--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<ArgumentI> 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<ArgumentI> 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<compbio.data.sequence.FastaSequence> 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<AlignmentAnnotation> 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<AlignmentAnnotation> 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<Float> 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();
+ * }
+ ***/
+}
git://source.jalview.org / jalview.git / blobdiff