* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.ws.jws2;
+package jalview.ws.jws2.jabaws2;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.jws2.AbstractJabaCalcWorker;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
-import java.util.Iterator;
import java.util.List;
-import compbio.data.msa.MsaWS;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.Score;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.WrongParameterException;
-
public abstract class JabawsMsaInterfaceAlignCalcWorker
extends AbstractJabaCalcWorker
{
- @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();
+ 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