X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FRangetype.java;h=ee4fa8306092c72a4db5d85cd237ffdf41531d27;hb=07c06919a5e944dd12f751a5f23bcb79887cc11e;hp=e7f8cf28a5a6c81fd13d85e19e4cbb06f5a5fdc2;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index e7f8cf2..ee4fa83 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -20,6 +20,10 @@
  */
 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;
@@ -28,8 +32,6 @@ 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.io.VamsasAppDatastore;
-import jalview.util.MessageManager;
 
 /**
  * Enhances DatastoreItem objects with additional functions to do with RangeType
@@ -51,7 +53,8 @@ public abstract class Rangetype extends DatastoreItem
     super(datastore);
   }
 
-  public Rangetype(VamsasAppDatastore datastore, Vobject vobj, Class jvClass)
+  public Rangetype(VamsasAppDatastore datastore, Vobject vobj,
+          Class jvClass)
   {
     super(datastore, vobj, jvClass);
   }
@@ -76,7 +79,8 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+        throw new Error(MessageManager.getString(
+                "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -99,8 +103,7 @@ public abstract class Rangetype extends DatastoreItem
         // could do a polarity for pos range too. and pass back indication of
         // discontinuities.
         int pos = dseta.getPos(0).getI();
-        se = new int[]
-        { pos, pos };
+        se = new int[] { pos, pos };
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
@@ -134,7 +137,8 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+        throw new Error(MessageManager.getString(
+                "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -181,7 +185,8 @@ public abstract class Rangetype extends DatastoreItem
       int[] se = null;
       if (range.getSegCount() > 0 && range.getPosCount() > 0)
       {
-        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+        throw new Error(MessageManager.getString(
+                "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (range.getSegCount() > 0)
       {
@@ -221,15 +226,15 @@ 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);
     }
@@ -240,8 +245,10 @@ public abstract 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
+   * @param default
+   *          unit for local
+   * @param default
+   *          unit for mapped
    * @return MapList
    */
   protected jalview.util.MapList parsemapType(MapType maprange, int localu,
@@ -252,8 +259,9 @@ public abstract class Rangetype extends DatastoreItem
     int[] mappedRange = getIntervals(maprange.getMapped());
     long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
             : localu;
-    long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
-            .getUnit() : mappedu;
+    long mu = maprange.getMapped().hasUnit()
+            ? maprange.getMapped().getUnit()
+            : mappedu;
     ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
             (int) mu);
     return ml;
@@ -297,7 +305,8 @@ public abstract class Rangetype extends DatastoreItem
   {
     if (ml == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_maplist_is_null"));
+      throw new Error(MessageManager
+              .getString("error.implementation_error_maplist_is_null"));
     }
     maprange.setLocal(new Local());
     maprange.setMapped(new Mapped());