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;
24 /** Data structure to hold and manipulate a multiple sequence alignment
26 public interface AlignmentI
29 * Calculates the number of sequences in an alignment
31 * @return Number of sequences in alignment
33 public int getHeight();
36 * Calculates the maximum width of the alignment, including gaps.
38 * @return Greatest sequence length within alignment.
40 public int getWidth();
44 * Calculates if this set of sequences is all the same length
46 * @return true if all sequences in alignment are the same length
48 public boolean isAligned();
51 * Gets sequences as a Vector
53 * @return All sequences in alignment.
55 public Vector getSequences();
58 * Gets sequences as a SequenceI[]
60 * @return All sequences in alignment.
62 public SequenceI [] getSequencesArray();
65 * Find a specific sequence in this alignment.
67 * @param i Index of required sequence.
69 * @return SequenceI at given index.
71 public SequenceI getSequenceAt(int i);
74 * Add a new sequence to this alignment.
76 * @param seq New sequence will be added at end of alignment.
78 public void addSequence(SequenceI seq);
81 * Used to set a particular index of the alignment with the given sequence.
83 * @param i Index of sequence to be updated.
84 * @param seq New sequence to be inserted.
86 public void setSequenceAt(int i, SequenceI seq);
89 * Deletes a sequence from the alignment
91 * @param s Sequence to be deleted.
93 public void deleteSequence(SequenceI s);
96 * Deletes a sequence from the alignment.
98 * @param i Index of sequence to be deleted.
100 public void deleteSequence(int i);
104 * Finds sequence in alignment using sequence name as query.
106 * @param name Id of sequence to search for.
108 * @return Sequence matching query, if found. If not found returns null.
110 public SequenceI findName(String name);
112 public SequenceI [] findSequenceMatch(String name);
115 * Finds index of a given sequence in the alignment.
117 * @param s Sequence to look for.
119 * @return Index of sequence within the alignment.
121 public int findIndex(SequenceI s);
125 * Finds group that given sequence is part of.
127 * @param s Sequence in alignment.
129 * @return First group found for sequence. WARNING :
130 * Sequences may be members of several groups. This method is incomplete.
132 public SequenceGroup findGroup(SequenceI s);
135 * Finds all groups that a given sequence is part of.
137 * @param s Sequence in alignment.
139 * @return All groups containing given sequence.
141 public SequenceGroup[] findAllGroups(SequenceI s);
144 * Adds a new SequenceGroup to this alignment.
146 * @param sg New group to be added.
148 public void addGroup(SequenceGroup sg);
151 * Deletes a specific SequenceGroup
153 * @param g Group will be deleted from alignment.
155 public void deleteGroup(SequenceGroup g);
158 * Get all the groups associated with this alignment.
160 * @return All groups as a Vector.
162 public Vector getGroups();
165 * Deletes all groups from this alignment.
167 public void deleteAllGroups();
171 * Adds a new AlignmentAnnotation to this alignment
173 public void addAnnotation(AlignmentAnnotation aa);
176 public void setAnnotationIndex(AlignmentAnnotation aa, int index);
179 * Deletes a specific AlignmentAnnotation from the alignment.
181 * @param aa DOCUMENT ME!
183 public void deleteAnnotation(AlignmentAnnotation aa);
188 * @return DOCUMENT ME!
190 public AlignmentAnnotation[] getAlignmentAnnotation();
195 * @param gc DOCUMENT ME!
197 public void setGapCharacter(char gc);
202 * @return DOCUMENT ME!
204 public char getGapCharacter();
208 * Returns true if alignment is nucleotide sequence
210 * @return DOCUMENT ME!
212 public boolean isNucleotide();
215 * Set true if the alignment is a nucleotide sequence
219 public void setNucleotide(boolean b);
222 public Alignment getDataset();
224 public void setDataset(Alignment dataset);
226 * pads sequences with gaps (to ensure the set looks like an alignment)
227 * @return boolean true if alignment was modified
229 public boolean padGaps();
231 public void adjustSequenceAnnotations();
233 public HiddenSequences getHiddenSequences();
235 * Compact representation of alignment
238 public CigarArray getCompactAlignment();