* 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.
*/
public interface AlignmentI extends AnnotatedCollectionI
{
/**
- * Calculates the number of sequences in an alignment
+ * Calculates the number of sequences in an alignment, excluding hidden
+ * sequences
*
* @return Number of sequences in alignment
*/
int getHeight();
/**
+ * Calculates the number of sequences in an alignment, including hidden
+ * sequences
+ *
+ * @return Number of sequences in alignment
+ */
+ int getAbsoluteHeight();
+
+ /**
*
* Calculates the maximum width of the alignment, including gaps.
*
boolean isAligned(boolean includeHidden);
/**
+ * Answers if the sequence at alignmentIndex is hidden
+ *
+ * @param alignmentIndex
+ * the index to check
+ * @return true if the sequence is hidden
+ */
+ boolean isHidden(int alignmentIndex);
+
+ /**
* Gets sequences as a Synchronized collection
*
* @return All sequences in alignment.
SequenceI getSequenceAt(int i);
/**
+ * Find a specific sequence in this alignment.
+ *
+ * @param i
+ * Index of required sequence in full alignment, i.e. if all columns
+ * were visible
+ *
+ * @return SequenceI at given index.
+ */
+ SequenceI getSequenceAtAbsoluteIndex(int i);
+
+ /**
* Returns a map of lists of sequences keyed by sequence name.
*
* @return
SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
- * Deletes a sequence from the alignment
+ * Deletes a sequence from the alignment. Updates hidden sequences to account
+ * for the removed sequence. Do NOT use this method to delete sequences which
+ * are just hidden.
*
* @param s
* Sequence to be deleted.
void deleteSequence(SequenceI s);
/**
- * Deletes a sequence from the alignment.
+ * Deletes a sequence from the alignment. Updates hidden sequences to account
+ * for the removed sequence. Do NOT use this method to delete sequences which
+ * are just hidden.
*
* @param i
* Index of sequence to be deleted.
void deleteSequence(int i);
/**
+ * Deletes a sequence in the alignment which has been hidden.
+ *
+ * @param i
+ * Index of sequence to be deleted
+ */
+ void deleteHiddenSequence(int i);
+
+ /**
* Finds sequence in alignment using sequence name as query.
*
* @param name
HiddenSequences getHiddenSequences();
+ HiddenColumns getHiddenColumns();
+
/**
* Compact representation of alignment
*
*/
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.
- *
- * @param hiddenCols
- * @return
- */
- public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+ public void setHiddenColumns(HiddenColumns cols);
+
}