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.datamodel.Annotation;
25 import jalview.datamodel.SequenceI;
26 import jalview.gui.AlignFrame;
27 import jalview.ws.jws2.jabaws2.Jws2Instance;
28 import jalview.ws.params.WsParamSetI;
30 import java.util.Iterator;
31 import java.util.List;
33 import compbio.data.msa.SequenceAnnotation;
34 import compbio.data.sequence.Score;
35 import compbio.data.sequence.ScoreManager;
36 import compbio.metadata.Argument;
37 import compbio.metadata.ChunkHolder;
38 import compbio.metadata.JobStatus;
39 import compbio.metadata.JobSubmissionException;
40 import compbio.metadata.ResultNotAvailableException;
41 import compbio.metadata.WrongParameterException;
43 public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
46 @SuppressWarnings("unchecked")
47 protected SequenceAnnotation aaservice;
49 protected ScoreManager scoremanager;
51 public JabawsCalcWorker(Jws2Instance service, AlignFrame alignFrame,
52 WsParamSetI preset, List<Argument> paramset)
54 super(service, alignFrame, preset, paramset);
55 aaservice = (SequenceAnnotation) service.service;
59 ChunkHolder pullExecStatistics(String rslt, long rpos)
61 return aaservice.pullExecStatistics(rslt, rpos);
65 boolean collectAnnotationResultsFor(String rslt)
66 throws ResultNotAvailableException
68 scoremanager = aaservice.getAnnotation(rslt);
69 if (scoremanager != null)
77 boolean cancelJob(String rslt) throws Exception
79 return aaservice.cancelJob(rslt);
83 protected JobStatus getJobStatus(String rslt) throws Exception
85 return aaservice.getJobStatus(rslt);
91 return aaservice != null;
95 protected boolean isInteractiveUpdate()
97 return this instanceof AAConClient;
101 protected String submitToService(
102 List<compbio.data.sequence.FastaSequence> seqs)
103 throws JobSubmissionException
106 if (preset == null && arguments == null)
108 rslt = aaservice.analize(seqs);
114 rslt = aaservice.customAnalize(seqs, getJabaArguments());
115 } catch (WrongParameterException x)
117 throw new JobSubmissionException(
118 "Invalid parameter set. Check Jalview implementation.", x);
125 protected void createAnnotationRowsForScores(
126 List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
129 // simple annotation row
130 AlignmentAnnotation annotation = alignViewport.getAlignment()
131 .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
133 if (alWidth == gapMap.length) // scr.getScores().size())
135 constructAnnotationFromScore(annotation, 0, alWidth, scr);
136 ourAnnot.add(annotation);
140 protected AlignmentAnnotation createAnnotationRowsForScores(
141 List<AlignmentAnnotation> ourAnnot, String typeName,
142 String calcId, SequenceI dseq, int base, Score scr)
144 System.out.println("Creating annotation on dseq:" + dseq.getStart()
145 + " base is " + base + " and length=" + dseq.getLength()
146 + " == " + scr.getScores().size());
147 // AlignmentAnnotation annotation = new AlignmentAnnotation(
148 // scr.getMethod(), typeName, new Annotation[]
149 // {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
150 // annotation.setCalcId(calcId);
151 AlignmentAnnotation annotation = alignViewport.getAlignment()
152 .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
153 constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
154 annotation.createSequenceMapping(dseq, base, false);
155 annotation.adjustForAlignment();
156 dseq.addAlignmentAnnotation(annotation);
157 ourAnnot.add(annotation);
161 private void constructAnnotationFromScore(AlignmentAnnotation annotation,
162 int base, int alWidth, Score scr)
164 Annotation[] elm = new Annotation[alWidth];
165 Iterator<Float> vals = scr.getScores().iterator();
166 float m = 0f, x = 0f;
167 for (int i = 0; vals.hasNext(); i++)
169 float val = vals.next().floatValue();
187 // if we're at a gapped column then skip to next ungapped position
188 if (gapMap != null && gapMap.length > 0)
192 elm[i++] = new Annotation("", "", ' ', Float.NaN);
195 elm[i] = new Annotation("", "" + val, ' ', val);
198 annotation.annotations = elm;
199 annotation.belowAlignment = true;
205 annotation.graphMax = x;
206 annotation.graphMin = m;
207 annotation.validateRangeAndDisplay();