X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=590e1c538278342b8c4a25af6c6933a0d70e48af;hb=0aa7f6fab658c9a203b410d4bead72217da5c9a0;hp=c8b5190865ab4ad30dc479ed73e1dbba0751b5a7;hpb=b26fefd329b60deb2025aa28cdbaae30bfb58382;p=jalview.git diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java index c8b5190..590e1c5 100644 --- a/src/jalview/util/MappingUtils.java +++ b/src/jalview/util/MappingUtils.java @@ -835,7 +835,7 @@ public final class MappingUtils { if (range.length % 2 != 0) { - System.err.println( + Cache.log.error( "Error unbalance start/end ranges: " + ranges.toString()); return 0; } @@ -991,7 +991,7 @@ public final class MappingUtils /* * not coded for [start1, end1, start2, end2, ...] */ - System.err.println( + Cache.log.error( "MappingUtils.removeEndPositions doesn't handle multiple ranges"); return; } @@ -1002,7 +1002,7 @@ public final class MappingUtils /* * not coded for a reverse strand range (end < start) */ - System.err.println( + Cache.log.error( "MappingUtils.removeEndPositions doesn't handle reverse strand"); return; } @@ -1039,4 +1039,66 @@ public final class MappingUtils } return result; } + + /* + * Returns the maximal start-end positions in the given (ordered) list of + * ranges which is overlapped by the given begin-end range, or null if there + * is no overlap. + * + *
+ * Examples: + * if ranges is {[4, 8], [10, 12], [16, 19]} + * then + * findOverlap(ranges, 1, 20) == [4, 19] + * findOverlap(ranges, 6, 11) == [6, 11] + * findOverlap(ranges, 9, 15) == [10, 12] + * findOverlap(ranges, 13, 15) == null + *+ * + * @param ranges + * @param begin + * @param end + * @return + */ + protected static int[] findOverlap(List