2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.ws.jws2;
20 import jalview.datamodel.AlignmentAnnotation;
21 import jalview.gui.AlignFrame;
22 import jalview.gui.AlignmentPanel;
23 import jalview.ws.jws2.dm.AAConSettings;
24 import jalview.ws.jws2.jabaws2.Jws2Instance;
25 import jalview.ws.params.WsParamSetI;
26 import jalview.ws.uimodel.AlignAnalysisUIText;
28 import java.util.ArrayList;
29 import java.util.List;
32 import java.util.TreeSet;
34 import compbio.data.sequence.Score;
35 import compbio.metadata.Argument;
37 public class AAConClient extends JabawsAlignCalcWorker
40 public AAConClient(Jws2Instance service, AlignFrame alignFrame,
41 WsParamSetI preset, List<Argument> paramset)
43 super(service, alignFrame, preset, paramset);
46 nucleotidesAllowed = false;
47 proteinAllowed = true;
48 gapMap = new boolean[0];
52 public String getServiceActionText()
54 return "calculating Amino acid consensus using AACon service";
58 * update the consensus annotation from the sequence profile data using
59 * current visualization settings.
62 public void updateResultAnnotation(boolean immediate)
64 if (immediate || !calcMan.isWorking(this) && scoremanager != null)
66 Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
67 int alWidth = alignViewport.getAlignment().getWidth();
68 ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
69 for (String score : scoremap.keySet())
71 Set<Score> scores = scoremap.get(score);
72 for (Score scr : scores)
74 if (scr.getRanges() != null && scr.getRanges().size() > 0)
77 * annotation in range annotation = findOrCreate(scr.getMethod(),
78 * true, null, null); Annotation[] elm = new Annotation[alWidth];
79 * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng
80 * : scr.getRanges()) { float val = vals.next().floatValue(); for
81 * (int i = rng.from; i <= rng.to; i++) { elm[i] = new
82 * Annotation("", "", ' ', val); } } annotation.annotations = elm;
83 * annotation.validateRangeAndDisplay();
88 createAnnotationRowsForScores(ourAnnot, getCalcId(), alWidth,
94 if (ourAnnot.size() > 0)
96 updateOurAnnots(ourAnnot);
102 public String getCalcId()
106 private static String CALC_ID="jabaws2.AACon";
108 public static AlignAnalysisUIText getAlignAnalysisUITest()
110 return new AlignAnalysisUIText(
111 compbio.ws.client.Services.AAConWS.toString(),
112 jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true,
113 "AACon Calculations",
114 "When checked, AACon calculations are updated automatically.",
115 "Change AACon Settings...",
116 "Modify settings for AACon calculations.");