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.api.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.Annotation;
27 import jalview.datamodel.SequenceI;
28 import jalview.gui.AlignFrame;
29 import jalview.util.MessageManager;
30 import jalview.ws.jws2.jabaws2.Jws2Instance;
31 import jalview.ws.params.WsParamSetI;
33 import java.util.Iterator;
34 import java.util.List;
36 import compbio.data.msa.MsaWS;
37 import compbio.data.sequence.Alignment;
38 import compbio.data.sequence.Score;
39 import compbio.metadata.Argument;
40 import compbio.metadata.ChunkHolder;
41 import compbio.metadata.JobStatus;
42 import compbio.metadata.JobSubmissionException;
43 import compbio.metadata.ResultNotAvailableException;
44 import compbio.metadata.WrongParameterException;
46 public abstract class JabawsMsaInterfaceAlignCalcWorker
47 extends AbstractJabaCalcWorker
50 @SuppressWarnings("unchecked")
51 protected MsaWS msaservice;
53 protected Alignment msascoreset;
55 public JabawsMsaInterfaceAlignCalcWorker(AlignViewportI alignViewport,
56 AlignmentViewPanel alignPanel)
58 super(alignViewport, alignPanel);
61 public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
62 AlignFrame alignFrame, WsParamSetI preset,
63 List<Argument> paramset)
65 this(alignFrame.getCurrentView(), alignFrame.alignPanel);
66 this.guiProgress = alignFrame;
68 this.arguments = paramset;
69 this.service = service;
70 msaservice = (MsaWS) service.service;
75 ChunkHolder pullExecStatistics(String rslt, long rpos)
77 return msaservice.pullExecStatistics(rslt, rpos);
81 boolean collectAnnotationResultsFor(String rslt)
82 throws ResultNotAvailableException
84 msascoreset = msaservice.getResult(rslt);
85 if (msascoreset != null)
93 boolean cancelJob(String rslt) throws Exception
95 return msaservice.cancelJob(rslt);
99 protected JobStatus getJobStatus(String rslt) throws Exception
101 return msaservice.getJobStatus(rslt);
107 return msaservice != null;
111 protected boolean isInteractiveUpdate()
113 return false; // this instanceof AAConClient;
117 protected String submitToService(
118 List<compbio.data.sequence.FastaSequence> seqs)
119 throws JobSubmissionException
122 if (preset == null && arguments == null)
124 rslt = msaservice.align(seqs);
130 rslt = msaservice.customAlign(seqs, getJabaArguments());
131 } catch (WrongParameterException x)
133 throw new JobSubmissionException(MessageManager.getString(
134 "exception.jobsubmission_invalid_params_set"), x);
140 protected void createAnnotationRowsForScores(
141 List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
144 // simple annotation row
145 AlignmentAnnotation annotation = alignViewport.getAlignment()
146 .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
148 if (alWidth == gapMap.length) // scr.getScores().size())
150 constructAnnotationFromScore(annotation, 0, alWidth, scr);
151 ourAnnot.add(annotation);
155 protected AlignmentAnnotation createAnnotationRowsForScores(
156 List<AlignmentAnnotation> ourAnnot, String typeName,
157 String calcId, SequenceI dseq, int base, Score scr)
159 jalview.bin.Console.outPrintln("Creating annotation on dseq:"
160 + dseq.getStart() + " base is " + base + " and length="
161 + dseq.getLength() + " == " + scr.getScores().size());
162 // AlignmentAnnotation annotation = new AlignmentAnnotation(
163 // scr.getMethod(), typeName, new Annotation[]
164 // {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
165 // annotation.setCalcId(calcId);
166 AlignmentAnnotation annotation = alignViewport.getAlignment()
167 .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
168 constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
169 annotation.createSequenceMapping(dseq, base, false);
170 annotation.adjustForAlignment();
171 dseq.addAlignmentAnnotation(annotation);
172 ourAnnot.add(annotation);
176 private void constructAnnotationFromScore(AlignmentAnnotation annotation,
177 int base, int alWidth, Score scr)
179 Annotation[] elm = new Annotation[alWidth];
180 Iterator<Float> vals = scr.getScores().iterator();
181 float m = 0f, x = 0f;
182 for (int i = 0; vals.hasNext(); i++)
184 float val = vals.next().floatValue();
202 // if we're at a gapped column then skip to next ungapped position
203 if (gapMap != null && gapMap.length > 0)
207 elm[i++] = new Annotation("", "", ' ', Float.NaN);
210 elm[i] = new Annotation("", "" + val, ' ', val);
213 annotation.annotations = elm;
214 annotation.belowAlignment = true;
220 annotation.graphMax = x;
221 annotation.graphMin = m;
222 annotation.validateRangeAndDisplay();