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ContactMapHolderI | 25 | 0 | 0 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.datamodel; | |
22 | ||
23 | import java.util.Collection; | |
24 | ||
25 | public interface ContactMapHolderI | |
26 | { | |
27 | /** | |
28 | * resolve a contact list instance (if any) associated with the annotation row | |
29 | * and column position Columns of ContactMap are indexed relative to context | |
30 | * object (columns of alignment, positions on sequence relative to | |
31 | * sequence.getStart()) | |
32 | * | |
33 | * @param _aa | |
34 | * @param column | |
35 | * - base 0 column index | |
36 | * @return | |
37 | */ | |
38 | ContactListI getContactListFor(AlignmentAnnotation _aa, int column); | |
39 | ||
40 | AlignmentAnnotation addContactList(ContactMatrixI cm); | |
41 | ||
42 | Collection<ContactMatrixI> getContactMaps(); | |
43 | ||
44 | public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann); | |
45 | ||
46 | void addContactListFor(AlignmentAnnotation annotation, ContactMatrixI cm); | |
47 | ||
48 | } |