2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.datamodel;
21 import jalview.util.ShiftList;
26 /** Data structure to hold and manipulate a multiple sequence alignment
28 public interface AlignmentI
31 * Calculates the number of sequences in an alignment
33 * @return Number of sequences in alignment
35 public int getHeight();
38 * Calculates the maximum width of the alignment, including gaps.
40 * @return Greatest sequence length within alignment.
42 public int getWidth();
46 * Calculates if this set of sequences is all the same length
48 * @return true if all sequences in alignment are the same length
50 public boolean isAligned();
53 * Gets sequences as a Vector
55 * @return All sequences in alignment.
57 public Vector getSequences();
60 * Gets sequences as a SequenceI[]
62 * @return All sequences in alignment.
64 public SequenceI [] getSequencesArray();
67 * Find a specific sequence in this alignment.
69 * @param i Index of required sequence.
71 * @return SequenceI at given index.
73 public SequenceI getSequenceAt(int i);
76 * Add a new sequence to this alignment.
78 * @param seq New sequence will be added at end of alignment.
80 public void addSequence(SequenceI seq);
83 * Used to set a particular index of the alignment with the given sequence.
85 * @param i Index of sequence to be updated.
86 * @param seq New sequence to be inserted.
88 public void setSequenceAt(int i, SequenceI seq);
91 * Deletes a sequence from the alignment
93 * @param s Sequence to be deleted.
95 public void deleteSequence(SequenceI s);
98 * Deletes a sequence from the alignment.
100 * @param i Index of sequence to be deleted.
102 public void deleteSequence(int i);
106 * Finds sequence in alignment using sequence name as query.
108 * @param name Id of sequence to search for.
110 * @return Sequence matching query, if found. If not found returns null.
112 public SequenceI findName(String name);
114 public SequenceI [] findSequenceMatch(String name);
117 * Finds index of a given sequence in the alignment.
119 * @param s Sequence to look for.
121 * @return Index of sequence within the alignment.
123 public int findIndex(SequenceI s);
127 * Finds group that given sequence is part of.
129 * @param s Sequence in alignment.
131 * @return First group found for sequence. WARNING :
132 * Sequences may be members of several groups. This method is incomplete.
134 public SequenceGroup findGroup(SequenceI s);
137 * Finds all groups that a given sequence is part of.
139 * @param s Sequence in alignment.
141 * @return All groups containing given sequence.
143 public SequenceGroup[] findAllGroups(SequenceI s);
146 * Adds a new SequenceGroup to this alignment.
148 * @param sg New group to be added.
150 public void addGroup(SequenceGroup sg);
153 * Deletes a specific SequenceGroup
155 * @param g Group will be deleted from alignment.
157 public void deleteGroup(SequenceGroup g);
160 * Get all the groups associated with this alignment.
162 * @return All groups as a Vector.
164 public Vector getGroups();
167 * Deletes all groups from this alignment.
169 public void deleteAllGroups();
173 * Adds a new AlignmentAnnotation to this alignment
175 public void addAnnotation(AlignmentAnnotation aa);
178 public void setAnnotationIndex(AlignmentAnnotation aa, int index);
181 * Deletes a specific AlignmentAnnotation from the alignment.
183 * @param aa DOCUMENT ME!
185 public void deleteAnnotation(AlignmentAnnotation aa);
190 * @return DOCUMENT ME!
192 public AlignmentAnnotation[] getAlignmentAnnotation();
197 * @param gc DOCUMENT ME!
199 public void setGapCharacter(char gc);
204 * @return DOCUMENT ME!
206 public char getGapCharacter();
210 * Returns true if alignment is nucleotide sequence
212 * @return DOCUMENT ME!
214 public boolean isNucleotide();
217 * Set true if the alignment is a nucleotide sequence
221 public void setNucleotide(boolean b);
224 public Alignment getDataset();
226 public void setDataset(Alignment dataset);
228 * pads sequences with gaps (to ensure the set looks like an alignment)
229 * @return boolean true if alignment was modified
231 public boolean padGaps();
233 public void adjustSequenceAnnotations();
235 public HiddenSequences getHiddenSequences();
237 * Compact representation of alignment
240 public CigarArray getCompactAlignment();