Coverage Report
File ContactGeometry.java
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29% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| ContactGeometry | 39 | 51 | 27 | ||
| ContactGeometry.contactInterval | 103 | 9 | 5 |
Contributing tests
This file is covered by 12 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 java.util.Arrays; | |
| 24 | import java.util.Iterator; | |
| 25 | import java.util.List; | |
| 26 | ||
| 27 | import jalview.datamodel.ColumnSelection; | |
| 28 | import jalview.datamodel.ContactListI; | |
| 29 | import jalview.datamodel.HiddenColumns; | |
| 30 | import jalview.renderer.ContactGeometry.contactInterval; | |
| 31 | ||
| 32 | /** | |
| 33 | * encapsulate logic for mapping between positions in a ContactList and their | |
| 34 | * rendered representation in a given number of pixels. | |
| 35 | * | |
| 36 | * @author jprocter | |
| 37 | * | |
| 38 | */ | |
| 39 | public class ContactGeometry | |
| 40 | { | |
| 41 | ||
| 42 | final ContactListI contacts; | |
| 43 | ||
| 44 | /** | |
| 45 | * how many pixels per contact (1..many) | |
| 46 | */ | |
| 47 | final int pixels_step; | |
| 48 | ||
| 49 | /** | |
| 50 | * how many contacts per pixel (many > 0) | |
| 51 | */ | |
| 52 | final double contacts_per_pixel; | |
| 53 | ||
| 54 | /** | |
| 55 | * number of contacts being mapped | |
| 56 | */ | |
| 57 | final int contact_height; | |
| 58 | ||
| 59 | /** | |
| 60 | * number of pixels to map contact_height to | |
| 61 | */ | |
| 62 | final int graphHeight; | |
| 63 | ||
| 64 | /** | |
| 65 | * number of contacts for each pixel_step - to last whole contact | |
| 66 | */ | |
| 67 | final double contacts_step; | |
| 68 | ||
| 69 | final int lastStep; | |
| 70 | ||
| 71 | /** | |
| 72 | * Bean used to map from a range of contacts to a range of pixels | |
| 73 | * | |
| 74 | * @param contacts | |
| 75 | * @param graphHeight | |
| 76 | * Number of pixels to map given range of contacts | |
| 77 | */ | |
| 78 | 145041 |  public ContactGeometry(final ContactListI contacts, int graphHeight) |
| 79 | { | |
| 80 | 145041 | this.contacts = contacts; |
| 81 | 145041 | this.graphHeight = graphHeight; |
| 82 | 145041 | contact_height = contacts.getContactHeight(); |
| 83 | // fractional number of contacts covering each pixel | |
| 84 | 145041 | contacts_per_pixel = (graphHeight <= 1) ? contact_height |
| 85 | : ((double) contact_height) / ((double) graphHeight); | |
| 86 | ||
| 87 | 145041 | if (contacts_per_pixel >= 1) |
| 88 | { | |
| 89 | // many contacts rendered per pixel | |
| 90 | 32006 | pixels_step = 1; |
| 91 | } | |
| 92 | else | |
| 93 | { | |
| 94 | // pixel height for each contact | |
| 95 | 113035 | pixels_step = (int) Math |
| 96 | .ceil(((double) graphHeight) / (double) contact_height); | |
| 97 | } | |
| 98 | 145041 | contacts_step = pixels_step * contacts_per_pixel; |
| 99 | 145041 | lastStep = (int) Math.min((double) graphHeight, |
| 100 | ((double) graphHeight) / ((double) pixels_step)); | |
| 101 | } | |
| 102 | ||
| 103 | public class contactInterval | |
| 104 | { | |
| 105 | 147128654 | public contactInterval(int cStart, int cEnd, int pStart, int pEnd) |
| 106 | { | |
| 107 | 147128654 | this.cStart = cStart; |
| 108 | 147128654 | this.cEnd = cEnd; |
| 109 | 147128655 | this.pStart = pStart; |
| 110 | 147128655 | this.pEnd = pEnd; |
| 111 | } | |
| 112 | ||
| 113 | // range on contact list | |
| 114 | public final int cStart; | |
| 115 | ||
| 116 | public final int cEnd; | |
| 117 | ||
| 118 | // range in pixels | |
| 119 | public final int pStart; | |
| 120 | ||
| 121 | public final int pEnd; | |
| 122 | ||
| 123 | 174 | @Override |
| 124 | public boolean equals(Object obj) | |
| 125 | { | |
| 126 | 174 | if (obj == null || !(obj instanceof contactInterval)) |
| 127 | { | |
| 128 | 0 | return false; |
| 129 | } | |
| 130 | 174 | contactInterval them = (contactInterval) obj; |
| 131 | 174 | return cStart == them.cStart && cEnd == them.cEnd && pEnd == them.pEnd |
| 132 | && pStart == them.pStart; | |
| 133 | } | |
| 134 | ||
| 135 | 4 | @Override |
| 136 | public String toString() | |
| 137 | { | |
| 138 | 4 | return "Contacts [" + cStart + "," + cEnd + "] : Pixels [" + pStart |
| 139 | + "," + pEnd + "]"; | |
| 140 | } | |
| 141 | } | |
| 142 | ||
| 143 | /** | |
| 144 | * | |
| 145 | * @param columnSelection | |
| 146 | * @param ci | |
| 147 | * @param visibleOnly | |
| 148 | * - when true, only test intersection of visible columns given | |
| 149 | * matrix range | |
| 150 | * @return true if the range on the matrix specified by ci intersects with | |
| 151 | * selected columns in the ContactListI's reference frame. | |
| 152 | */ | |
| 153 | ||
| 154 | 146452 | boolean intersects(contactInterval ci, ColumnSelection columnSelection, |
| 155 | HiddenColumns hiddenColumns, boolean visibleOnly) | |
| 156 | { | |
| 157 | 146452 | boolean rowsel = false; |
| 158 | 146452 | final int[] mappedRange = contacts.getMappedPositionsFor(ci.cStart, |
| 159 | ci.cEnd); | |
| 160 | 146452 | if (mappedRange == null) |
| 161 | { | |
| 162 | 0 | return false; |
| 163 | } | |
| 164 | 292902 | for (int p = 0; p < mappedRange.length && !rowsel; p += 2) |
| 165 | { | |
| 166 | 146452 | boolean containsHidden = false; |
| 167 | 146451 | if (visibleOnly && hiddenColumns != null |
| 168 | && hiddenColumns.hasHiddenColumns()) | |
| 169 | { | |
| 170 | // TODO: turn into function on hiddenColumns and create test !! | |
| 171 | 0 | Iterator<int[]> viscont = hiddenColumns.getVisContigsIterator( |
| 172 | -1 + mappedRange[p], -1 + mappedRange[p + 1], false); | |
| 173 | 0 | containsHidden = !viscont.hasNext(); |
| 174 | 0 | if (!containsHidden) |
| 175 | { | |
| 176 | 0 | for (int[] interval = viscont.next(); viscont |
| 177 | .hasNext(); rowsel |= columnSelection | |
| 178 | .intersects(interval[p], interval[p + 1])) | |
| 179 | 0 | ; |
| 180 | } | |
| 181 | } | |
| 182 | else | |
| 183 | { | |
| 184 | 146451 | rowsel = columnSelection.intersects(-1 + mappedRange[p], |
| 185 | -1 + mappedRange[p + 1]); | |
| 186 | } | |
| 187 | } | |
| 188 | 146451 | return rowsel; |
| 189 | ||
| 190 | } | |
| 191 | ||
| 192 | /** | |
| 193 | * Return mapped cell intersecting pStart \ | |
| 194 | * | |
| 195 | * FIXME: REDUNDANT METHOD - COULD DELETE FIXME: OR RE-IMPLEMENT AS EFFICIENT | |
| 196 | * RANGE QUERY | |
| 197 | * | |
| 198 | * @param pStart | |
| 199 | * [0..) | |
| 200 | * @param pEnd | |
| 201 | * @return nearest full cell containing pStart - does not set | |
| 202 | * contactInterval.pEnd or cEnd to equivalent position on pEnd ! | |
| 203 | */ | |
| 204 | 84 | public contactInterval mapFor(int pStart, int pEnd) |
| 205 | { | |
| 206 | 84 | if (pStart < 0) |
| 207 | { | |
| 208 | 0 | pStart = 0; |
| 209 | } | |
| 210 | 84 | if (pEnd < pStart) |
| 211 | { | |
| 212 | 0 | pEnd = pStart; |
| 213 | } | |
| 214 | 84 | if (pEnd >= graphHeight) |
| 215 | { | |
| 216 | 4 | pEnd = graphHeight - 1; |
| 217 | } | |
| 218 | 84 | if (pStart >= graphHeight) |
| 219 | { | |
| 220 | 0 | pStart = graphHeight - pixels_step; |
| 221 | } | |
| 222 | 84 | int step = Math.floorDiv(pStart, pixels_step); |
| 223 | 84 | return findStep(step); |
| 224 | } | |
| 225 | ||
| 226 | /** | |
| 227 | * | |
| 228 | * @param step | |
| 229 | * [0..) n steps covering height and contactHeight | |
| 230 | * @return contactInterval for step, or null if out of bounds | |
| 231 | */ | |
| 232 | 147128655 | contactInterval findStep(int step) |
| 233 | { | |
| 234 | 147128654 | if (step < 0 || step > lastStep) |
| 235 | { | |
| 236 | 0 | return null; |
| 237 | } | |
| 238 | 147128654 | return new contactInterval((int) Math.floor(contacts_step * step), |
| 239 | -1 + (int) Math.min(contact_height, | |
| 240 | Math.floor(contacts_step * (step + 1))), | |
| 241 | pixels_step * step, | |
| 242 | Math.min(graphHeight, (step + 1) * pixels_step) - 1); | |
| 243 | } | |
| 244 | ||
| 245 | /** | |
| 246 | * return the cell containing given pixel | |
| 247 | * | |
| 248 | * @param pCentre | |
| 249 | * @return range for pCEntre | |
| 250 | */ | |
| 251 | 146537 | public contactInterval mapFor(int pCentre) |
| 252 | { | |
| 253 | 146537 | if (pCentre >= graphHeight + pixels_step) |
| 254 | { | |
| 255 | 0 | return null; |
| 256 | } | |
| 257 | 146537 | int step = Math.floorDiv(pCentre, pixels_step); |
| 258 | 146537 | return findStep(step); |
| 259 | } | |
| 260 | ||
| 261 | 141374 | public List<contactInterval> allSteps() |
| 262 | { | |
| 263 | 141374 | contactInterval[] array = new contactInterval[lastStep + 1]; |
| 264 | 141374 | int csum = 0, psum = 0; |
| 265 | 147123408 | for (int i = 0; i <= lastStep; i++) |
| 266 | { | |
| 267 | 146982034 | array[i] = findStep(i); |
| 268 | 146982034 | csum += 1 + array[i].cEnd - array[i].cStart; |
| 269 | 146982034 | psum += 1 + array[i].pEnd - array[i].pStart; |
| 270 | } | |
| 271 | 141374 | if (csum != contact_height || psum != graphHeight) |
| 272 | { | |
| 273 | 0 | System.err.println("csum = " + csum + " not " + contact_height + "\n" |
| 274 | + "psum = " + psum + " not " + graphHeight); | |
| 275 | 0 | return null; |
| 276 | } | |
| 277 | 141374 | return Arrays.asList(array); |
| 278 | } | |
| 279 | ||
| 280 | 0 | public Iterator<contactInterval> iterateOverContactIntervals( |
| 281 | int graphHeight) | |
| 282 | { | |
| 283 | // NOT YET IMPLEMENTED | |
| 284 | 0 | return null; |
| 285 | // int cstart = 0, cend; | |
| 286 | // | |
| 287 | // for (int ht = y2, | |
| 288 | // eht = y2 - graphHeight; ht >= eht; ht -= pixels_step) | |
| 289 | // { | |
| 290 | // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel); | |
| 291 | // cend = (int) Math.min(contact_height, | |
| 292 | // Math.ceil(cstart + contacts_per_pixel * pixels_step)); | |
| 293 | // | |
| 294 | // return new Iterator<contactIntervals>() { | |
| 295 | // | |
| 296 | // @Override | |
| 297 | // public boolean hasNext() | |
| 298 | // { | |
| 299 | // // TODO Auto-generated method stub | |
| 300 | // return false; | |
| 301 | // } | |
| 302 | // | |
| 303 | // @Override | |
| 304 | // public contactIntervals next() | |
| 305 | // { | |
| 306 | // // TODO Auto-generated method stub | |
| 307 | // return null; | |
| 308 | // } | |
| 309 | // | |
| 310 | // } | |
| 311 | } | |
| 312 | } |