* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General License for more details.
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General License
+ * You should have received a copy of the GNU General Public License
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
* - null or specific sequence reference
* @param groupRef
* - null or specific group reference
- * @param method
- * - CalcId for the annotation (must match)
*
* @return existing annotation matching the given attributes
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
/**
- * Calculate the visible start and end index of an alignment. The result is
- * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+ * Set the hidden columns collection on the alignment
*
- * @param hiddenCols
- * @return
+ * @param cols
*/
- public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
-
public void setHiddenColumns(HiddenColumns cols);
-
- /**
- * Returns all HMM consensus sequences.
- *
- * @param remove
- * If true, remove all HMM consensus sequences from the alignment.
- * @return
- */
- public List<SequenceI> getHMMConsensusSequences(boolean remove);
/**
* Insert a sequence at a position in an alignment
*
* @param i
- * The idnex of the position.
+ * The index of the position.
* @param snew
* The new sequence.
*/
void insertSequenceAt(int i, SequenceI snew);
-
+ /**
+ * Set the first sequence as representative and hide its insertions. Typically
+ * used when loading JPred files.
+ */
+ public void setupJPredAlignment();
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * sequence in al which sequences are aligned to
+ * @param input
+ * alignment view where sequence corresponding to profileseq is first
+ * entry
+ * @return new HiddenColumns for new alignment view, with insertions into
+ * profileseq marked as hidden.
+ */
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input);
}