/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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.
- *
- * 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 - 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 file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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;
import java.util.*;
-/** Data structure to hold and manipulate a multiple sequence alignment
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
*/
public interface AlignmentI
{
/**
- * Calculates the number of sequences in an alignment
- *
+ * Calculates the number of sequences in an alignment
+ *
* @return Number of sequences in alignment
*/
public int getHeight();
/**
* Calculates the maximum width of the alignment, including gaps.
- *
+ *
* @return Greatest sequence length within alignment.
*/
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.
*/
public Vector getSequences();
/**
* Gets sequences as a SequenceI[]
- *
+ *
* @return All sequences in alignment.
*/
public SequenceI[] getSequencesArray();
/**
* Find a specific sequence in this alignment.
- *
- * @param i Index of required sequence.
- *
+ *
+ * @param i
+ * Index of required sequence.
+ *
* @return SequenceI at given index.
*/
public SequenceI getSequenceAt(int i);
/**
* Add a new sequence to this alignment.
- *
- * @param seq New sequence will be added at end of alignment.
+ *
+ * @param seq
+ * 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.
- * @param seq New sequence to be inserted.
+ *
+ * @param i
+ * Index of sequence to be updated.
+ * @param seq
+ * New sequence to be inserted.
*/
public void setSequenceAt(int i, SequenceI seq);
/**
* Deletes a sequence from the alignment
- *
- * @param s Sequence to be deleted.
+ *
+ * @param s
+ * Sequence to be deleted.
*/
public void deleteSequence(SequenceI s);
/**
* Deletes a sequence from the alignment.
- *
- * @param i Index of sequence to be deleted.
+ *
+ * @param i
+ * 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.
- *
+ *
+ * @param name
+ * Id of sequence to search for.
+ *
* @return Sequence matching query, if found. If not found returns null.
*/
public SequenceI findName(String name);
/**
* Finds index of a given sequence in the alignment.
- *
- * @param s Sequence to look for.
- *
- * @return Index of sequence within the alignment.
+ *
+ * @param s
+ * Sequence to look for.
+ *
+ * @return Index of sequence within the alignment or -1 if not found
*/
public int findIndex(SequenceI s);
/**
* Finds group that given sequence is part of.
- *
- * @param s Sequence in alignment.
- *
- * @return First group found for sequence. WARNING :
- * Sequences may be members of several groups. This method is incomplete.
+ *
+ * @param s
+ * Sequence in alignment.
+ *
+ * @return First group found for sequence. WARNING : Sequences may be members
+ * of several groups. This method is incomplete.
*/
public SequenceGroup findGroup(SequenceI s);
/**
* Finds all groups that a given sequence is part of.
- *
- * @param s Sequence in alignment.
- *
+ *
+ * @param s
+ * Sequence in alignment.
+ *
* @return All groups containing given sequence.
*/
public SequenceGroup[] findAllGroups(SequenceI s);
/**
* Adds a new SequenceGroup to this alignment.
- *
- * @param sg New group to be added.
+ *
+ * @param sg
+ * New group to be added.
*/
public void addGroup(SequenceGroup sg);
/**
* Deletes a specific SequenceGroup
- *
- * @param g Group will be deleted from alignment.
+ *
+ * @param g
+ * Group will be deleted from alignment.
*/
public void deleteGroup(SequenceGroup g);
/**
* Get all the groups associated with this alignment.
- *
+ *
* @return All groups as a Vector.
*/
public Vector getGroups();
-
/**
* Deletes all groups from this alignment.
*/
/**
* Adds a new AlignmentAnnotation to this alignment
- * @note Care should be taken to ensure that annotation is at
- * least as wide as the longest sequence in the alignment
- * for rendering purposes.
+ *
+ * @note Care should be taken to ensure that annotation is at least as wide as
+ * the longest sequence in the alignment for rendering purposes.
*/
public void addAnnotation(AlignmentAnnotation aa);
+
/**
* moves annotation to a specified index in alignment annotation display stack
- * @param aa the annotation object to be moved
- * @param index the destination position
+ *
+ * @param aa
+ * the annotation object to be moved
+ * @param index
+ * the destination position
*/
public void setAnnotationIndex(AlignmentAnnotation aa, int index);
/**
- * Deletes a specific AlignmentAnnotation from the alignment.
- *
- * @param aa the annotation to delete
+ * Deletes a specific AlignmentAnnotation from the alignment, and removes its
+ * 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
+ * @return true if annotation was deleted from this alignment.
+ */
+ public boolean deleteAnnotation(AlignmentAnnotation aa);
+
+ /**
+ * 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 void deleteAnnotation(AlignmentAnnotation aa);
+ public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
/**
- * Get the annotation associated with this alignment
- *
+ * 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
*/
public AlignmentAnnotation[] getAlignmentAnnotation();
/**
* Change the gap character used in this alignment to 'gc'
- *
- * @param gc the new gap character.
+ *
+ * @param gc
+ * the new gap character.
*/
public void setGapCharacter(char gc);
/**
* Get the gap character used in this alignment
- *
+ *
* @return gap character
*/
public char getGapCharacter();
/**
* Test for all nucleotide alignment
- *
+ *
* @return true if alignment is nucleotide sequence
*/
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
- *
+ *
*/
public void setNucleotide(boolean b);
/**
* Get the associated dataset for the alignment.
- * @return Alignment containing dataset sequences or null of this is a dataset.
+ *
+ * @return Alignment containing dataset sequences or null of this is a
+ * dataset.
*/
public Alignment getDataset();
/**
* Set the associated dataset for the alignment, or create one.
- * @param dataset The dataset alignment or null to construct one.
+ *
+ * @param dataset
+ * The dataset alignment or null to construct one.
*/
public void setDataset(Alignment dataset);
/**
* pads sequences with gaps (to ensure the set looks like an alignment)
+ *
* @return boolean true if alignment was modified
*/
public boolean padGaps();
/**
* Compact representation of alignment
+ *
* @return CigarArray
*/
public CigarArray getCompactAlignment();
/**
- * Set an arbitrary key value pair for an alignment.
- * Note: both key and value objects should return a
- * meaningful, human readable response to .toString()
+ * Set an arbitrary key value pair for an alignment. Note: both key and value
+ * objects should return a meaningful, human readable response to .toString()
+ *
* @param key
* @param value
*/
public void setProperty(Object key, Object value);
+
/**
- * Get a named property from the alignment.
+ * Get a named property from the alignment.
+ *
* @param key
* @return value of property
*/
public Object getProperty(Object key);
+
/**
* Get the property hashtable.
- * @return hashtable of alignment properties (if any)
+ *
+ * @return hashtable of alignment properties (or null if none are defined)
*/
public Hashtable getProperties();
+
+ /**
+ * add a reference to a frame of aligned codons for this alignment
+ *
+ * @param codons
+ */
+ public void addCodonFrame(AlignedCodonFrame codons);
+
+ /**
+ * remove a particular codon frame reference from this alignment
+ *
+ * @param codons
+ * @return true if codon frame was removed.
+ */
+ public boolean removeCodonFrame(AlignedCodonFrame codons);
+
+ /**
+ * get all codon frames associated with this alignment
+ *
+ * @return
+ */
+ public AlignedCodonFrame[] getCodonFrames();
+
+ /**
+ * get a particular codon frame
+ *
+ * @param index
+ * @return
+ */
+ public AlignedCodonFrame getCodonFrame(int index);
+
+ /**
+ * get codon frames involving sequenceI
+ */
+ public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+
+ /**
+ * find sequence with given name in alignment
+ *
+ * @param token
+ * name to find
+ * @param b
+ * true implies that case insensitive matching will <em>also</em> be
+ * tried
+ * @return matched sequence or null
+ */
+ public SequenceI findName(String token, boolean b);
+
+ /**
+ * find next sequence with given name in alignment starting after a given
+ * sequence
+ *
+ * @param startAfter
+ * the sequence after which the search will be started (usually the
+ * result of the last call to findName)
+ * @param token
+ * name to find
+ * @param b
+ * 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
+ *
+ * @param results
+ * @return -1 or index of sequence in alignment
+ */
+ public int findIndex(SearchResults results);
+
+ /**
+ * 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.
+ */
+ 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
+ */
+ public boolean justify(boolean right);
+
+ /**
+ * add given annotation row at given position (0 is start, -1 is end)
+ *
+ * @param consensus
+ * @param i
+ */
+ public void addAnnotation(AlignmentAnnotation consensus, int i);
}
git://source.jalview.org / jalview.git / blobdiff