2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.datamodel;
23 import java.awt.Color;
25 public interface ContactListProviderI
30 * @return position index for this contact List (usually sequence position or
36 * dimension of list where getContactAt(column<getContactHeight()) may return
41 int getContactHeight();
44 * get a value representing contact at column for this site
47 * @return Double.NaN or a contact strength for this site
49 double getContactAt(int column);
52 * Return positions in local reference corresponding to cStart and cEnd in
53 * matrix data. Positions are base 1 column indices for sequence associated
58 * @return int[] { start, end (inclusive) for each contiguous segment}
60 default int[] getMappedPositionsFor(int cStart, int cEnd)
62 return new int[] { cStart, cEnd };
65 default Color getColourForGroup()