2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ws.jws2;
23 import jalview.datamodel.AlignmentAnnotation;
24 import jalview.gui.AlignFrame;
25 import jalview.gui.AlignmentPanel;
26 import jalview.ws.jws2.dm.AAConSettings;
27 import jalview.ws.jws2.jabaws2.Jws2Instance;
28 import jalview.ws.params.WsParamSetI;
29 import jalview.ws.uimodel.AlignAnalysisUIText;
31 import java.util.ArrayList;
32 import java.util.List;
35 import java.util.TreeSet;
37 import compbio.data.sequence.FastaSequence;
38 import compbio.data.sequence.Score;
39 import compbio.metadata.Argument;
41 public class AAConClient extends JabawsCalcWorker
44 public AAConClient(Jws2Instance service, AlignFrame alignFrame,
45 WsParamSetI preset, List<Argument> paramset)
47 super(service, alignFrame, preset, paramset);
50 nucleotidesAllowed = false;
51 proteinAllowed = true;
52 gapMap = new boolean[0];
56 public String getServiceActionText()
58 return "calculating Amino acid consensus using AACon service";
62 * update the consensus annotation from the sequence profile data using
63 * current visualization settings.
66 public void updateResultAnnotation(boolean immediate)
68 if (immediate || !calcMan.isWorking(this) && scoremanager != null)
70 Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
71 int alWidth = alignViewport.getAlignment().getWidth();
72 ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
73 for (String score : scoremap.keySet())
75 Set<Score> scores = scoremap.get(score);
76 for (Score scr : scores)
78 if (scr.getRanges() != null && scr.getRanges().size() > 0)
81 * annotation in range annotation = findOrCreate(scr.getMethod(),
82 * true, null, null); Annotation[] elm = new Annotation[alWidth];
83 * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng
84 * : scr.getRanges()) { float val = vals.next().floatValue(); for
85 * (int i = rng.from; i <= rng.to; i++) { elm[i] = new
86 * Annotation("", "", ' ', val); } } annotation.annotations = elm;
87 * annotation.validateRangeAndDisplay();
92 createAnnotationRowsForScores(ourAnnot, getCalcId(), alWidth,
98 if (ourAnnot.size() > 0)
100 updateOurAnnots(ourAnnot);
106 boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
108 return (seqs.size() > 1);
112 public String getCalcId()
117 private static String CALC_ID = "jabaws2.AACon";
119 public static AlignAnalysisUIText getAlignAnalysisUITest()
121 return new AlignAnalysisUIText(
122 compbio.ws.client.Services.AAConWS.toString(),
123 jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true,
124 "AACon Calculations",
125 "When checked, AACon calculations are updated automatically.",
126 "Change AACon Settings...",
127 "Modify settings for AACon calculations.");