Coverage Report
File ContactListImpl.java
Coverage histogram
12% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| ContactListImpl | 33 | 35 | 17 |
Contributing tests
This file is covered by 21 tests.
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Source view
| 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.awt.Color; | |
| 24 | ||
| 25 | import jalview.renderer.ContactGeometry.contactInterval; | |
| 26 | ||
| 27 | /** | |
| 28 | * helper class to compute min/max/mean for a range on a contact list | |
| 29 | * | |
| 30 | * @author jprocter | |
| 31 | * | |
| 32 | */ | |
| 33 | public class ContactListImpl implements ContactListI | |
| 34 | { | |
| 35 | ContactListProviderI clist; | |
| 36 | ||
| 37 | 0 |  public static ContactListI newContactList(ContactListProviderI list) |
| 38 | { | |
| 39 | 0 | return new ContactListImpl(list); |
| 40 | } | |
| 41 | ||
| 42 | 7948 | public ContactListImpl(ContactListProviderI list) |
| 43 | { | |
| 44 | 7948 | clist = list; |
| 45 | } | |
| 46 | ||
| 47 | 0 | @Override |
| 48 | public int getPosition() | |
| 49 | { | |
| 50 | 0 | return clist.getPosition(); |
| 51 | } | |
| 52 | ||
| 53 | 4693839 | @Override |
| 54 | public double getContactAt(int column) | |
| 55 | { | |
| 56 | 4693839 | return clist.getContactAt(column); |
| 57 | } | |
| 58 | ||
| 59 | 4304432 | @Override |
| 60 | public int getContactHeight() | |
| 61 | { | |
| 62 | 4304432 | return clist.getContactHeight(); |
| 63 | } | |
| 64 | ||
| 65 | 156600 | @Override |
| 66 | public ContactRange getRangeFor(int from_column, int to_column) | |
| 67 | { | |
| 68 | // TODO: consider caching ContactRange for a particular call ? | |
| 69 | 156600 | if (clist instanceof ContactListI) |
| 70 | { | |
| 71 | // clist may implement getRangeFor in a more efficient way, so use theirs | |
| 72 | 0 | return ((ContactListI) clist).getRangeFor(from_column, to_column); |
| 73 | } | |
| 74 | 156600 | if (from_column < 0) |
| 75 | { | |
| 76 | 0 | from_column = 0; |
| 77 | } | |
| 78 | 156600 | if (to_column >= getContactHeight()) |
| 79 | { | |
| 80 | 0 | to_column = getContactHeight() - 1; |
| 81 | } | |
| 82 | 156600 | ContactRange cr = new ContactRange(); |
| 83 | 156600 | cr.setFrom_column(from_column); |
| 84 | 156600 | cr.setTo_column(to_column); |
| 85 | 156600 | double tot = 0; |
| 86 | 639605 | for (int i = from_column; i <= to_column; i++) |
| 87 | { | |
| 88 | 483013 | double contact = getContactAt(i); |
| 89 | 483016 | tot += contact; |
| 90 | 483037 | if (i == from_column) |
| 91 | { | |
| 92 | 156600 | cr.setMin(contact); |
| 93 | 156600 | cr.setMax(contact); |
| 94 | 156600 | cr.setMinPos(i); |
| 95 | 156599 | cr.setMaxPos(i); |
| 96 | } | |
| 97 | else | |
| 98 | { | |
| 99 | 326443 | if (cr.getMax() < contact) |
| 100 | { | |
| 101 | 76102 | cr.setMax(contact); |
| 102 | 76102 | cr.setMaxPos(i); |
| 103 | } | |
| 104 | 326441 | if (cr.getMin() < contact) |
| 105 | { | |
| 106 | 76102 | cr.setMin(contact); |
| 107 | 76103 | cr.setMinPos(i); |
| 108 | } | |
| 109 | } | |
| 110 | } | |
| 111 | 156592 | if (tot > 0 && to_column > from_column) |
| 112 | { | |
| 113 | 133108 | cr.setMean(tot / (1 + to_column - from_column)); |
| 114 | } | |
| 115 | else | |
| 116 | { | |
| 117 | 23484 | cr.setMean(tot); |
| 118 | } | |
| 119 | 156592 | return cr; |
| 120 | } | |
| 121 | ||
| 122 | 156549 | @Override |
| 123 | public int[] getMappedPositionsFor(int cStart, int cEnd) | |
| 124 | { | |
| 125 | 156549 | return clist.getMappedPositionsFor(cStart, cEnd); |
| 126 | } | |
| 127 | ||
| 128 | 3913 | @Override |
| 129 | public Color getColourForGroup() | |
| 130 | { | |
| 131 | 3913 | return clist.getColourForGroup(); |
| 132 | } | |
| 133 | } |