X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=33decb4b838da9dec3f5dbe496dcdafc6d9c3d9d;hp=4e07a08ba6c739402fa7f10389b05a4889ca3a28;hb=217bacee24ea08305c3187a0c54bbaf867e25082;hpb=34524f89f84e7d9b85743300a6407aa1c0e2751a diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java index 4e07a08..33decb4 100644 --- a/src/jalview/util/MappingUtils.java +++ b/src/jalview/util/MappingUtils.java @@ -29,6 +29,7 @@ import java.util.Map; import jalview.analysis.AlignmentSorter; import jalview.api.AlignViewportI; +import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -78,7 +79,7 @@ public final class MappingUtils action = action.getUndoAction(); } // TODO write this - System.err.println("MappingUtils.mapCutOrPaste not yet implemented"); + Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented"); } /** @@ -835,7 +836,7 @@ 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 +992,7 @@ 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 +1003,7 @@ 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 +1040,66 @@ 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