+ mappedColumns.hideColumns(mappedTo[0] - 1, mappedTo[1] - 1);
+ }
+ }
+ }
+
+ /**
+ * Helper method to map one column selection
+ *
+ * @param col
+ * the column number (base 0)
+ * @param mappings
+ * the sequence mappings
+ * @param mappedColumns
+ * the mapped column selections to add to
+ * @param fromSequences
+ * @param toSequences
+ * @param fromGapChar
+ */
+ protected static void mapColumn(int col,
+ List<AlignedCodonFrame> mappings,
+ ColumnSelection mappedColumns, List<SequenceI> fromSequences,
+ List<SequenceI> toSequences, char fromGapChar)
+ {
+ int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
+ toSequences, fromGapChar);
+
+ /*
+ * Add the range of mapped columns to the mapped selection (converting
+ * base 1 to base 0). Note that this may include intron-only regions which
+ * lie between the start and end ranges of the selection.
+ */
+ if (mappedTo != null)
+ {
+ for (int i = mappedTo[0]; i <= mappedTo[1]; i++)
+ {
+ mappedColumns.addElement(i - 1);
+ }
+ }
+ }
+
+ /**
+ * Helper method to find the range of columns mapped to from one column.
+ * Returns the maximal range of columns mapped to from all sequences in the
+ * source column, or null if no mappings were found.
+ *
+ * @param col
+ * @param mappings
+ * @param fromSequences
+ * @param toSequences
+ * @param fromGapChar
+ * @return
+ */
+ protected static int[] findMappedColumns(int col,
+ List<AlignedCodonFrame> mappings, List<SequenceI> fromSequences,
+ List<SequenceI> toSequences, char fromGapChar)
+ {
+ int[] mappedTo = new int[] { Integer.MAX_VALUE, Integer.MIN_VALUE };
+ boolean found = false;
+
+ /*
+ * For each sequence in the 'from' alignment
+ */
+ for (SequenceI fromSeq : fromSequences)
+ {
+ /*
+ * Ignore gaps (unmapped anyway)
+ */
+ if (fromSeq.getCharAt(col) == fromGapChar)
+ {
+ continue;
+ }
+
+ /*
+ * Get the residue position and find the mapped position.
+ */
+ int residuePos = fromSeq.findPosition(col);
+ SearchResults sr = buildSearchResults(fromSeq, residuePos,
+ mappings);
+ for (Match m : sr.getResults())
+ {
+ int mappedStartResidue = m.getStart();
+ int mappedEndResidue = m.getEnd();
+ SequenceI mappedSeq = m.getSequence();