Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop

[jalview.git] / src / jalview / io / vamsas / Rangetype.java

diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index c4b817d..08b1b52 100644 (file)
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -1,34 +1,37 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
+
+import java.util.List;
 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.DBRefEntry;
-import jalview.datamodel.Mapping;
-import jalview.io.VamsasAppDatastore;
 
 /**
  * Enhances DatastoreItem objects with additional functions to do with RangeType
@@ -75,8 +78,7 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -134,8 +136,7 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -182,8 +183,7 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (range.getSegCount() > 0 && range.getPosCount() > 0)
       {
-        throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (range.getSegCount() > 0)
       {
@@ -223,15 +223,15 @@ public abstract class Rangetype extends DatastoreItem
    * initialise a range type object from a set of start/end inclusive intervals
    * 
    * @param mrt
-   * @param range
+   * @param ranges
    */
-  protected void initRangeType(RangeType mrt, int[] range)
+  protected void initRangeType(RangeType mrt, List<int[]> ranges)
   {
-    for (int i = 0; i < range.length; i += 2)
+    for (int[] range : ranges)
     {
       Seg vSeg = new Seg();
-      vSeg.setStart(range[i]);
-      vSeg.setEnd(range[i + 1]);
+      vSeg.setStart(range[0]);
+      vSeg.setEnd(range[1]);
       vSeg.setInclusive(true);
       mrt.addSeg(vSeg);
     }
@@ -299,8 +299,7 @@ public abstract class Rangetype extends DatastoreItem
   {
     if (ml == null)
     {
-      throw new Error(
-              "Implementation error. MapList is null for initMapType.");
+      throw new Error(MessageManager.getString("error.implementation_error_maplist_is_null"));
     }
     maprange.setLocal(new Local());
     maprange.setMapped(new Mapped());