/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
- *
- * @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
- *
- * @return true if all sequences in alignment are the same length
- */
- public boolean isAligned();
-
- /**
- * 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.
- *
- * @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.
- */
- 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.
- */
- public void setSequenceAt(int i, SequenceI seq);
-
- /**
- * Deletes a sequence from the alignment
- *
- * @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.
- */
- public void deleteSequence(int i);
-
-
- /**
- * Finds sequence in alignment using sequence name as query.
- *
- * @param name Id of sequence to search for.
- *
- * @return Sequence matching query, if found. If not found returns null.
- */
- public SequenceI findName(String name);
-
- public SequenceI [] findSequenceMatch(String name);
-
- /**
- * Finds index of a given sequence in the alignment.
- *
- * @param s Sequence to look for.
- *
- * @return Index of sequence within the alignment.
- */
- 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.
- */
- public SequenceGroup findGroup(SequenceI s);
-
- /**
- * Finds all groups that a given sequence is part of.
- *
- * @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.
- */
- public void addGroup(SequenceGroup sg);
-
- /**
- * Deletes a specific SequenceGroup
- *
- * @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.
- */
- public void deleteAllGroups();
-
-
- /**
- * Adds a new AlignmentAnnotation to this alignment
- */
- public void addAnnotation(AlignmentAnnotation aa);
-
-
- public void setAnnotationIndex(AlignmentAnnotation aa, int index);
-
- /**
- * Deletes a specific AlignmentAnnotation from the alignment.
- *
- * @param aa DOCUMENT ME!
- */
- public void deleteAnnotation(AlignmentAnnotation aa);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public AlignmentAnnotation[] getAlignmentAnnotation();
-
- /**
- * DOCUMENT ME!
- *
- * @param gc DOCUMENT ME!
- */
- public void setGapCharacter(char gc);
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getGapCharacter();
-
-
- /**
- * Returns true if alignment is nucleotide sequence
- *
- * @return DOCUMENT ME!
- */
- public boolean isNucleotide();
-
- /**
- * Set true if the alignment is a nucleotide sequence
- *
- * @return
- */
- public void setNucleotide(boolean b);
-
-
- public Alignment getDataset();
-
- 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();
-
-
- public HiddenSequences getHiddenSequences();
- /**
- * Compact representation of alignment
- * @return CigarArray
- */
- public CigarArray getCompactAlignment();
+ /**
+ * 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 (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.
+ *
+ * @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.
+ */
+ 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.
+ */
+ public void setSequenceAt(int i, SequenceI seq);
+
+ /**
+ * Deletes a sequence from the alignment
+ *
+ * @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.
+ */
+ public void deleteSequence(int i);
+
+ /**
+ * Finds sequence in alignment using sequence name as query.
+ *
+ * @param name
+ * Id of sequence to search for.
+ *
+ * @return Sequence matching query, if found. If not found returns null.
+ */
+ public SequenceI findName(String name);
+
+ public SequenceI[] findSequenceMatch(String name);
+
+ /**
+ * Finds index of a given sequence in 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.
+ */
+ public SequenceGroup findGroup(SequenceI s);
+
+ /**
+ * Finds all groups that a given sequence is part of.
+ *
+ * @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.
+ */
+ public void addGroup(SequenceGroup sg);
+
+ /**
+ * Deletes a specific SequenceGroup
+ *
+ * @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.
+ */
+ public void deleteAllGroups();
+
+ /**
+ * 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.
+ */
+ 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
+ */
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index);
+
+ /**
+ * 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 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
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation();
+
+ /**
+ * Change the gap character used in this alignment to 'gc'
+ *
+ * @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.
+ */
+ public Alignment getDataset();
+
+ /**
+ * Set the associated dataset for the alignment, or create 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();
+
+ public HiddenSequences getHiddenSequences();
+
+ /**
+ * 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()
+ *
+ * @param key
+ * @param value
+ */
+ public void setProperty(Object key, Object value);
+
+ /**
+ * 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 (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);
}
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