Coverage Report
File StartRegionIterator.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| StartRegionIterator | 31 | 24 | 10 |
Contributing tests
This file is covered by 16 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.datamodel; | |
| 22 | ||
| 23 | import java.util.ArrayList; | |
| 24 | import java.util.Iterator; | |
| 25 | import java.util.List; | |
| 26 | ||
| 27 | /** | |
| 28 | * An iterator which iterates over visible start positions of hidden column | |
| 29 | * regions in a range. | |
| 30 | */ | |
| 31 | public class StartRegionIterator implements Iterator<Integer> | |
| 32 | { | |
| 33 | // start position to iterate from | |
| 34 | private int start; | |
| 35 | ||
| 36 | // end position to iterate to | |
| 37 | private int end; | |
| 38 | ||
| 39 | // current index in hiddenColumns | |
| 40 | private int currentPosition = 0; | |
| 41 | ||
| 42 | // local copy or reference to hiddenColumns | |
| 43 | private List<Integer> positions = null; | |
| 44 | ||
| 45 | /** | |
| 46 | * Construct an iterator over hiddenColums bounded at [lowerBound,upperBound] | |
| 47 | * | |
| 48 | * @param lowerBound | |
| 49 | * lower bound to iterate from | |
| 50 | * @param upperBound | |
| 51 | * upper bound to iterate to | |
| 52 | * @param useCopyCols | |
| 53 | * whether to make a local copy of hiddenColumns for iteration (set | |
| 54 | * to true if calling from outwith the HiddenColumns class) | |
| 55 | */ | |
| 56 | 7 |  StartRegionIterator(int lowerBound, int upperBound, |
| 57 | List<int[]> hiddenColumns) | |
| 58 | { | |
| 59 | 7 | this(null, lowerBound, upperBound, hiddenColumns); |
| 60 | } | |
| 61 | ||
| 62 | /** | |
| 63 | * Construct an iterator over hiddenColums bounded at [lowerBound,upperBound] | |
| 64 | * | |
| 65 | * @param pos | |
| 66 | * a hidden cursor position to start from - may be null | |
| 67 | * @param lowerBound | |
| 68 | * lower bound to iterate from - will be ignored if pos != null | |
| 69 | * @param upperBound | |
| 70 | * upper bound to iterate to | |
| 71 | * @param hiddenColumns | |
| 72 | * the hidden columns collection to use | |
| 73 | */ | |
| 74 | 452 | StartRegionIterator(HiddenCursorPosition pos, int lowerBound, |
| 75 | int upperBound, List<int[]> hiddenColumns) | |
| 76 | { | |
| 77 | 452 | start = lowerBound; |
| 78 | 452 | end = upperBound; |
| 79 | ||
| 80 | 452 | if (hiddenColumns != null) |
| 81 | { | |
| 82 | 450 | positions = new ArrayList<>(hiddenColumns.size()); |
| 83 | ||
| 84 | // navigate to start, keeping count of hidden columns | |
| 85 | 450 | int i = 0; |
| 86 | 450 | int hiddenSoFar = 0; |
| 87 | ||
| 88 | 450 | if (pos != null) |
| 89 | { | |
| 90 | // use the cursor position provided | |
| 91 | 437 | i = pos.getRegionIndex(); |
| 92 | 437 | hiddenSoFar = pos.getHiddenSoFar(); |
| 93 | } | |
| 94 | else | |
| 95 | { | |
| 96 | // navigate to start | |
| 97 | 15 | while ((i < hiddenColumns.size()) |
| 98 | && (hiddenColumns.get(i)[0] < start + hiddenSoFar)) | |
| 99 | { | |
| 100 | 2 | int[] region = hiddenColumns.get(i); |
| 101 | 2 | hiddenSoFar += region[1] - region[0] + 1; |
| 102 | 2 | i++; |
| 103 | } | |
| 104 | } | |
| 105 | ||
| 106 | // iterate from start to end, adding start positions of each | |
| 107 | // hidden region. Positions are visible columns count, not absolute | |
| 108 | 898 | while (i < hiddenColumns.size() |
| 109 | && (hiddenColumns.get(i)[0] <= end + hiddenSoFar)) | |
| 110 | { | |
| 111 | 448 | int[] region = hiddenColumns.get(i); |
| 112 | 448 | positions.add(region[0] - hiddenSoFar); |
| 113 | 448 | hiddenSoFar += region[1] - region[0] + 1; |
| 114 | 448 | i++; |
| 115 | } | |
| 116 | } | |
| 117 | else | |
| 118 | { | |
| 119 | 2 | positions = new ArrayList<>(); |
| 120 | } | |
| 121 | ||
| 122 | } | |
| 123 | ||
| 124 | 898 | @Override |
| 125 | public boolean hasNext() | |
| 126 | { | |
| 127 | 898 | return (currentPosition < positions.size()); |
| 128 | } | |
| 129 | ||
| 130 | /** | |
| 131 | * Get next hidden region start position | |
| 132 | * | |
| 133 | * @return the start position in *visible* coordinates | |
| 134 | */ | |
| 135 | 448 | @Override |
| 136 | public Integer next() | |
| 137 | { | |
| 138 | 448 | int result = positions.get(currentPosition); |
| 139 | 448 | currentPosition++; |
| 140 | 448 | return result; |
| 141 | } | |
| 142 | } |