/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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 Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.datamodel;
public int getWidth();
/**
- * Calculates if this set of sequences is all the same length
+ * Calculates if this set of sequences (visible and invisible) are all the
+ * same length
*
* @return true if all sequences in alignment are the same length
*/
public boolean isAligned();
/**
+ * Calculates if this set of sequences is all the same length
+ *
+ * @param includeHidden
+ * optionally exclude hidden sequences from test
+ * @return true if all (or just visible) sequences are the same length
+ */
+ public boolean isAligned(boolean includeHidden);
+
+ /**
* Gets sequences as a Vector
*
* @return All sequences in alignment.
* Find a specific sequence in this alignment.
*
* @param i
- * Index of required sequence.
+ * Index of required sequence.
*
* @return SequenceI at given index.
*/
* Add a new sequence to this alignment.
*
* @param seq
- * New sequence will be added at end of alignment.
+ * New sequence will be added at end of alignment.
*/
public void addSequence(SequenceI seq);
* Used to set a particular index of the alignment with the given sequence.
*
* @param i
- * Index of sequence to be updated.
+ * Index of sequence to be updated.
* @param seq
- * New sequence to be inserted.
+ * New sequence to be inserted.
*/
public void setSequenceAt(int i, SequenceI seq);
* Deletes a sequence from the alignment
*
* @param s
- * Sequence to be deleted.
+ * Sequence to be deleted.
*/
public void deleteSequence(SequenceI s);
* Deletes a sequence from the alignment.
*
* @param i
- * Index of sequence to be deleted.
+ * Index of sequence to be deleted.
*/
public void deleteSequence(int i);
* Finds sequence in alignment using sequence name as query.
*
* @param name
- * Id of sequence to search for.
+ * Id of sequence to search for.
*
* @return Sequence matching query, if found. If not found returns null.
*/
* Finds index of a given sequence in the alignment.
*
* @param s
- * Sequence to look for.
+ * Sequence to look for.
*
* @return Index of sequence within the alignment or -1 if not found
*/
* Finds group that given sequence is part of.
*
* @param s
- * Sequence in alignment.
+ * Sequence in alignment.
*
* @return First group found for sequence. WARNING : Sequences may be members
* of several groups. This method is incomplete.
* Finds all groups that a given sequence is part of.
*
* @param s
- * Sequence in alignment.
+ * Sequence in alignment.
*
* @return All groups containing given sequence.
*/
* Adds a new SequenceGroup to this alignment.
*
* @param sg
- * New group to be added.
+ * New group to be added.
*/
public void addGroup(SequenceGroup sg);
* Deletes a specific SequenceGroup
*
* @param g
- * Group will be deleted from alignment.
+ * Group will be deleted from alignment.
*/
public void deleteGroup(SequenceGroup g);
* moves annotation to a specified index in alignment annotation display stack
*
* @param aa
- * the annotation object to be moved
+ * the annotation object to be moved
* @param index
- * the destination position
+ * the destination position
*/
public void setAnnotationIndex(AlignmentAnnotation aa, int index);
/**
* Deletes a specific AlignmentAnnotation from the alignment, and removes its
- * reference from any SequenceI object's annotation if and only if aa is
- * contained within the alignment's annotation vector. Otherwise, it will do
- * nothing.
+ * reference from any SequenceI or SequenceGroup object's annotation if and
+ * only if aa is contained within the alignment's annotation vector.
+ * Otherwise, it will do nothing.
*
* @param aa
- * the annotation to delete
+ * the annotation to delete
* @return true if annotation was deleted from this alignment.
*/
public boolean deleteAnnotation(AlignmentAnnotation aa);
/**
- * Get the annotation associated with this alignment
+ * Deletes a specific AlignmentAnnotation from the alignment, and optionally
+ * removes any reference from any SequenceI or SequenceGroup object's
+ * annotation if and only if aa is contained within the alignment's annotation
+ * vector. Otherwise, it will do nothing.
+ *
+ * @param aa
+ * the annotation to delete
+ * @param unhook
+ * flag indicating if any references should be removed from
+ * annotation - use this if you intend to add the annotation back
+ * into the alignment
+ * @return true if annotation was deleted from this alignment.
+ */
+ public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
+
+ /**
+ * Get the annotation associated with this alignment (this can be null if no
+ * annotation has ever been created on the alignment)
*
* @return array of AlignmentAnnotation objects
*/
* Change the gap character used in this alignment to 'gc'
*
* @param gc
- * the new gap character.
+ * the new gap character.
*/
public void setGapCharacter(char gc);
public boolean isNucleotide();
/**
+ * Test if alignment contains RNA structure
+ *
+ * @return true if RNA structure AligmnentAnnotation was added to alignment
+ */
+ public boolean hasRNAStructure();
+
+ /**
* Set alignment to be a nucleotide sequence
*
*/
* Set the associated dataset for the alignment, or create one.
*
* @param dataset
- * The dataset alignment or null to construct one.
+ * The dataset alignment or null to construct one.
*/
public void setDataset(Alignment dataset);
* find sequence with given name in alignment
*
* @param token
- * name to find
+ * name to find
* @param b
- * true implies that case insensitive matching will
- * <em>also</em> be tried
+ * true implies that case insensitive matching will <em>also</em> be
+ * tried
* @return matched sequence or null
*/
public SequenceI findName(String token, boolean b);
* sequence
*
* @param startAfter
- * the sequence after which the search will be started (usually
- * the result of the last call to findName)
+ * the sequence after which the search will be started (usually the
+ * result of the last call to findName)
* @param token
- * name to find
+ * name to find
* @param b
- * true implies that case insensitive matching will
- * <em>also</em> be tried
+ * true implies that case insensitive matching will <em>also</em> be
+ * tried
* @return matched sequence or null
*/
public SequenceI findName(SequenceI startAfter, String token, boolean b);
/**
- * find first sequence in alignment which is involved in the given search result object
+ * find first sequence in alignment which is involved in the given search
+ * result object
+ *
* @param results
* @return -1 or index of sequence in alignment
*/
/**
* append sequences and annotation from another alignment object to this one.
- * Note: this is a straight transfer of object references, and may result in
- * toappend's dependent data being transformed to fit the alignment (changing gap characters, etc...).
- * If you are uncertain, use the copy Alignment copy constructor to create a new version
- * which can be appended without side effect.
- * @param toappend - the alignment to be appended.
+ * Note: this is a straight transfer of object references, and may result in
+ * toappend's dependent data being transformed to fit the alignment (changing
+ * gap characters, etc...). If you are uncertain, use the copy Alignment copy
+ * constructor to create a new version which can be appended without side
+ * effect.
+ *
+ * @param toappend
+ * - the alignment to be appended.
*/
public void append(AlignmentI toappend);
+
/**
- * Justify the sequences to the left or right by deleting and inserting gaps before the initial residue or after the terminal residue
- * @param right true if alignment padded to right, false to justify to left
- * @return true if alignment was changed
- * TODO: return undo object
+ * Justify the sequences to the left or right by deleting and inserting gaps
+ * before the initial residue or after the terminal residue
+ *
+ * @param right
+ * true if alignment padded to right, false to justify to left
+ * @return true if alignment was changed TODO: return undo object
*/
public boolean justify(boolean right);
/**
* add given annotation row at given position (0 is start, -1 is end)
+ *
* @param consensus
* @param i
*/
git://source.jalview.org / jalview.git / blobdiff