Coverage Report
File ContactMatrixI.java
Coverage histogram
52% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| ContactMatrixI | 31 | 50 | 35 |
Contributing tests
This file is covered by 10 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.awt.Color; | |
| 24 | import java.util.Arrays; | |
| 25 | import java.util.BitSet; | |
| 26 | import java.util.List; | |
| 27 | ||
| 28 | import jalview.util.ColorUtils; | |
| 29 | import jalview.ws.datamodel.MappableContactMatrixI; | |
| 30 | ||
| 31 | public interface ContactMatrixI | |
| 32 | { | |
| 33 | ||
| 34 | ContactListI getContactList(int column); | |
| 35 | ||
| 36 | float getMin(); | |
| 37 | ||
| 38 | float getMax(); | |
| 39 | ||
| 40 | String getAnnotDescr(); | |
| 41 | ||
| 42 | String getAnnotLabel(); | |
| 43 | ||
| 44 | /** | |
| 45 | * string indicating how the contactMatrix should be rendered - stored in | |
| 46 | * calcId | |
| 47 | * | |
| 48 | * @return | |
| 49 | */ | |
| 50 | String getType(); | |
| 51 | ||
| 52 | int getWidth(); | |
| 53 | ||
| 54 | int getHeight(); | |
| 55 | ||
| 56 | public GroupSetI getGroupSet(); | |
| 57 | ||
| 58 | /// proxy methods to simplify use of the interface | |
| 59 | /// Mappable contact matrices can override these to perform mapping | |
| 60 | ||
| 61 | 7135 |  default public boolean hasGroupSet() |
| 62 | { | |
| 63 | 7135 | return getGroupSet() != null; |
| 64 | } | |
| 65 | ||
| 66 | 5 | default boolean hasGroups() |
| 67 | { | |
| 68 | 5 | return hasGroupSet() && getGroupSet().hasGroups(); |
| 69 | } | |
| 70 | ||
| 71 | 3552 | default BitSet getGroupsFor(int column) |
| 72 | { | |
| 73 | 3552 | if (!hasGroupSet()) |
| 74 | { | |
| 75 | 0 | BitSet colbitset = new BitSet(); |
| 76 | 0 | colbitset.set(column); |
| 77 | 0 | return colbitset; |
| 78 | } | |
| 79 | 3552 | return getGroupSet().getGroupsFor(column); |
| 80 | } | |
| 81 | ||
| 82 | 6 | default List<BitSet> getGroups() |
| 83 | { | |
| 84 | 6 | if (!hasGroupSet()) |
| 85 | { | |
| 86 | 0 | return Arrays.asList(); |
| 87 | } | |
| 88 | 6 | return getGroupSet().getGroups(); |
| 89 | } | |
| 90 | ||
| 91 | 5 | default boolean hasTree() |
| 92 | { | |
| 93 | 5 | return hasGroupSet() ? getGroupSet().hasTree() : false; |
| 94 | } | |
| 95 | ||
| 96 | /** | |
| 97 | * Newick representation of clustered matrix | |
| 98 | * | |
| 99 | * @return null unless hasTree is true | |
| 100 | */ | |
| 101 | 6 | default String getNewick() |
| 102 | { | |
| 103 | 6 | return hasGroupSet() ? getGroupSet().getNewick() : null; |
| 104 | } | |
| 105 | ||
| 106 | 3 | default String getTreeMethod() |
| 107 | { | |
| 108 | 3 | return hasGroupSet() ? getGroupSet().getTreeMethod() : null; |
| 109 | } | |
| 110 | ||
| 111 | 3 | default boolean hasCutHeight() |
| 112 | { | |
| 113 | 3 | return hasGroupSet() ? getGroupSet().hasCutHeight() : false; |
| 114 | } | |
| 115 | ||
| 116 | 3 | default double getCutHeight() |
| 117 | { | |
| 118 | 3 | return hasGroupSet() ? getGroupSet().getCutHeight() : 0; |
| 119 | } | |
| 120 | ||
| 121 | 0 | default void updateGroups(List<BitSet> colGroups) |
| 122 | { | |
| 123 | 0 | if (hasGroupSet()) |
| 124 | { | |
| 125 | 0 | getGroupSet().updateGroups(colGroups); |
| 126 | } | |
| 127 | } | |
| 128 | ||
| 129 | 0 | default void setColorForGroup(BitSet bs, Color color) |
| 130 | { | |
| 131 | 0 | if (hasGroupSet()) |
| 132 | { | |
| 133 | 0 | getGroupSet().setColorForGroup(bs, color); |
| 134 | } | |
| 135 | } | |
| 136 | ||
| 137 | 3552 | default Color getColourForGroup(BitSet bs) |
| 138 | { | |
| 139 | 3552 | if (hasGroupSet()) |
| 140 | { | |
| 141 | 3552 | return getGroupSet().getColourForGroup(bs); |
| 142 | } | |
| 143 | else | |
| 144 | { | |
| 145 | 0 | return Color.white; |
| 146 | } | |
| 147 | } | |
| 148 | ||
| 149 | void setGroupSet(GroupSet makeGroups); | |
| 150 | ||
| 151 | 0 | default void randomlyReColourGroups() |
| 152 | { | |
| 153 | 0 | if (hasGroupSet()) |
| 154 | { | |
| 155 | 0 | GroupSetI groups = getGroupSet(); |
| 156 | 0 | for (BitSet group : groups.getGroups()) |
| 157 | { | |
| 158 | 0 | groups.setColorForGroup(group, ColorUtils.getARandomColor()); |
| 159 | } | |
| 160 | } | |
| 161 | } | |
| 162 | ||
| 163 | 0 | default void transferGroupColorsTo(AlignmentAnnotation aa) |
| 164 | { | |
| 165 | 0 | if (hasGroupSet()) |
| 166 | { | |
| 167 | 0 | GroupSetI groups = getGroupSet(); |
| 168 | // stash colors in linked annotation row. | |
| 169 | // doesn't work yet. TESTS! | |
| 170 | 0 | int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1 |
| 171 | : 0; | |
| 172 | 0 | Annotation ae; |
| 173 | 0 | Color gpcol = null; |
| 174 | 0 | int[] seqpos = null; |
| 175 | 0 | for (BitSet gp : groups.getGroups()) |
| 176 | { | |
| 177 | 0 | gpcol = groups.getColourForGroup(gp); |
| 178 | 0 | for (int p = gp.nextSetBit(0); p >= 0 |
| 179 | && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1)) | |
| 180 | { | |
| 181 | 0 | if (this instanceof MappableContactMatrixI) |
| 182 | { | |
| 183 | 0 | MappableContactMatrixI mcm = (MappableContactMatrixI) this; |
| 184 | 0 | seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p); |
| 185 | 0 | if (seqpos == null) |
| 186 | { | |
| 187 | // no mapping for this column. | |
| 188 | 0 | continue; |
| 189 | } | |
| 190 | // TODO: handle ranges... | |
| 191 | 0 | ae = aa.getAnnotationForPosition(seqpos[0]); |
| 192 | } | |
| 193 | else | |
| 194 | { | |
| 195 | 0 | ae = aa.getAnnotationForPosition(p + sstart); |
| 196 | } | |
| 197 | 0 | if (ae != null) |
| 198 | { | |
| 199 | 0 | ae.colour = gpcol.brighter().darker(); |
| 200 | } | |
| 201 | } | |
| 202 | } | |
| 203 | } | |
| 204 | } | |
| 205 | ||
| 206 | /** | |
| 207 | * look up the colour for a column in the associated contact matrix | |
| 208 | * | |
| 209 | * @return Color.white or assigned colour | |
| 210 | */ | |
| 211 | 0 | default Color getGroupColorForPosition(int column) |
| 212 | { | |
| 213 | 0 | if (hasGroupSet()) |
| 214 | { | |
| 215 | 0 | GroupSetI groups = getGroupSet(); |
| 216 | 0 | for (BitSet gp : groups.getGroups()) |
| 217 | { | |
| 218 | 0 | if (gp.get(column)) |
| 219 | { | |
| 220 | 0 | return groups.getColourForGroup(gp); |
| 221 | } | |
| 222 | } | |
| 223 | } | |
| 224 | 0 | return Color.white; |
| 225 | } | |
| 226 | ||
| 227 | /** | |
| 228 | * direct access to column and row position of matrix | |
| 229 | * | |
| 230 | * Implementations are allowed to throw RunTimeExceptions if _column/i are out | |
| 231 | * of bounds | |
| 232 | * | |
| 233 | * @param column | |
| 234 | * @param row | |
| 235 | * @return | |
| 236 | */ | |
| 237 | double getElementAt(int column, int row); | |
| 238 | ||
| 239 | } |