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.jabaws2;
23 import jalview.api.AlignViewportI;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.util.MessageManager;
26 import jalview.ws.gui.AnnotationWsJob;
27 import jalview.ws.uimodel.AlignAnalysisUIText;
29 import java.util.ArrayList;
30 import java.util.List;
33 import java.util.TreeSet;
35 import compbio.data.sequence.Score;
37 public class AAConClient extends JabawsAnnotationInstance
39 // configuration for factory
40 public static String getServiceActionText()
42 return "calculating Amino acid consensus using AACon service";
47 private static String CALC_ID = "jabaws2.AACon";
49 public static AlignAnalysisUIText getAlignAnalysisUIText()
51 return new AlignAnalysisUIText(
52 compbio.ws.client.Services.AAConWS.toString(),
53 AAConClient.class, CALC_ID, false, true, true, true,
54 true, 2, MessageManager.getString("label.aacon_calculations"),
55 MessageManager.getString("tooltip.aacon_calculations"),
56 MessageManager.getString("label.aacon_settings"),
57 MessageManager.getString("tooltip.aacon_settings"));
61 public AAConClient(Jws2Instance handle)
67 List<AlignmentAnnotation> annotationFromScoreManager(
68 AnnotationWsJob running, AlignViewportI alignViewport,
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 (int i
87 * = rng.from; i <= rng.to; i++) { elm[i] = new Annotation("", "", '
88 * ', val); } } annotation.annotations = elm;
89 * annotation.validateRangeAndDisplay();
94 createAnnotationRowsForScores(alignViewport, gapMap, ourAnnot,
95 getCalcId(), alWidth, scr);