/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.jabaws2;
import jalview.gui.AlignFrame;
import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.List;
public abstract class JabawsMsaInterfaceAlignCalcWorker
extends SeqAnnotationServiceCalcWorker
{
public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
AlignFrame alignFrame, WsParamSetI preset,
List paramset)
{
super(service, alignFrame, preset, paramset);
// TODO Auto-generated constructor stub
}
// TODO: REFACTOR if needed !
// may be able to get away with overriding run() only, but maybe not.
/***
* @SuppressWarnings("unchecked") protected MsaWS msaservice;
*
* protected Alignment msascoreset;
*
* public JabawsMsaInterfaceAlignCalcWorker(AlignViewportI alignViewport,
* AlignmentViewPanel alignPanel) { super(alignViewport, alignPanel); }
*
* public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service, AlignFrame
* alignFrame, WsParamSetI preset, List paramset) {
* this(alignFrame.getCurrentView(), alignFrame.alignPanel); this.guiProgress
* = alignFrame; this.preset = preset; this.arguments = paramset; this.service
* = service; msaservice = (MsaWS) service.service;
*
* }
*
* @Override ChunkHolder pullExecStatistics(String rslt, long rpos) { return
* msaservice.pullExecStatistics(rslt, rpos); }
*
* @Override boolean collectAnnotationResultsFor(String rslt) throws
* ResultNotAvailableException { msascoreset =
* msaservice.getResult(rslt); if (msascoreset != null) { return
* true; } return false; }
*
* @Override boolean cancelJob(String rslt) throws Exception { return
* msaservice.cancelJob(rslt); }
*
* @Override protected JobStatus getJobStatus(String rslt) throws Exception {
* return msaservice.getJobStatus(rslt); }
*
* @Override boolean hasService() { return msaservice != null; }
*
* @Override protected boolean isInteractiveUpdate() { return false; // this
* instanceof AAConClient; }
*
* @Override protected String submitToService(
* List seqs) throws
* JobSubmissionException { String rslt; if (preset == null &&
* arguments == null) { rslt = msaservice.align(seqs); } else { try
* { rslt = msaservice.customAlign(seqs, getJabaArguments()); }
* catch (WrongParameterException x) { throw new
* JobSubmissionException(MessageManager.getString(
* "exception.jobsubmission_invalid_params_set"), x); } } return
* rslt; }
*
* protected void createAnnotationRowsForScores(
* List ourAnnot, String calcId, int alWidth,
* Score scr) { // simple annotation row AlignmentAnnotation
* annotation = alignViewport.getAlignment()
* .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
* null); if (alWidth == gapMap.length) // scr.getScores().size()) {
* constructAnnotationFromScore(annotation, 0, alWidth, scr);
* ourAnnot.add(annotation); } }
*
* protected AlignmentAnnotation createAnnotationRowsForScores(
* List ourAnnot, String typeName, String
* calcId, SequenceI dseq, int base, Score scr) {
* System.out.println("Creating annotation on dseq:" +
* dseq.getStart() + " base is " + base + " and length=" +
* dseq.getLength() + " == " + scr.getScores().size()); //
* AlignmentAnnotation annotation = new AlignmentAnnotation( //
* scr.getMethod(), typeName, new Annotation[] // {}, 0, -1,
* AlignmentAnnotation.LINE_GRAPH); // annotation.setCalcId(calcId);
* AlignmentAnnotation annotation = alignViewport.getAlignment()
* .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
* constructAnnotationFromScore(annotation, 0, dseq.getLength(),
* scr); annotation.createSequenceMapping(dseq, base, false);
* annotation.adjustForAlignment();
* dseq.addAlignmentAnnotation(annotation);
* ourAnnot.add(annotation); return annotation; }
*
* private void constructAnnotationFromScore(AlignmentAnnotation
* annotation, int base, int alWidth, Score scr) { Annotation[] elm
* = new Annotation[alWidth]; Iterator vals =
* scr.getScores().iterator(); float m = 0f, x = 0f; for (int i = 0;
* vals.hasNext(); i++) { float val = vals.next().floatValue(); if
* (i == 0) { m = val; x = val; } else { if (m > val) { m = val; } ;
* if (x < val) { x = val; } } // if we're at a gapped column then
* skip to next ungapped position if (gapMap != null &&
* gapMap.length > 0) { while (!gapMap[i]) { elm[i++] = new
* Annotation("", "", ' ', Float.NaN); } } elm[i] = new
* Annotation("", "" + val, ' ', val); }
*
* annotation.annotations = elm; annotation.belowAlignment = true;
* if (x < 0) { x = 0; } x += (x - m) * 0.1; annotation.graphMax =
* x; annotation.graphMin = m; annotation.validateRangeAndDisplay();
* }
***/
}