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.renderer;
23 import jalview.api.AlignViewportI;
24 import jalview.datamodel.SequenceI;
26 import java.util.ArrayList;
27 import java.util.List;
30 * Calculate and display alignment rulers
35 public class ScaleRenderer
38 * calculate positions markers on the alignment ruler
40 * @return List { Object { .. } } Boolean: true/false for major/minor mark,
41 * Integer: marker position in alignment column coords, String: null
42 * or a String to be rendered at the position.
44 public static List<Object[]> calculateMarks(AlignViewportI av,
47 new ArrayList<Object[]>();
49 int scalestartx = (startx / 10) * 10;
51 SequenceI refSeq = av.getAlignment().getSeqrep();
52 int refSp = 0, refStartI = 0, refEndI = -1;
55 // find bounds and set origin appopriately
56 // locate first visible position for this sequence
57 int[] refbounds = av.getColumnSelection()
58 .locateVisibleBoundsOfSequence(refSeq);
61 refStartI = refbounds[4];
62 refEndI = refbounds[5];
63 scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
66 if (refSeq == null && scalestartx % 10 == 0)
70 List<Object[]> marks = new ArrayList<Object[]>();
73 // todo: add a 'reference origin column' to set column number relative to
74 for (int i = scalestartx; i < endx; i += 5)
76 Object[] amark = new Object[3];
77 if (((i - refSp) % 10) == 0)
81 iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1) + 1;
82 string = String.valueOf(iadj);
86 iadj = av.getColumnSelection().adjustForHiddenColumns(i - 1);
87 refN = refSeq.findPosition(iadj);
88 // TODO show bounds if position is a gap
89 // - ie L--R -> "1L|2R" for
93 string = String.valueOf(iadj - refStartI);
95 else if (iadj > refEndI)
97 string = "+" + String.valueOf(iadj - refEndI);
101 string = String.valueOf(refN) + refSeq.getCharAt(iadj);
104 amark[0] = Boolean.TRUE;
105 amark[1] = Integer.valueOf(i - startx - 1);
111 amark[0] = Boolean.FALSE;
112 amark[1] = Integer.valueOf(i - startx - 1);