JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

[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 a83a34f..bd25c62 100644 (file)
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,11 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Console;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
+
+import java.util.List;
 import java.util.Vector;
 
 import uk.ac.vamsas.client.Vobject;
@@ -28,8 +33,6 @@ 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 +54,8 @@ 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 +80,8 @@ 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 +104,7 @@ 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 +138,8 @@ 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)
       {
@@ -144,7 +149,7 @@ public abstract class Rangetype extends DatastoreItem
           int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
           for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
           {
-            posList.add(new Integer(p));
+            posList.add(Integer.valueOf(p));
           }
         }
       }
@@ -155,7 +160,7 @@ public abstract class Rangetype extends DatastoreItem
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
-          posList.add(new Integer(pos));
+          posList.add(Integer.valueOf(pos));
         }
       }
     }
@@ -181,15 +186,16 @@ 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)
       {
         for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)
         {
           se = getSegRange(range.getSeg(s), false);
-          posList.addElement(new Integer(se[0]));
-          posList.addElement(new Integer(se[1]));
+          posList.addElement(Integer.valueOf(se[0]));
+          posList.addElement(Integer.valueOf(se[1]));
         }
       }
       else if (range.getPosCount() > 0)
@@ -199,8 +205,8 @@ public abstract class Rangetype extends DatastoreItem
         for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
         {
           pos = range.getPos(p).getI();
-          posList.add(new Integer(pos));
-          posList.add(new Integer(pos));
+          posList.add(Integer.valueOf(pos));
+          posList.add(Integer.valueOf(pos));
         }
       }
     }
@@ -221,15 +227,15 @@ 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 +246,10 @@ 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 +260,9 @@ 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;
@@ -263,8 +272,7 @@ public abstract class Rangetype extends DatastoreItem
   {
     if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
     {
-      jalview.bin.Cache.log
-              .warn("using default mapping length of 1:1 for map "
+      Console.warn("using default mapping length of 1:1 for map "
                       + (map.isRegistered() ? map.getVorbaId().toString()
                               : ("<no Id registered> " + map.toString())));
     }
@@ -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(
+              "Implementation error. MapList is null for initMapType.");
     }
     maprange.setLocal(new Local());
     maprange.setMapped(new Mapped());