2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.util.MessageManager;
26 import jalview.ws.jws2.jabaws2.Jws2Instance;
27 import jalview.ws.params.WsParamSetI;
28 import jalview.ws.uimodel.AlignAnalysisUIText;
30 import java.util.ArrayList;
31 import java.util.List;
34 import java.util.TreeSet;
36 import compbio.data.sequence.FastaSequence;
37 import compbio.data.sequence.Score;
38 import compbio.metadata.Argument;
40 public class AAConClient extends JabawsCalcWorker
43 public AAConClient(Jws2Instance service, AlignFrame alignFrame,
44 WsParamSetI preset, List<Argument> paramset)
46 super(service, alignFrame, preset, paramset);
49 nucleotidesAllowed = false;
50 proteinAllowed = true;
51 filterNonStandardResidues = true;
52 gapMap = new boolean[0];
57 public String getServiceActionText()
59 return "calculating Amino acid consensus using AACon service";
63 * update the consensus annotation from the sequence profile data using
64 * current visualization settings.
68 public void updateResultAnnotation(boolean immediate)
70 if (immediate || !calcMan.isWorking(this) && scoremanager != null)
72 Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
73 int alWidth = alignViewport.getAlignment().getWidth();
74 ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
75 for (String score : scoremap.keySet())
77 Set<Score> scores = scoremap.get(score);
78 for (Score scr : scores)
80 if (scr.getRanges() != null && scr.getRanges().size() > 0)
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();
94 createAnnotationRowsForScores(ourAnnot, getCalcId(), alWidth,
100 if (ourAnnot.size() > 0)
102 updateOurAnnots(ourAnnot);
108 boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
110 return (seqs.size() > 1);
114 public String getCalcId()
119 private static String CALC_ID = "jabaws2.AACon";
121 public static AlignAnalysisUIText getAlignAnalysisUITest()
123 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"));