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.FeatureColourI;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.features.FeatureMatcherSetI;
27 import jalview.util.MessageManager;
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.Score;
38 public class AAConClient extends JabawsAnnotationInstance
40 // configuration for factory
41 public static String getServiceActionText()
43 return "calculating Amino acid consensus using AACon service";
48 private static String CALC_ID = "jabaws2.AACon";
50 public static AlignAnalysisUIText getAlignAnalysisUIText()
52 return new AlignAnalysisUIText(
53 compbio.ws.client.Services.AAConWS.toString(),
54 AAConClient.class, CALC_ID, false, true, true, true,
55 true, 2, MessageManager.getString("label.aacon_calculations"),
56 MessageManager.getString("tooltip.aacon_calculations"),
57 MessageManager.getString("label.aacon_settings"),
58 MessageManager.getString("tooltip.aacon_settings"));
62 public AAConClient(Jws2Instance handle)
68 List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
69 Map<String, FeatureColourI> featureColours,
70 Map<String, FeatureMatcherSetI> featureFilters)
72 return aacons_annotation(seqs.getWidth(), seqs, null);
75 private List<AlignmentAnnotation> aacons_annotation(int alWidth,
76 AlignmentI alignViewport, boolean[] gapMap)
78 Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
79 ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
80 for (String score : scoremap.keySet())
82 Set<Score> scores = scoremap.get(score);
83 for (Score scr : scores)
85 if (scr.getRanges() != null && scr.getRanges().size() > 0)
88 * annotation in range annotation = findOrCreate(scr.getMethod(),
89 * true, null, null); Annotation[] elm = new Annotation[alWidth];
90 * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng :
91 * scr.getRanges()) { float val = vals.next().floatValue(); for (int i
92 * = rng.from; i <= rng.to; i++) { elm[i] = new Annotation("", "", '
93 * ', val); } } annotation.annotations = elm;
94 * annotation.validateRangeAndDisplay();
99 createAnnotationRowsForScores(alignViewport, null, ourAnnot,
101 scr.getScores().size(), scr);