X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencefeature.java;h=0525cf91fbac7e85236d9a0d6ead0fa2cd5331ed;hb=cb105dfc09cebd040a202758a3756fdf6c5fa3b6;hp=1348227a20e9c6b491fd74008dc43667d8f3e8e4;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index 1348227..0525cf9 100644
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.io.vamsas;
 
@@ -64,7 +63,8 @@ public class Sequencefeature extends Rangetype
   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
           DataSetAnnotations dseta, SequenceI dsSeq)
   {
-    super(vamsasAppDatastore, dseta, jalview.datamodel.SequenceFeature.class);
+    super(vamsasAppDatastore, dseta,
+            jalview.datamodel.SequenceFeature.class);
     this.dsSeq = dsSeq;
     doJvUpdate();
   }
@@ -90,9 +90,12 @@ public class Sequencefeature extends Rangetype
   public void addFromDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
-    if (dsa.getSeqRefCount()!=1)
+    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;
@@ -107,9 +110,10 @@ public class Sequencefeature extends Rangetype
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
-    replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature to newly created feature
+    replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
+                                      // to newly created feature
     dsSeq.addSequenceFeature(sf); // add new imported feature
-    addToDocument(); // and create a new feature in the document        
+    addToDocument(); // and create a new feature in the document
   }
 
   public void updateToDoc()
@@ -137,6 +141,7 @@ public class Sequencefeature extends Rangetype
     }
 
   }
+
   public void updateFromDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -146,19 +151,26 @@ 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.");
-       // - consider deleting the feature ?
+              .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();
     }
     else
     {
-      // Sync the features to Jalview - easiest to delete and add the feature again
+      // Sync the features to Jalview - easiest to delete and add the feature
+      // again
       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
       dsSeq.deleteFeature(feature);
       replaceJvObjMapping(feature, newsf);
       dsSeq.addSequenceFeature(newsf);
-      feature.otherDetails.clear();
+      if (feature.otherDetails != null)
+      {
+        // TODO later: leave this to finalise method ?
+        feature.otherDetails.clear();
+      }
     }
   }
 
@@ -167,10 +179,9 @@ public class Sequencefeature extends Rangetype
    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
    * 
    * @param dsa
-   *                (typically DataSetAnnotations or
-   *                AlignmentSequenceAnnotation)
+   *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
    * @param feature
-   *                (the feature to be mapped from)
+   *          (the feature to be mapped from)
    * @return
    */
   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
@@ -197,15 +208,14 @@ public class Sequencefeature extends Rangetype
       {
         String link = (String) feature.links.elementAt(i);
         UrlLink ulink = new UrlLink(link);
-        /*
-         * int sep = link.indexOf('|'); if (sep > -1) { Link vLink = new Link();
-         * if (sep > 0) { vLink.setContent(link.substring(0, sep - 1)); } else {
-         * vLink.setContent(""); } vLink.setHref(link.substring(sep + 1)); //
-         * TODO: validate href. dsa.addLink(vLink); }
-         */
-        Link vLink = new Link();
-        vLink.setContent(ulink.getLabel());
-        vLink.setHref(ulink.getUrl_prefix());
+        if (ulink.isValid())
+        {
+          // We only add static links to the document.
+          Link vLink = new Link();
+          vLink.setContent(ulink.getLabel());
+          vLink.setHref(ulink.getTarget());
+          dsa.addLink(vLink);
+        }
       }
     }
     dsa.setGroup(feature.getFeatureGroup());
@@ -240,8 +250,7 @@ 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)
           {
@@ -265,21 +274,23 @@ public class Sequencefeature extends Rangetype
     }
     return dsa;
   }
+
   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());
+    SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+            dseta.getType(), dseta.getDescription(), dseta.getStatus(),
+            se[0], se[1], dseta.getGroup());
     if (dseta.getLinkCount() > 0)
     {
       Link[] links = dseta.getLink();
       for (int i = 0; i < links.length; i++)
       {
+        // TODO: use URLLink parsing/validation here.
         sf.addLink(links[i].getContent() + "|" + links[i].getHref());
       }
     }
-    if (dseta.getScoreCount()>0)
+    if (dseta.getScoreCount() > 0)
     {
       Enumeration scr = dseta.enumerateScore();
       while (scr.hasMoreElements())
@@ -288,8 +299,10 @@ public class Sequencefeature extends Rangetype
         if (score.getName().equals(sf.getType()))
         {
           sf.setScore(score.getContent());
-        } else {
-          sf.setValue(score.getName(), ""+score.getContent());
+        }
+        else
+        {
+          sf.setValue(score.getName(), "" + score.getContent());
         }
       }
     }
@@ -299,36 +312,41 @@ public class Sequencefeature extends Rangetype
     {
       Property p = (Property) props.nextElement();
       Object val = null;
-      if (Properties.isValid(p)) 
+      if (Properties.isValid(p))
       {
         if (Properties.isString(p))
         {
-        val = p.getContent();
+          val = p.getContent();
         }
         if (Properties.isBoolean(p))
         {
-          try {
+          try
+          {
             val = new Boolean(p.getContent());
-          } catch (Exception e) {}
+          } catch (Exception e)
+          {
+          }
         }
         if (Properties.isFloat(p))
         {
-          try {
-              val = new Float(p.getContent());
-              
-            } catch (Exception e)
-            {
-            }
+          try
+          {
+            val = new Float(p.getContent());
+
+          } catch (Exception e)
+          {
           }
-        if(Properties.isInteger(p))
+        }
+        if (Properties.isInteger(p))
         {
-          try {
-                val = new Integer(p.getContent());
+          try
+          {
+            val = new Integer(p.getContent());
           } catch (Exception e)
           {
-              } 
+          }
         }
-        if (val!=null)
+        if (val != null)
         {
           sf.setValue(p.getName(), val);
         }