.setGroup(feature.getFeatureGroup());
-    if (feature.getScore() != Float.NaN)
+    if (!Float.isNaN(feature.getScore()))
     {
       Score fscore = new Score();
-      dsa.setScore(new Score[]
-      { fscore });
+      dsa.setScore(new Score[] { fscore });
       fscore.setContent(feature.getScore());
       fscore.setName(feature.getType());
     }
     if (feature.otherDetails != null)
     {
-      Enumeration iter = feature.otherDetails.keys();
+      Iterator<String> iter = feature.otherDetails.keySet().iterator();
       Vector props = dsa.getPropertyAsReference();
-      while (iter.hasMoreElements())
+      while (iter.hasNext())
       {
-        String key = (String) iter.nextElement();
+        String key = iter.next();
         if (!key.equalsIgnoreCase("score")
                 && !key.equalsIgnoreCase("status"))
         {
@@ -250,7 +252,8 @@ public class Sequencefeature extends Rangetype
           else if (vlu instanceof Integer)
           {
             valid = true;
-            nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
+            nprop.setType(
+                    uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
           }
           else if (vlu instanceof Float)
           {
@@ -278,9 +281,39 @@ public class Sequencefeature extends Rangetype
   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
   {
     int[] se = getBounds(dseta);
-    SequenceFeature sf = new jalview.datamodel.SequenceFeature(
-            dseta.getType(), dseta.getDescription(), dseta.getStatus(),
-            se[0], se[1], dseta.getGroup());
+
+    /*
+     * try to identify feature score
+     */
+    boolean scoreFound = false;
+    float theScore = 0f;
+    String featureType = dseta.getType();
+    if (dseta.getScoreCount() > 0)
+    {
+      Enumeration scr = dseta.enumerateScore();
+      while (scr.hasMoreElements())
+      {
+        Score score = (Score) scr.nextElement();
+        if (score.getName().equals(featureType))
+        {
+          theScore = score.getContent();
+          scoreFound = true;
+        }
+      }
+    }
+
+    SequenceFeature sf = null;
+    if (scoreFound)
+    {
+      sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
+              se[1], theScore, dseta.getGroup());
+    }
+    else
+    {
+      sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
+              se[1], dseta.getGroup());
+    }
+    sf.setStatus(dseta.getStatus());
     if (dseta.getLinkCount() > 0)
     {
       Link[] links = dseta.getLink();
@@ -296,11 +329,7 @@ public class Sequencefeature extends Rangetype
       while (scr.hasMoreElements())
       {
         Score score = (Score) scr.nextElement();
-        if (score.getName().equals(sf.getType()))
-        {
-          sf.setScore(score.getContent());
-        }
-        else
+        if (!score.getName().equals(sf.getType()))
         {
           sf.setValue(score.getName(), "" + score.getContent());
         }
@@ -322,7 +351,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Boolean(p.getContent());
+            val = Boolean.valueOf(p.getContent());
           } catch (Exception e)
           {
           }
@@ -331,7 +360,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Float(p.getContent());
+            val = Float.valueOf(p.getContent());
 
           } catch (Exception e)
           {
@@ -341,7 +370,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Integer(p.getContent());
+            val = Integer.valueOf(p.getContent());
           } catch (Exception e)
           {
           }