Coverage Report
File ShiftList.java
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21% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| ShiftList | 31 | 47 | 26 |
Contributing tests
This file is covered by 18 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.util; | |
| 22 | ||
| 23 | import java.util.ArrayList; | |
| 24 | import java.util.List; | |
| 25 | ||
| 26 | /** | |
| 27 | * ShiftList Simple way of mapping a linear series to a new linear range with | |
| 28 | * new points introduced. Use at your own risk! Now growing to be used for | |
| 29 | * interval ranges (position, offset) storing deletions/insertions | |
| 30 | */ | |
| 31 | public class ShiftList | |
| 32 | { | |
| 33 | private List<int[]> shifts; | |
| 34 | ||
| 35 | 40 |  public ShiftList() |
| 36 | { | |
| 37 | 40 | shifts = new ArrayList<int[]>(); |
| 38 | } | |
| 39 | ||
| 40 | /** | |
| 41 | * addShift | |
| 42 | * | |
| 43 | * @param pos | |
| 44 | * start position for shift (in original reference frame) | |
| 45 | * @param shift | |
| 46 | * length of shift | |
| 47 | */ | |
| 48 | 36 | public void addShift(int pos, int shift) |
| 49 | { | |
| 50 | 36 | synchronized (shifts) |
| 51 | { | |
| 52 | 36 | int sidx = 0; |
| 53 | 36 | int[] rshift = null; |
| 54 | ? | while (sidx < shifts.size() && (rshift = shifts.get(sidx))[0] < pos) |
| 55 | { | |
| 56 | 8 | sidx++; |
| 57 | } | |
| 58 | 36 | if (sidx == shifts.size() || pos!=rshift[0]) |
| 59 | { | |
| 60 | 33 | shifts.add(sidx, new int[] { pos, shift }); |
| 61 | } | |
| 62 | else | |
| 63 | { | |
| 64 | 3 | rshift[1] += shift; |
| 65 | } | |
| 66 | } | |
| 67 | } | |
| 68 | ||
| 69 | /** | |
| 70 | * update the shiftList with a new insertion. | |
| 71 | * If a shift already exists at that position the shift will be extended if this one is bigger. | |
| 72 | * @param pos | |
| 73 | * @param shift | |
| 74 | * @return true if the shiftList was modified | |
| 75 | */ | |
| 76 | 599 | public boolean extendShift(int pos, int shift) |
| 77 | { | |
| 78 | 599 | boolean modified=false; |
| 79 | 599 | synchronized (shifts) |
| 80 | { | |
| 81 | 599 | int sidx = 0; |
| 82 | 599 | int[] rshift = null; |
| 83 | ? | while (sidx < shifts.size() && (rshift = shifts.get(sidx))[0] < pos) |
| 84 | { | |
| 85 | 15008 | sidx++; |
| 86 | } | |
| 87 | 599 | if (sidx == shifts.size() || pos!=rshift[0]) |
| 88 | { | |
| 89 | 225 | modified=true; |
| 90 | 225 | shifts.add(sidx, new int[] { pos, shift }); |
| 91 | } | |
| 92 | else | |
| 93 | { | |
| 94 | 374 | if (rshift[1]<shift) { |
| 95 | 12 | modified=true; |
| 96 | 12 | rshift[1] = shift; |
| 97 | } | |
| 98 | } | |
| 99 | } | |
| 100 | 599 | return modified; |
| 101 | } | |
| 102 | /** | |
| 103 | * get shifted position for pos | |
| 104 | * | |
| 105 | * @param pos | |
| 106 | * int | |
| 107 | * @return int shifted position | |
| 108 | */ | |
| 109 | 211 | public int shift(int pos) |
| 110 | { | |
| 111 | 211 | if (shifts.size() == 0) |
| 112 | { | |
| 113 | 3 | return pos; |
| 114 | } | |
| 115 | 208 | int shifted = pos; |
| 116 | 208 | int sidx = 0; |
| 117 | 208 | int rshift[]; |
| 118 | ? | while (sidx < shifts.size() |
| 119 | && (rshift = (shifts.get(sidx++)))[0] <= pos) | |
| 120 | { | |
| 121 | 212 | shifted += rshift[1]; |
| 122 | } | |
| 123 | 208 | return shifted; |
| 124 | } | |
| 125 | ||
| 126 | /** | |
| 127 | * clear all shifts | |
| 128 | */ | |
| 129 | 0 | public synchronized void clear() |
| 130 | { | |
| 131 | 0 | shifts.clear(); |
| 132 | } | |
| 133 | ||
| 134 | /** | |
| 135 | * invert the shifts | |
| 136 | * | |
| 137 | * @return ShiftList with inverse shift operations | |
| 138 | */ | |
| 139 | 0 | public ShiftList getInverse() |
| 140 | { | |
| 141 | 0 | ShiftList inverse = new ShiftList(); |
| 142 | 0 | synchronized (shifts) |
| 143 | { | |
| 144 | 0 | if (shifts != null) |
| 145 | { | |
| 146 | 0 | for (int[] sh : shifts) |
| 147 | { | |
| 148 | 0 | if (sh != null) |
| 149 | { | |
| 150 | 0 | inverse.shifts.add(new int[] { sh[0], -sh[1] }); |
| 151 | } | |
| 152 | } | |
| 153 | } | |
| 154 | } | |
| 155 | 0 | return inverse; |
| 156 | } | |
| 157 | ||
| 158 | /** | |
| 159 | * parse a 1d map of position 1<i<n to L<pos[i]<N such as that | |
| 160 | * returned from SequenceI.gapMap() | |
| 161 | * | |
| 162 | * @param gapMap | |
| 163 | * @return shifts from map index to mapped position | |
| 164 | */ | |
| 165 | 3 | public static ShiftList parseMap(int[] gapMap) |
| 166 | { | |
| 167 | 3 | ShiftList shiftList = null; |
| 168 | 3 | if (gapMap != null && gapMap.length > 0) |
| 169 | { | |
| 170 | 1 | shiftList = new ShiftList(); |
| 171 | 8 | for (int i = 0, p = 0; i < gapMap.length; p++, i++) |
| 172 | { | |
| 173 | 7 | if (p != gapMap[i]) |
| 174 | { | |
| 175 | 4 | shiftList.addShift(p, gapMap[i] - p); |
| 176 | 4 | p = gapMap[i]; |
| 177 | } | |
| 178 | } | |
| 179 | } | |
| 180 | 3 | return shiftList; |
| 181 | } | |
| 182 | ||
| 183 | 87 | public List<int[]> getShifts() |
| 184 | { | |
| 185 | 87 | return shifts; |
| 186 | } | |
| 187 | } |