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.gui.AlignFrame;
24 import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
25 import jalview.ws.params.ArgumentI;
26 import jalview.ws.params.WsParamSetI;
28 import java.util.List;
30 public abstract class JabawsMsaInterfaceAlignCalcWorker
31 extends SeqAnnotationServiceCalcWorker
34 public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
35 AlignFrame alignFrame, WsParamSetI preset,
36 List<ArgumentI> paramset)
38 super(service, alignFrame, preset, paramset);
39 // TODO Auto-generated constructor stub
42 // TODO: REFACTOR if needed !
43 // may be able to get away with overriding run() only, but maybe not.
45 * @SuppressWarnings("unchecked") protected MsaWS msaservice;
47 * protected Alignment msascoreset;
49 * public JabawsMsaInterfaceAlignCalcWorker(AlignViewportI alignViewport,
50 * AlignmentViewPanel alignPanel) { super(alignViewport, alignPanel); }
52 * public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame
53 * alignFrame, WsParamSetI preset, List<ArgumentI> paramset) {
54 * this(alignFrame.getCurrentView(), alignFrame.alignPanel); this.guiProgress
55 * = alignFrame; this.preset = preset; this.arguments = paramset; this.service
56 * = service; msaservice = (MsaWS) service.service;
60 * @Override ChunkHolder pullExecStatistics(String rslt, long rpos) { return
61 * msaservice.pullExecStatistics(rslt, rpos); }
63 * @Override boolean collectAnnotationResultsFor(String rslt) throws
64 * ResultNotAvailableException { msascoreset =
65 * msaservice.getResult(rslt); if (msascoreset != null) { return
66 * true; } return false; }
68 * @Override boolean cancelJob(String rslt) throws Exception { return
69 * msaservice.cancelJob(rslt); }
71 * @Override protected JobStatus getJobStatus(String rslt) throws Exception {
72 * return msaservice.getJobStatus(rslt); }
74 * @Override boolean hasService() { return msaservice != null; }
76 * @Override protected boolean isInteractiveUpdate() { return false; // this
77 * instanceof AAConClient; }
79 * @Override protected String submitToService(
80 * List<compbio.data.sequence.FastaSequence> seqs) throws
81 * JobSubmissionException { String rslt; if (preset == null &&
82 * arguments == null) { rslt = msaservice.align(seqs); } else { try
83 * { rslt = msaservice.customAlign(seqs, getJabaArguments()); }
84 * catch (WrongParameterException x) { throw new
85 * JobSubmissionException(MessageManager.getString(
86 * "exception.jobsubmission_invalid_params_set"), x); } } return
89 * protected void createAnnotationRowsForScores(
90 * List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
91 * Score scr) { // simple annotation row AlignmentAnnotation
92 * annotation = alignViewport.getAlignment()
93 * .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
94 * null); if (alWidth == gapMap.length) // scr.getScores().size()) {
95 * constructAnnotationFromScore(annotation, 0, alWidth, scr);
96 * ourAnnot.add(annotation); } }
98 * protected AlignmentAnnotation createAnnotationRowsForScores(
99 * List<AlignmentAnnotation> ourAnnot, String typeName, String
100 * calcId, SequenceI dseq, int base, Score scr) {
101 * System.out.println("Creating annotation on dseq:" +
102 * dseq.getStart() + " base is " + base + " and length=" +
103 * dseq.getLength() + " == " + scr.getScores().size()); //
104 * AlignmentAnnotation annotation = new AlignmentAnnotation( //
105 * scr.getMethod(), typeName, new Annotation[] // {}, 0, -1,
106 * AlignmentAnnotation.LINE_GRAPH); // annotation.setCalcId(calcId);
107 * AlignmentAnnotation annotation = alignViewport.getAlignment()
108 * .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
109 * constructAnnotationFromScore(annotation, 0, dseq.getLength(),
110 * scr); annotation.createSequenceMapping(dseq, base, false);
111 * annotation.adjustForAlignment();
112 * dseq.addAlignmentAnnotation(annotation);
113 * ourAnnot.add(annotation); return annotation; }
115 * private void constructAnnotationFromScore(AlignmentAnnotation
116 * annotation, int base, int alWidth, Score scr) { Annotation[] elm
117 * = new Annotation[alWidth]; Iterator<Float> vals =
118 * scr.getScores().iterator(); float m = 0f, x = 0f; for (int i = 0;
119 * vals.hasNext(); i++) { float val = vals.next().floatValue(); if
120 * (i == 0) { m = val; x = val; } else { if (m > val) { m = val; } ;
121 * if (x < val) { x = val; } } // if we're at a gapped column then
122 * skip to next ungapped position if (gapMap != null &&
123 * gapMap.length > 0) { while (!gapMap[i]) { elm[i++] = new
124 * Annotation("", "", ' ', Float.NaN); } } elm[i] = new
125 * Annotation("", "" + val, ' ', val); }
127 * annotation.annotations = elm; annotation.belowAlignment = true;
128 * if (x < 0) { x = 0; } x += (x - m) * 0.1; annotation.graphMax =
129 * x; annotation.graphMin = m; annotation.validateRangeAndDisplay();