Coverage Report
File TreeBuilder.java
Coverage histogram
21% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| TreeBuilder | 42 | 57 | 21 |
Contributing tests
This file is covered by 1 test.
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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.analysis; | |
| 22 | ||
| 23 | import jalview.api.analysis.ScoreModelI; | |
| 24 | import jalview.api.analysis.SimilarityParamsI; | |
| 25 | import jalview.datamodel.AlignmentAnnotation; | |
| 26 | import jalview.datamodel.AlignmentView; | |
| 27 | import jalview.datamodel.BinaryNode; | |
| 28 | import jalview.datamodel.CigarArray; | |
| 29 | import jalview.datamodel.SeqCigar; | |
| 30 | import jalview.datamodel.SequenceI; | |
| 31 | import jalview.datamodel.SequenceNode; | |
| 32 | import jalview.util.Constants; | |
| 33 | import jalview.viewmodel.AlignmentViewport; | |
| 34 | ||
| 35 | ||
| 36 | import java.util.ArrayList; | |
| 37 | import java.util.BitSet; | |
| 38 | import java.util.HashMap; | |
| 39 | import java.util.List; | |
| 40 | import java.util.Vector; | |
| 41 | ||
| 42 | public abstract class TreeBuilder extends TreeEngine | |
| 43 | { | |
| 44 | public static final String AVERAGE_DISTANCE = "AV"; | |
| 45 | ||
| 46 | public static final String NEIGHBOUR_JOINING = "NJ"; | |
| 47 | ||
| 48 | protected SequenceI[] sequences; | |
| 49 | ||
| 50 | protected List<String> labels; | |
| 51 | ||
| 52 | // Map to store node pos : annotation details | |
| 53 | // (additional details from annotation property) | |
| 54 | protected HashMap<Integer, String> annotationDetails; | |
| 55 | ||
| 56 | public AlignmentView seqData; | |
| 57 | ||
| 58 | private AlignmentView seqStrings; | |
| 59 | ||
| 60 | /** | |
| 61 | * Constructor | |
| 62 | * | |
| 63 | * @param av | |
| 64 | * @param sm | |
| 65 | * @param scoreParameters | |
| 66 | */ | |
| 67 | 1 |  public TreeBuilder(AlignmentViewport av, ScoreModelI sm, |
| 68 | SimilarityParamsI scoreParameters) | |
| 69 | { | |
| 70 | 1 | int start, end; |
| 71 | 1 | boolean selview = av.getSelectionGroup() != null |
| 72 | && av.getSelectionGroup().getSize() >= 1; | |
| 73 | 1 | seqStrings = av.getAlignmentView(selview); |
| 74 | // FIXME @RENIA - we should check that there are enough annotation tracks to | |
| 75 | // build a tree! | |
| 76 | 1 | if (!selview)// && !sm.isSecondaryStructure()) |
| 77 | { | |
| 78 | 0 | start = 0; |
| 79 | 0 | end = av.getAlignment().getWidth(); |
| 80 | 0 | this.sequences = av.getAlignment().getSequencesArray(); |
| 81 | } | |
| 82 | else | |
| 83 | { | |
| 84 | 1 | start = av.getSelectionGroup().getStartRes(); |
| 85 | 1 | end = av.getSelectionGroup().getEndRes() + 1; |
| 86 | 1 | this.sequences = av.getSelectionGroup() |
| 87 | .getSequencesInOrder(av.getAlignment()); | |
| 88 | } | |
| 89 | ||
| 90 | 1 | init(seqStrings, start, end); |
| 91 | ||
| 92 | 1 | computeTree(sm, scoreParameters); |
| 93 | } | |
| 94 | ||
| 95 | 1 | public SequenceI[] getSequences() |
| 96 | { | |
| 97 | 1 | return sequences; |
| 98 | } | |
| 99 | ||
| 100 | /** | |
| 101 | * | |
| 102 | * @return true if tree has real distances | |
| 103 | */ | |
| 104 | 1 | public boolean hasDistances() |
| 105 | { | |
| 106 | 1 | return true; |
| 107 | } | |
| 108 | ||
| 109 | /** | |
| 110 | * | |
| 111 | * @return true if tree has real bootstrap values | |
| 112 | */ | |
| 113 | 1 | public boolean hasBootstrap() |
| 114 | { | |
| 115 | 1 | return false; |
| 116 | } | |
| 117 | ||
| 118 | 1 | public boolean hasRootDistance() |
| 119 | { | |
| 120 | 1 | return true; |
| 121 | } | |
| 122 | ||
| 123 | 1 | public List<String> getLabels(){ |
| 124 | 1 | return this.labels; |
| 125 | } | |
| 126 | ||
| 127 | ArrayList<AlignmentAnnotation> ssAnnotationForSeqs; | |
| 128 | ||
| 129 | /** | |
| 130 | * Calculates the tree using the given score model and parameters, and the | |
| 131 | * configured tree type | |
| 132 | * <p> | |
| 133 | * If the score model computes pairwise distance scores, then these are used | |
| 134 | * directly to derive the tree | |
| 135 | * <p> | |
| 136 | * If the score model computes similarity scores, then the range of the scores | |
| 137 | * is reversed to give a distance measure, and this is used to derive the tree | |
| 138 | * | |
| 139 | * @param sm | |
| 140 | * @param scoreOptions | |
| 141 | */ | |
| 142 | 1 | protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions) |
| 143 | { | |
| 144 | 1 | labels = new ArrayList<String>(); |
| 145 | 1 | annotationDetails = new HashMap<Integer, String>(); |
| 146 | 1 | ssAnnotationForSeqs = new ArrayList<AlignmentAnnotation>(); |
| 147 | 1 | sequences = sm.expandSeqData(sequences, seqData, scoreOptions, |
| 148 | labels, ssAnnotationForSeqs, annotationDetails); | |
| 149 | 1 | noseqs = sequences.length; |
| 150 | ||
| 151 | 1 | distances = sm.findDistances(seqData, scoreOptions); |
| 152 | ||
| 153 | 1 | makeLeaves(); |
| 154 | ||
| 155 | 1 | noClus = clusters.size(); |
| 156 | ||
| 157 | 1 | cluster(); |
| 158 | } | |
| 159 | ||
| 160 | 1 | protected void init(AlignmentView seqView, int start, int end) |
| 161 | { | |
| 162 | 1 | this.node = new Vector<BinaryNode>(); |
| 163 | 1 | if (seqView != null) |
| 164 | { | |
| 165 | 1 | this.seqData = seqView; |
| 166 | } | |
| 167 | else | |
| 168 | { | |
| 169 | 0 | SeqCigar[] seqs = new SeqCigar[sequences.length]; |
| 170 | 0 | for (int i = 0; i < sequences.length; i++) |
| 171 | { | |
| 172 | 0 | seqs[i] = new SeqCigar(sequences[i], start, end); |
| 173 | } | |
| 174 | 0 | CigarArray sdata = new CigarArray(seqs); |
| 175 | 0 | sdata.addOperation(CigarArray.M, end - start + 1); |
| 176 | 0 | this.seqData = new AlignmentView(sdata, start); |
| 177 | } | |
| 178 | ||
| 179 | /* | |
| 180 | * count the non-null sequences | |
| 181 | */ | |
| 182 | 1 | noseqs = 0; |
| 183 | ||
| 184 | 1 | done = new BitSet(); |
| 185 | ||
| 186 | 1 | for (SequenceI seq : sequences) |
| 187 | { | |
| 188 | 15 | if (seq != null) |
| 189 | { | |
| 190 | 15 | noseqs++; |
| 191 | } | |
| 192 | } | |
| 193 | } | |
| 194 | ||
| 195 | /** | |
| 196 | * Start by making a cluster for each individual sequence | |
| 197 | */ | |
| 198 | 1 | void makeLeaves() |
| 199 | { | |
| 200 | 1 | clusters = new Vector<BitSet>(); |
| 201 | ||
| 202 | 19 | for (int i = 0; i < noseqs; i++) |
| 203 | { | |
| 204 | 18 | SequenceNode sn = new SequenceNode(); |
| 205 | ||
| 206 | 18 | sn.setElement(sequences[i]); |
| 207 | ||
| 208 | 18 | if (labels.size() == noseqs) |
| 209 | { | |
| 210 | 18 | sn.setLabel(labels.get(i)); |
| 211 | } | |
| 212 | ||
| 213 | 18 | if (ssAnnotationForSeqs != null && !ssAnnotationForSeqs.isEmpty() && ssAnnotationForSeqs.get(i) != null) |
| 214 | { | |
| 215 | ||
| 216 | 4 | sn.setAlignmentAnnotation(ssAnnotationForSeqs.get(i)); |
| 217 | ||
| 218 | // Initialise AnnotationDetails if present for the annotation | |
| 219 | 4 | String annotationData = annotationDetails.get(i); |
| 220 | 4 | if(annotationData != null && annotationData.length() > 0) |
| 221 | { | |
| 222 | 0 | sn.setAnnotationDetails(annotationData); |
| 223 | } | |
| 224 | ||
| 225 | } | |
| 226 | ||
| 227 | 18 | sn.setName(sequences[i].getName()); |
| 228 | ||
| 229 | 18 | node.addElement(sn); |
| 230 | 18 | BitSet bs = new BitSet(); |
| 231 | 18 | bs.set(i); |
| 232 | 18 | clusters.addElement(bs); |
| 233 | } | |
| 234 | } | |
| 235 | ||
| 236 | 1 | public AlignmentView getOriginalData() |
| 237 | { | |
| 238 | 1 | return seqStrings; |
| 239 | } | |
| 240 | ||
| 241 | } |