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
37 public final class ScaleMark
39 public final boolean major;
41 public final int column;
43 public final String text;
45 ScaleMark(boolean isMajor, int col, String txt)
54 * calculate positions markers on the alignment ruler
58 * left-most column in visible view
60 * - right-most column in visible view
61 * @return List of ScaleMark holding boolean: true/false for major/minor mark,
62 * marker position in alignment column coords, a String to be rendered
63 * at the position (or null)
65 public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
68 int scalestartx = (startx / 10) * 10;
70 SequenceI refSeq = av.getAlignment().getSeqrep();
71 int refSp = 0, refStartI = 0, refEndI = -1;
74 // find bounds and set origin appopriately
75 // locate first visible position for this sequence
76 int[] refbounds = av.getAlignment().getHiddenColumns()
77 .locateVisibleBoundsOfSequence(refSeq);
80 refStartI = refbounds[4];
81 refEndI = refbounds[5];
82 scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
85 if (refSeq == null && scalestartx % 10 == 0)
89 List<ScaleMark> marks = new ArrayList<ScaleMark>();
92 // todo: add a 'reference origin column' to set column number relative to
93 for (int i = scalestartx; i < endx; i += 5)
95 if (((i - refSp) % 10) == 0)
99 iadj = av.getAlignment().getHiddenColumns()
100 .adjustForHiddenColumns(i - 1) + 1;
101 string = String.valueOf(iadj);
105 iadj = av.getAlignment().getHiddenColumns()
106 .adjustForHiddenColumns(i - 1);
107 refN = refSeq.findPosition(iadj);
108 // TODO show bounds if position is a gap
109 // - ie L--R -> "1L|2R" for
111 if (iadj < refStartI)
113 string = String.valueOf(iadj - refStartI);
115 else if (iadj > refEndI)
117 string = "+" + String.valueOf(iadj - refEndI);
121 string = String.valueOf(refN) + refSeq.getCharAt(iadj);
124 marks.add(new ScaleMark(true, i - startx - 1, string));
128 marks.add(new ScaleMark(false, i - startx - 1, null));