jalviewX
File VisibleContigsIterator.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| VisibleContigsIterator | 32 | 31 | 11 | 0 |
Contributing tests
This file is covered by 32 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 regions in a range. Provides a | |
| 29 | * special "endsAtHidden" indicator to allow callers to determine if the final | |
| 30 | * visible column is adjacent to a hidden region. | |
| 31 | */ | |
| 32 | public class VisibleContigsIterator implements Iterator<int[]> | |
| 33 | { | |
| 34 | private List<int[]> vcontigs = new ArrayList<>(); | |
| 35 | ||
| 36 | private int currentPosition = 0; | |
| 37 | ||
| 38 | private boolean endsAtHidden = false; | |
| 39 | ||
| 40 | 682 |  VisibleContigsIterator(int start, int end, |
| 41 | List<int[]> hiddenColumns) | |
| 42 | { | |
| 43 | 682 | if (hiddenColumns != null && hiddenColumns.size() > 0) |
| 44 | { | |
| 45 | 670 | int vstart = start; |
| 46 | 670 | int hideStart; |
| 47 | 670 | int hideEnd; |
| 48 | ||
| 49 | 670 | for (int[] region : hiddenColumns) |
| 50 | { | |
| 51 | 1013 | endsAtHidden = false; |
| 52 | 1013 | hideStart = region[0]; |
| 53 | 1013 | hideEnd = region[1]; |
| 54 | ||
| 55 | // navigate to start | |
| 56 | 1013 | if (hideEnd < vstart) |
| 57 | { | |
| 58 | 435 | continue; |
| 59 | } | |
| 60 | 578 | if (hideStart > vstart) |
| 61 | { | |
| 62 | 379 | if (end - 1 > hideStart - 1) |
| 63 | { | |
| 64 | 254 | int[] contig = new int[] { vstart, hideStart - 1 }; |
| 65 | 254 | vcontigs.add(contig); |
| 66 | 254 | endsAtHidden = true; |
| 67 | } | |
| 68 | else | |
| 69 | { | |
| 70 | 125 | int[] contig = new int[] { vstart, end - 1 }; |
| 71 | 125 | vcontigs.add(contig); |
| 72 | } | |
| 73 | } | |
| 74 | 578 | vstart = hideEnd + 1; |
| 75 | ||
| 76 | // exit if we're past the end | |
| 77 | 578 | if (vstart >= end) |
| 78 | { | |
| 79 | 345 | break; |
| 80 | } | |
| 81 | } | |
| 82 | ||
| 83 | 670 | if (vstart < end) |
| 84 | { | |
| 85 | 325 | int[] contig = new int[] { vstart, end - 1 }; |
| 86 | 325 | vcontigs.add(contig); |
| 87 | 325 | endsAtHidden = false; |
| 88 | } | |
| 89 | } | |
| 90 | else | |
| 91 | { | |
| 92 | 12 | int[] contig = new int[] { start, end - 1 }; |
| 93 | 12 | vcontigs.add(contig); |
| 94 | } | |
| 95 | } | |
| 96 | ||
| 97 | 2053 | @Override |
| 98 | public boolean hasNext() | |
| 99 | { | |
| 100 | 2053 | return (currentPosition < vcontigs.size()); |
| 101 | } | |
| 102 | ||
| 103 | 716 | @Override |
| 104 | public int[] next() | |
| 105 | { | |
| 106 | 716 | int[] result = vcontigs.get(currentPosition); |
| 107 | 716 | currentPosition++; |
| 108 | 716 | return result; |
| 109 | } | |
| 110 | ||
| 111 | 451 | public boolean endsAtHidden() |
| 112 | { | |
| 113 | 451 | return endsAtHidden; |
| 114 | } | |
| 115 | } | |
| 116 |