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JAL-3210 removed 'all' core due to problems
[jalview.git]
/
src
/
jalview
/
util
/
MapList.java
diff --git
a/src/jalview/util/MapList.java
b/src/jalview/util/MapList.java
index
c944345
..
731e976
100644
(file)
--- a/
src/jalview/util/MapList.java
+++ b/
src/jalview/util/MapList.java
@@
-116,8
+116,17
@@
public class MapList
{
int hashCode = 31 * fromRatio;
hashCode = 31 * hashCode + toRatio;
{
int hashCode = 31 * fromRatio;
hashCode = 31 * hashCode + toRatio;
- hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
- hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+ for (int[] shift : fromShifts)
+ {
+ hashCode = 31 * hashCode + shift[0];
+ hashCode = 31 * hashCode + shift[1];
+ }
+ for (int[] shift : toShifts)
+ {
+ hashCode = 31 * hashCode + shift[0];
+ hashCode = 31 * hashCode + shift[1];
+ }
+
return hashCode;
}
return hashCode;
}
@@
-318,6
+327,13
@@
public class MapList
fromHighest = Integer.MIN_VALUE;
for (int[] range : fromRange)
{
fromHighest = Integer.MIN_VALUE;
for (int[] range : fromRange)
{
+ if (range.length != 2)
+ {
+ // throw new IllegalArgumentException(range);
+ System.err.println(
+ "Invalid format for fromRange " + Arrays.toString(range)
+ + " may cause errors");
+ }
fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
fromHighest = Math.max(fromHighest, Math.max(range[0], range[1]));
}
fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
fromHighest = Math.max(fromHighest, Math.max(range[0], range[1]));
}
@@
-326,6
+342,13
@@
public class MapList
toHighest = Integer.MIN_VALUE;
for (int[] range : toRange)
{
toHighest = Integer.MIN_VALUE;
for (int[] range : toRange)
{
+ if (range.length != 2)
+ {
+ // throw new IllegalArgumentException(range);
+ System.err.println("Invalid format for toRange "
+ + Arrays.toString(range)
+ + " may cause errors");
+ }
toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
}
toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
}
@@
-1194,14
+1217,33
@@
public class MapList
for (int[] range : getToRanges())
{
int[] transferred = map.locateInTo(range[0], range[1]);
for (int[] range : getToRanges())
{
int[] transferred = map.locateInTo(range[0], range[1]);
- if (transferred == null)
+ if (transferred == null || transferred.length % 2 != 0)
{
return null;
}
{
return null;
}
- toRanges.add(transferred);
+
+ /*
+ * convert [start1, end1, start2, end2, ...]
+ * to [[start1, end1], [start2, end2], ...]
+ */
+ for (int i = 0; i < transferred.length;)
+ {
+ toRanges.add(new int[] { transferred[i], transferred[i + 1] });
+ i += 2;
+ }
}
return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
}
}
return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);
}
+ /**
+ * Answers true if the mapping is from one contiguous range to another, else
+ * false
+ *
+ * @return
+ */
+ public boolean isContiguous()
+ {
+ return fromShifts.size() == 1 && toShifts.size() == 1;
+ }
}
}