*/
package jalview.util;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewportI;
import jalview.commands.CommandI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
/**
* Helper methods for manipulations involving sequence mappings.
*
toSequences, fromGapChar);
}
- for (int[] hidden : hiddencols.getHiddenColumnsCopy())
+ Iterator<int[]> regions = hiddencols.iterator();
+ while (regions.hasNext())
{
- mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
- toSequences, fromGapChar);
+ mapHiddenColumns(regions.next(), codonFrames, newHidden,
+ fromSequences, toSequences, fromGapChar);
}
return; // mappedColumns;
}
int min = Math.min(range[0], range[1]);
int max = Math.max(range[0], range[1]);
-
+
return (min <= queryRange[0] && max >= queryRange[0]
&& min <= queryRange[1] && max >= queryRange[1]);
}
+
+ /**
+ * Removes the specified number of positions from the given ranges. Provided
+ * to allow a stop codon to be stripped from a CDS sequence so that it matches
+ * the peptide translation length.
+ *
+ * @param positions
+ * @param ranges
+ * a list of (single) [start, end] ranges
+ * @return
+ */
+ public static void removeEndPositions(int positions, List<int[]> ranges)
+ {
+ int toRemove = positions;
+ Iterator<int[]> it = new ReverseListIterator<>(ranges);
+ while (toRemove > 0)
+ {
+ int[] endRange = it.next();
+ if (endRange.length != 2)
+ {
+ /*
+ * not coded for [start1, end1, start2, end2, ...]
+ */
+ System.err.println(
+ "MappingUtils.removeEndPositions doesn't handle multiple ranges");
+ return;
+ }
+
+ int length = endRange[1] - endRange[0] + 1;
+ if (length <= 0)
+ {
+ /*
+ * not coded for a reverse strand range (end < start)
+ */
+ System.err.println(
+ "MappingUtils.removeEndPositions doesn't handle reverse strand");
+ return;
+ }
+ if (length > toRemove)
+ {
+ endRange[1] -= toRemove;
+ toRemove = 0;
+ }
+ else
+ {
+ toRemove -= length;
+ it.remove();
+ }
+ }
+ }
+
+ /**
+ * Converts a list of {@code start-end} ranges to a single array of
+ * {@code start1, end1, start2, ... } ranges
+ *
+ * @param ranges
+ * @return
+ */
+ public static int[] rangeListToArray(List<int[]> ranges)
+ {
+ int rangeCount = ranges.size();
+ int[] result = new int[rangeCount * 2];
+ int j = 0;
+ for (int i = 0; i < rangeCount; i++)
+ {
+ int[] range = ranges.get(i);
+ result[j++] = range[0];
+ result[j++] = range[1];
+ }
+ return result;
+ }
}