Coverage Report
File ScaleRenderer.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| ScaleRenderer | 37 | 35 | 9 | ||
| ScaleRenderer.ScaleMark | 42 | 3 | 1 |
Contributing tests
This file is covered by 21 tests.
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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.renderer; | |
| 22 | ||
| 23 | import jalview.api.AlignViewportI; | |
| 24 | import jalview.datamodel.HiddenColumns; | |
| 25 | import jalview.datamodel.SequenceI; | |
| 26 | ||
| 27 | import java.util.ArrayList; | |
| 28 | import java.util.Iterator; | |
| 29 | import java.util.List; | |
| 30 | ||
| 31 | /** | |
| 32 | * Calculate and display alignment rulers | |
| 33 | * | |
| 34 | * @author jprocter | |
| 35 | * | |
| 36 | */ | |
| 37 | public class ScaleRenderer | |
| 38 | { | |
| 39 | /** | |
| 40 | * Represents one major or minor scale mark | |
| 41 | */ | |
| 42 | public final class ScaleMark | |
| 43 | { | |
| 44 | /** | |
| 45 | * true for a major scale mark, false for minor | |
| 46 | */ | |
| 47 | public final boolean major; | |
| 48 | ||
| 49 | /** | |
| 50 | * visible column position (0..) e.g. 19 | |
| 51 | */ | |
| 52 | public final int column; | |
| 53 | ||
| 54 | /** | |
| 55 | * text (if any) to show e.g. "20" | |
| 56 | */ | |
| 57 | public final String text; | |
| 58 | ||
| 59 | 8472 |  ScaleMark(boolean isMajor, int col, String txt) |
| 60 | { | |
| 61 | 8472 | major = isMajor; |
| 62 | 8472 | column = col; |
| 63 | 8472 | text = txt; |
| 64 | } | |
| 65 | } | |
| 66 | ||
| 67 | /** | |
| 68 | * calculate positions markers on the alignment ruler | |
| 69 | * | |
| 70 | * @param av | |
| 71 | * @param startx | |
| 72 | * left-most column in visible view | |
| 73 | * @param endx | |
| 74 | * - right-most column in visible view | |
| 75 | * @return List of ScaleMark holding boolean: true/false for major/minor mark, | |
| 76 | * marker position in alignment column coords, a String to be rendered | |
| 77 | * at the position (or null) | |
| 78 | */ | |
| 79 | 715 | public List<ScaleMark> calculateMarks(AlignViewportI av, int startx, |
| 80 | int endx) | |
| 81 | { | |
| 82 | 715 | int scalestartx = (startx / 10) * 10; |
| 83 | ||
| 84 | 715 | SequenceI refSeq = av.getAlignment().getSeqrep(); |
| 85 | 715 | int refSp = 0; |
| 86 | 715 | int refStartI = 0; |
| 87 | 715 | int refEndI = -1; |
| 88 | ||
| 89 | 715 | HiddenColumns hc = av.getAlignment().getHiddenColumns(); |
| 90 | ||
| 91 | 715 | if (refSeq != null) |
| 92 | { | |
| 93 | // find bounds and set origin appropriately | |
| 94 | // locate first residue in sequence which is not hidden | |
| 95 | 115 | Iterator<int[]> it = hc.iterator(); |
| 96 | 115 | int index = refSeq.firstResidueOutsideIterator(it); |
| 97 | 115 | refSp = hc.absoluteToVisibleColumn(index); |
| 98 | ||
| 99 | 115 | refStartI = refSeq.findIndex(refSeq.getStart()) - 1; |
| 100 | ||
| 101 | 115 | int seqlength = refSeq.getLength(); |
| 102 | // get sequence position past the end of the sequence | |
| 103 | 115 | int pastEndPos = refSeq.findPosition(seqlength + 1); |
| 104 | 115 | refEndI = refSeq.findIndex(pastEndPos - 1) - 1; |
| 105 | ||
| 106 | 115 | scalestartx = refSp + ((scalestartx - refSp) / 10) * 10; |
| 107 | } | |
| 108 | ||
| 109 | 715 | if (refSeq == null && scalestartx % 10 == 0) |
| 110 | { | |
| 111 | 600 | scalestartx += 5; |
| 112 | } | |
| 113 | 715 | List<ScaleMark> marks = new ArrayList<>(); |
| 114 | 715 | String string; |
| 115 | 715 | int refN, iadj; |
| 116 | // todo: add a 'reference origin column' to set column number relative to | |
| 117 | 9187 | for (int i = scalestartx; i <= endx; i += 5) |
| 118 | { | |
| 119 | 8472 | if (((i - refSp) % 10) == 0) |
| 120 | { | |
| 121 | 4061 | if (refSeq == null) |
| 122 | { | |
| 123 | 3269 | iadj = hc.visibleToAbsoluteColumn(i - 1) + 1; |
| 124 | 3269 | string = String.valueOf(iadj); |
| 125 | } | |
| 126 | else | |
| 127 | { | |
| 128 | 792 | iadj = hc.visibleToAbsoluteColumn(i - 1); |
| 129 | 792 | refN = refSeq.findPosition(iadj); |
| 130 | // TODO show bounds if position is a gap | |
| 131 | // - ie L--R -> "1L|2R" for | |
| 132 | // marker | |
| 133 | 792 | if (iadj < refStartI) |
| 134 | { | |
| 135 | 13 | string = String.valueOf(iadj - refStartI); |
| 136 | } | |
| 137 | 779 | else if (iadj > refEndI) |
| 138 | { | |
| 139 | 0 | string = "+" + String.valueOf(iadj - refEndI); |
| 140 | } | |
| 141 | else | |
| 142 | { | |
| 143 | 779 | string = String.valueOf(refN) + refSeq.getCharAt(iadj); |
| 144 | } | |
| 145 | } | |
| 146 | 4061 | marks.add(new ScaleMark(true, i - startx - 1, string)); |
| 147 | } | |
| 148 | else | |
| 149 | { | |
| 150 | 4411 | marks.add(new ScaleMark(false, i - startx - 1, null)); |
| 151 | } | |
| 152 | } | |
| 153 | 715 | return marks; |
| 154 | } | |
| 155 | ||
| 156 | } |