X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FRangetype.java;h=281e8a46952ac58dfef996f6babd557bf68a5068;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=2686e858334d6e348fc1ed3ab8807f53e7b4ddce;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index 2686e85..281e8a4 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -1,35 +1,41 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 java.util.Vector;
 
+import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.Local;
-import uk.ac.vamsas.objects.core.Map;
 import uk.ac.vamsas.objects.core.MapType;
 import uk.ac.vamsas.objects.core.Mapped;
 import uk.ac.vamsas.objects.core.RangeType;
 import uk.ac.vamsas.objects.core.Seg;
-import jalview.datamodel.Mapping;
 import jalview.io.VamsasAppDatastore;
 
-public class Rangetype extends DatastoreItem
+/**
+ * Enhances DatastoreItem objects with additional functions to do with RangeType
+ * objects
+ * 
+ * @author JimP
+ * 
+ */
+public abstract class Rangetype extends DatastoreItem
 {
 
   public Rangetype()
@@ -42,6 +48,16 @@ public class Rangetype extends DatastoreItem
     super(datastore);
   }
 
+  public Rangetype(VamsasAppDatastore datastore, Vobject vobj, Class jvClass)
+  {
+    super(datastore, vobj, jvClass);
+  }
+
+  public Rangetype(VamsasAppDatastore datastore, Object jvobj, Class vClass)
+  {
+    super(datastore, jvobj, vClass);
+  }
+
   /**
    * get real bounds of a RangeType's specification. start and end are an
    * inclusive range within which all segments and positions lie. TODO: refactor
@@ -222,12 +238,10 @@ public class Rangetype extends DatastoreItem
   /**
    * 
    * @param maprange
-   *                where the from range is the local mapped range, and the to
-   *                range is the 'mapped' range in the MapRangeType
-   * @param default
-   *                unit for local
-   * @param default
-   *                unit for mapped
+   *          where the from range is the local mapped range, and the to range
+   *          is the 'mapped' range in the MapRangeType
+   * @param default unit for local
+   * @param default unit for mapped
    * @return MapList
    */
   protected jalview.util.MapList parsemapType(MapType maprange, int localu,
@@ -275,9 +289,8 @@ public class Rangetype extends DatastoreItem
    * @param maprange
    * @param ml
    * @param setUnits
-   * @param reverse -
-   *                reverse MapList mapping for Local and Mapped ranges and
-   *                units
+   * @param reverse
+   *          - reverse MapList mapping for Local and Mapped ranges and units
    */
   protected void initMapType(MapType maprange, jalview.util.MapList ml,
           boolean setUnits, boolean reverse)
@@ -311,6 +324,10 @@ public class Rangetype extends DatastoreItem
         maprange.getLocal().setUnit(ml.getToRatio());
         maprange.getMapped().setUnit(ml.getFromRatio());
       }
+      // TODO: and verify - raise an implementation fault notice if local/mapped
+      // range % Local/Mapped Ratio != 0
+      // if (uk.ac.vamsas.objects.utils.Range.getIntervals(range))
+
     }
   }