1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.datamodel

File ContactMapHolderI.java

 

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ContactMapHolderI 25 0 0
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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    }