Coverage Report
File AAConClient.java
Coverage histogram
59% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AAConClient | 40 | 23 | 12 |
Contributing tests
This file is covered by 3 tests.
.
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.ws.jws2; | |
| 22 | ||
| 23 | import jalview.datamodel.AlignmentAnnotation; | |
| 24 | import jalview.gui.AlignFrame; | |
| 25 | import jalview.util.MessageManager; | |
| 26 | import jalview.ws.jws2.jabaws2.Jws2Instance; | |
| 27 | import jalview.ws.params.WsParamSetI; | |
| 28 | import jalview.ws.uimodel.AlignAnalysisUIText; | |
| 29 | ||
| 30 | import java.util.ArrayList; | |
| 31 | import java.util.List; | |
| 32 | import java.util.Map; | |
| 33 | import java.util.Set; | |
| 34 | import java.util.TreeSet; | |
| 35 | ||
| 36 | import compbio.data.sequence.FastaSequence; | |
| 37 | import compbio.data.sequence.Score; | |
| 38 | import compbio.metadata.Argument; | |
| 39 | ||
| 40 | public class AAConClient extends JabawsCalcWorker | |
| 41 | { | |
| 42 | ||
| 43 | 0 |  public AAConClient(Jws2Instance service, AlignFrame alignFrame, |
| 44 | WsParamSetI preset, List<Argument> paramset) | |
| 45 | { | |
| 46 | 0 | super(service, alignFrame, preset, paramset); |
| 47 | 0 | submitGaps = true; |
| 48 | 0 | alignedSeqs = true; |
| 49 | 0 | nucleotidesAllowed = false; |
| 50 | 0 | proteinAllowed = true; |
| 51 | 0 | filterNonStandardResidues = true; |
| 52 | 0 | gapMap = new boolean[0]; |
| 53 | 0 | initViewportParams(); |
| 54 | } | |
| 55 | ||
| 56 | 0 | @Override |
| 57 | public String getServiceActionText() | |
| 58 | { | |
| 59 | 0 | return "calculating Amino acid consensus using AACon service"; |
| 60 | } | |
| 61 | ||
| 62 | /** | |
| 63 | * update the consensus annotation from the sequence profile data using | |
| 64 | * current visualization settings. | |
| 65 | */ | |
| 66 | ||
| 67 | 0 | @Override |
| 68 | public void updateResultAnnotation(boolean immediate) | |
| 69 | { | |
| 70 | 0 | if (immediate || !calcMan.isWorking(this) && scoremanager != null) |
| 71 | { | |
| 72 | 0 | Map<String, TreeSet<Score>> scoremap = scoremanager.asMap(); |
| 73 | 0 | int alWidth = alignViewport.getAlignment().getWidth(); |
| 74 | 0 | ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>(); |
| 75 | 0 | for (String score : scoremap.keySet()) |
| 76 | { | |
| 77 | 0 | Set<Score> scores = scoremap.get(score); |
| 78 | 0 | for (Score scr : scores) |
| 79 | { | |
| 80 | 0 | if (scr.getRanges() != null && scr.getRanges().size() > 0) |
| 81 | { | |
| 82 | /** | |
| 83 | * annotation in range annotation = findOrCreate(scr.getMethod(), | |
| 84 | * true, null, null); Annotation[] elm = new Annotation[alWidth]; | |
| 85 | * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng | |
| 86 | * : scr.getRanges()) { float val = vals.next().floatValue(); for | |
| 87 | * (int i = rng.from; i <= rng.to; i++) { elm[i] = new | |
| 88 | * Annotation("", "", ' ', val); } } annotation.annotations = elm; | |
| 89 | * annotation.validateRangeAndDisplay(); | |
| 90 | */ | |
| 91 | } | |
| 92 | else | |
| 93 | { | |
| 94 | 0 | createAnnotationRowsForScores(ourAnnot, getCalcId(), alWidth, |
| 95 | scr); | |
| 96 | } | |
| 97 | } | |
| 98 | } | |
| 99 | ||
| 100 | 0 | if (ourAnnot.size() > 0) |
| 101 | { | |
| 102 | 0 | updateOurAnnots(ourAnnot); |
| 103 | } | |
| 104 | } | |
| 105 | } | |
| 106 | ||
| 107 | 0 | @Override |
| 108 | boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs) | |
| 109 | { | |
| 110 | 0 | return (seqs.size() > 1); |
| 111 | } | |
| 112 | ||
| 113 | 0 | @Override |
| 114 | public String getCalcId() | |
| 115 | { | |
| 116 | 0 | return CALC_ID; |
| 117 | } | |
| 118 | ||
| 119 | private static String CALC_ID = "jabaws2.AACon"; | |
| 120 | ||
| 121 | 6 | public static AlignAnalysisUIText getAlignAnalysisUITest() |
| 122 | { | |
| 123 | 6 | return new AlignAnalysisUIText( |
| 124 | compbio.ws.client.Services.AAConWS.toString(), | |
| 125 | jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true, | |
| 126 | MessageManager.getString("label.aacon_calculations"), | |
| 127 | MessageManager.getString("tooltip.aacon_calculations"), | |
| 128 | MessageManager.getString("label.aacon_settings"), | |
| 129 | MessageManager.getString("tooltip.aacon_settings")); | |
| 130 | } | |
| 131 | } |