}
}
+ public AlignViewportI getAlignViewport()
+ {
+ return alignViewport;
+ }
}
--- /dev/null
+package jalview.ws.api;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.ws.gui.AnnotationWsJob;
+import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.List;
+
+public interface SequenceAnnotationServiceI extends JalviewWebServiceI
+{
+
+
+ /**
+ * submit sequences to service with no parameters, or preset or parameter set.
+ * Nb- almost the same as the 'align' method in the Msa service :)
+ *
+ * @param seqs
+ * @param preset
+ * @param paramset
+ * @return
+ * @throws Throwable
+ */
+ JobId submitToService(List<SequenceI> seqs, WsParamSetI preset,
+ List<ArgumentI> paramset) throws Throwable;
+
+ /**
+ * todo: move to SequenceAnnotationResult
+ *
+ * @param running
+ * @param abstractJabaCalcWorker
+ * @return
+ */
+ List<AlignmentAnnotation> getAlignmentAnnotation(AnnotationWsJob running,
+ AbstractJabaCalcWorker abstractJabaCalcWorker) throws Throwable;
+
+
+}
--- /dev/null
+package jalview.ws.api;
+
+public interface WSAnnotationCalcManagerI
+{
+
+}
--- /dev/null
+package jalview.ws.gui;
+
+import jalview.api.FeatureRenderer;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+import java.util.Map;
+
+public class AnnotationWsJob extends WsJob
+{
+ /**
+ * sequences (anonymised)
+ */
+ List<SequenceI> seqs;
+
+ /**
+ * mapping to original sequences
+ */
+ Map<String, SequenceI> seqNames;
+
+ /**
+ * first column in the segment of the alignment view that was submitted
+ */
+ int startPos;
+
+ public int getStartPos()
+ {
+ return startPos;
+ }
+
+ public void setStartPos(int startPos)
+ {
+ this.startPos = startPos;
+ }
+
+ /**
+ * outputs
+ */
+ List<AlignmentAnnotation> annotation = null;
+
+ boolean transferSequenceFeatures = false;
+
+ public boolean isTransferSequenceFeatures()
+ {
+ return transferSequenceFeatures;
+ }
+
+ public void setTransferSequenceFeatures(boolean transferSequenceFeatures)
+ {
+ this.transferSequenceFeatures = transferSequenceFeatures;
+ }
+
+ public List<AlignmentAnnotation> getAnnotation()
+ {
+ return annotation;
+ }
+
+ public void setAnnotation(List<AlignmentAnnotation> annotation)
+ {
+ this.annotation = annotation;
+ }
+
+ @Override
+ public boolean hasResults()
+ {
+ return (isSubmitted() && isFinished()
+ && (annotation != null || transferSequenceFeatures));
+ }
+
+ public List<SequenceI> getSeqs()
+ {
+ return seqs;
+ }
+
+ public void setSeqs(List<SequenceI> seqs)
+ {
+ this.seqs = seqs;
+ }
+
+ public Map<String, SequenceI> getSeqNames()
+ {
+ return seqNames;
+ }
+
+ public void setSeqNames(Map<String, SequenceI> seqNames)
+ {
+ this.seqNames = seqNames;
+ }
+
+ /**
+ * configured by the WS framework just before results are collected
+ */
+ FeatureRenderer featureRenderer;
+
+ public void setFeatureRenderer(FeatureRenderer fr)
+ {
+ this.featureRenderer = fr;
+ }
+ public FeatureRenderer getFeatureRenderer()
+ {
+ // TODO Auto-generated method stub
+ return featureRenderer;
+ }
+
+}
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
-import jalview.ws.api.JobId;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.params.ArgumentI;
{
// TODO: get attributes for this MsaWS instance to check if it can do two
// sequence alignment.
+ // TODO: check type of sequences are valid for this service
if (seqs != null && seqs.size() >= 2) // two or more sequences is valid ?
{
return true;
jobProgress.append("\nJob Output:\n");
}
}
-
- JobId jobHandle = null;
- public void setJobHandle(JobId align)
- {
- jobHandle = align;
- setJobId(jobHandle.getJobId());
-
- }
-
- public JobId getJobHandle()
- {
- return jobHandle;
- }
-
}
\ No newline at end of file
package jalview.ws.gui;
import jalview.ws.AWsJob;
+import jalview.ws.api.JobId;
/**
* Bean that holds state for a job
}
+ /*
+ * bean holding submission info for a next-gen ws job
+ */
+ JobId jobHandle = null;
+
+ /**
+ * stash the handle for the job and mark it as submitted
+ *
+ * @param align
+ */
+ public void setJobHandle(JobId align)
+ {
+ jobHandle = align;
+ setJobId(jobHandle.getJobId());
+ submitted = true;
+
+ }
+
+ public JobId getJobHandle()
+ {
+ return jobHandle;
+ }
+
}
+++ /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;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.gui.AlignFrame;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.WsParamSetI;
-import jalview.ws.uimodel.AlignAnalysisUIText;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
-
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Score;
-
-public class AAConClient extends JabawsCalcWorker
-{
-
- public AAConClient(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<ArgumentI> paramset)
- {
- super(service, alignFrame, preset, paramset);
- submitGaps = true;
- alignedSeqs = true;
- nucleotidesAllowed = false;
- proteinAllowed = true;
- filterNonStandardResidues = true;
- gapMap = new boolean[0];
- initViewportParams();
- }
-
- @Override
- public String getServiceActionText()
- {
- return "calculating Amino acid consensus using AACon service";
- }
-
- /**
- * update the consensus annotation from the sequence profile data using
- * current visualization settings.
- */
-
- @Override
- public void updateResultAnnotation(boolean immediate)
- {
- if (immediate || !calcMan.isWorking(this) && scoremanager != null)
- {
- Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
- int alWidth = alignViewport.getAlignment().getWidth();
- ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
- for (String score : scoremap.keySet())
- {
- Set<Score> scores = scoremap.get(score);
- for (Score scr : scores)
- {
- if (scr.getRanges() != null && scr.getRanges().size() > 0)
- {
- /**
- * annotation in range annotation = findOrCreate(scr.getMethod(),
- * true, null, null); Annotation[] elm = new Annotation[alWidth];
- * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng
- * : scr.getRanges()) { float val = vals.next().floatValue(); for
- * (int i = rng.from; i <= rng.to; i++) { elm[i] = new
- * Annotation("", "", ' ', val); } } annotation.annotations = elm;
- * annotation.validateRangeAndDisplay();
- */
- }
- else
- {
- createAnnotationRowsForScores(ourAnnot, getCalcId(), alWidth,
- scr);
- }
- }
- }
-
- if (ourAnnot.size() > 0)
- {
- updateOurAnnots(ourAnnot);
- }
- }
- }
-
- @Override
- boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
- {
- return (seqs.size() > 1);
- }
-
- @Override
- public String getCalcId()
- {
- return CALC_ID;
- }
-
- private static String CALC_ID = "jabaws2.AACon";
-
- public static AlignAnalysisUIText getAlignAnalysisUITest()
- {
- return new AlignAnalysisUIText(
- compbio.ws.client.Services.AAConWS.toString(),
- jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true,
- MessageManager.getString("label.aacon_calculations"),
- MessageManager.getString("tooltip.aacon_calculations"),
- MessageManager.getString("label.aacon_settings"),
- MessageManager.getString("tooltip.aacon_settings"));
- }
-}
+++ /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;
-
-import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.schemes.FeatureColour;
-import jalview.util.ColorUtils;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.WsParamSetI;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Range;
-import compbio.data.sequence.Score;
-import compbio.data.sequence.ScoreManager.ScoreHolder;
-
-public class AADisorderClient extends JabawsCalcWorker
-{
-
- private static final String THRESHOLD = "THRESHOLD";
-
- private static final String RANGE = "RANGE";
-
- String typeName;
-
- String methodName;
-
- String groupName;
-
- AlignFrame af;
-
- public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
- WsParamSetI thePreset, List<ArgumentI> paramset)
- {
- super(sh, alignFrame, thePreset, paramset);
- af = alignFrame;
- typeName = sh.getAction();
- methodName = sh.getName();
-
- submitGaps = false;
- alignedSeqs = false;
- nucleotidesAllowed = false;
- proteinAllowed = true;
- bySequence = true;
- }
-
- @Override
- public String getServiceActionText()
- {
- return "Submitting amino acid sequences for disorder prediction.";
- }
-
- @Override
- boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
- {
- return (seqs.size() > 0);
- }
-
- private static Map<String, Map<String, String[]>> featureMap;
-
- private static Map<String, Map<String, Map<String, Object>>> annotMap;
-
- private static String DONTCOMBINE = "DONTCOMBINE";
-
- private static String INVISIBLE = "INVISIBLE";
- static
- {
- // TODO: turn this into some kind of configuration file that's a bit easier
- // to edit
- featureMap = new HashMap<>();
- Map<String, String[]> fmap;
- featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
- fmap = new HashMap<>());
- fmap.put("Glob",
- new String[]
- { "Globular Domain", "Predicted globular domain" });
- featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
- fmap = new HashMap<>());
- featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
- fmap = new HashMap<>());
- fmap.put("REM465", new String[] { "REM465", "Missing density" });
- fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
- fmap.put("COILS", new String[] { "COILS", "Random coil" });
- featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
- fmap = new HashMap<>());
- fmap.put("GlobDoms",
- new String[]
- { "Globular Domain", "Predicted globular domain" });
- fmap.put("Disorder",
- new String[]
- { "Protein Disorder", "Probable unstructured peptide region" });
- Map<String, Map<String, Object>> amap;
- annotMap = new HashMap<>();
- annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
- amap = new HashMap<>());
- amap.put("Dydx", new HashMap<String, Object>());
- amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
- amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
- amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
-
- amap.put("SmoothedScore", new HashMap<String, Object>());
- amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
- amap.put("RawScore", new HashMap<String, Object>());
- amap.get("RawScore").put(INVISIBLE, INVISIBLE);
- annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
- amap = new HashMap<>());
- amap.put("COILS", new HashMap<String, Object>());
- amap.put("HOTLOOPS", new HashMap<String, Object>());
- amap.put("REM465", new HashMap<String, Object>());
- amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
- amap.get("COILS").put(RANGE, new float[] { 0, 1 });
-
- amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
- amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
- amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
- amap.get("REM465").put(RANGE, new float[] { 0, 1 });
-
- annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
- amap = new HashMap<>());
- amap.put("Long", new HashMap<String, Object>());
- amap.put("Short", new HashMap<String, Object>());
- amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
- amap.get("Long").put(RANGE, new float[] { 0, 1 });
- amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
- amap.get("Short").put(RANGE, new float[] { 0, 1 });
- annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
- amap = new HashMap<>());
- amap.put("JRonn", new HashMap<String, Object>());
- amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
- amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
- }
-
- @Override
- public void updateResultAnnotation(boolean immediate)
- {
-
- if (immediate || !calcMan.isWorking(this) && scoremanager != null)
- {
- Map<String, String[]> featureTypeMap = featureMap
- .get(service.getName());
- Map<String, Map<String, Object>> annotTypeMap = annotMap
- .get(service.getName());
- boolean dispFeatures = false;
- Map<String, Object> fc = new Hashtable<>();
- List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
- /**
- * grouping for any annotation rows created
- */
- int graphGroup = 1;
- if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
- {
- for (AlignmentAnnotation ala : alignViewport.getAlignment()
- .getAlignmentAnnotation())
- {
- if (ala.graphGroup > graphGroup)
- {
- graphGroup = ala.graphGroup;
- }
- }
- }
-
- for (String seqId : seqNames.keySet())
- {
- boolean sameGroup = false;
- SequenceI dseq, aseq, seq = seqNames.get(seqId);
- int base = seq.findPosition(start) - 1;
- aseq = seq;
- while ((dseq = seq).getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- ScoreHolder scores = null;
- try
- {
- scores = scoremanager.getAnnotationForSequence(seqId);
- } catch (Exception q)
- {
- Cache.log
- .info("Couldn't recover disorder prediction for sequence "
- + seq.getName() + "(Prediction name was " + seqId
- + ")"
- + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
- }
- float last = Float.NaN, val = Float.NaN;
- int lastAnnot = ourAnnot.size();
- if (scores != null && scores.scores != null)
- {
- for (Score scr : scores.scores)
- {
-
- if (scr.getRanges() != null && scr.getRanges().size() > 0)
- {
- Iterator<Float> vals = scr.getScores().iterator();
- // make features on sequence
- for (Range rn : scr.getRanges())
- {
-
- SequenceFeature sf;
- String[] type = featureTypeMap.get(scr.getMethod());
- if (type == null)
- {
- // create a default type for this feature
- type = new String[] {
- typeName + " (" + scr.getMethod() + ")",
- service.getActionText() };
- }
- if (vals.hasNext())
- {
- val = vals.next().floatValue();
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, val, methodName);
- }
- else
- {
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, methodName);
- }
- dseq.addSequenceFeature(sf);
- if (last != val && !Float.isNaN(last))
- {
- fc.put(sf.getType(), sf);
- }
- last = val;
- dispFeatures = true;
- }
- }
- else
- {
- if (scr.getScores().size() == 0)
- {
- continue;
- }
- String typename, calcName;
- AlignmentAnnotation annot = createAnnotationRowsForScores(
- ourAnnot,
- typename = service.getName() + " ("
- + scr.getMethod() + ")",
- calcName = service.getNameURI() + "/"
- + scr.getMethod(),
- aseq, base + 1, scr);
- annot.graph = AlignmentAnnotation.LINE_GRAPH;
-
- Map<String, Object> styleMap = (annotTypeMap == null) ? null
- : annotTypeMap.get(scr.getMethod());
-
- annot.visible = (styleMap == null
- || styleMap.get(INVISIBLE) == null);
- double[] thrsh = (styleMap == null) ? null
- : (double[]) styleMap.get(THRESHOLD);
- float[] range = (styleMap == null) ? null
- : (float[]) styleMap.get(RANGE);
- if (range != null)
- {
- annot.graphMin = range[0];
- annot.graphMax = range[1];
- }
- if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
- {
- {
- if (!sameGroup)
- {
- graphGroup++;
- sameGroup = true;
- }
-
- annot.graphGroup = graphGroup;
- }
- }
-
- annot.description = "<html>" + service.getActionText()
- + " - raw scores";
- if (thrsh != null)
- {
- String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
- + thrsh[1] + " indicates disorder";
- annot.threshold = new GraphLine((float) thrsh[1],
- threshNote, Color.red);
- annot.description += "<br/>" + threshNote;
- }
- annot.description += "</html>";
- Color col = ColorUtils
- .createColourFromName(typeName + scr.getMethod());
- for (int p = 0, ps = annot.annotations.length; p < ps; p++)
- {
- if (annot.annotations[p] != null)
- {
- annot.annotations[p].colour = col;
- }
- }
- annot._linecolour = col;
- // finally, update any dataset annotation
- replaceAnnotationOnAlignmentWith(annot, typename, calcName,
- aseq);
- }
- }
- }
- if (lastAnnot + 1 == ourAnnot.size())
- {
- // remove singleton alignment annotation row
- ourAnnot.get(lastAnnot).graphGroup = -1;
- }
- }
- {
- if (dispFeatures)
- {
- jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
- .cloneFeatureRenderer();
- for (String ft : fc.keySet())
- {
- FeatureColourI gc = fr.getFeatureStyle(ft);
- if (gc.isSimpleColour())
- {
- // set graduated color as fading to white for minimum, and
- // autoscaling to values on alignment
- FeatureColourI ggc = new FeatureColour(gc.getColour(),
- Color.white, gc.getColour(), Color.white,
- Float.MIN_VALUE, Float.MAX_VALUE);
- ggc.setAutoScaled(true);
- fr.setColour(ft, ggc);
- }
- }
- // TODO: JAL-1150 - create sequence feature settings API for defining
- // styles and enabling/disabling feature overlay on alignment panel
- ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
- if (af.alignPanel == ap)
- {
- // only do this if the alignFrame is currently showing this view.
- af.setShowSeqFeatures(true);
- }
- }
- if (ourAnnot.size() > 0)
- {
- // Modify the visible annotation on the alignment viewport with the
- // new alignment annotation rows created.
- updateOurAnnots(ourAnnot);
- ap.adjustAnnotationHeight();
- ap.paintAlignment(true, true);
- }
- }
- }
- }
-
- @Override
- public String getCalcId()
- {
- // Disorder predictions are not dynamically updated so we return null
- return null;
- }
-
-}
import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
import jalview.gui.IProgressIndicator;
import jalview.gui.IProgressIndicatorHandler;
+import jalview.gui.JvOptionPane;
import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
import jalview.workers.AlignCalcWorker;
+import jalview.ws.api.CancellableI;
+import jalview.ws.api.JobId;
+import jalview.ws.api.WSAnnotationCalcManagerI;
+import jalview.ws.gui.AnnotationWsJob;
import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
import java.util.List;
import java.util.Map;
-import compbio.data.sequence.FastaSequence;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Option;
-import compbio.metadata.ResultNotAvailableException;
-
-public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
+public class AbstractJabaCalcWorker extends AlignCalcWorker
+ implements WSAnnotationCalcManagerI
{
protected Jws2Instance service;
* @return null or a string used to recover all annotation generated by this
* worker
*/
- public abstract String getCalcId();
+ public String getCalcId()
+ {
+ return service.getAlignAnalysisUI() == null ? null
+ : service.getAlignAnalysisUI().getCalcId();
+ }
public WsParamSetI getPreset()
{
calcMan.startWorker(this);
initViewportParams();
}
-
- public List<Option> getJabaArguments()
- {
- List<Option> newargs = new ArrayList<>();
- if (preset != null && preset instanceof JabaWsParamSet)
- {
- newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
- }
- if (arguments != null && arguments.size() > 0)
- {
- for (Object rg : JabaParamStore.getJabafromJwsArgs(arguments))
- {
- if (Option.class.isAssignableFrom(rg.getClass()))
- {
- newargs.add((Option) rg);
- }
- }
- }
- return newargs;
- }
-
protected boolean alignedSeqs = true;
protected boolean nucleotidesAllowed = false;
protected Map<String, SequenceI> seqNames;
+ // TODO: convert to bitset
protected boolean[] gapMap;
int realw;
int end;
+ private AlignFrame alignFrame;
+
+ public boolean[] getGapMap()
+ {
+ return gapMap;
+ }
+
public AbstractJabaCalcWorker(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
WsParamSetI preset, List<ArgumentI> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
+ // TODO: both these fields needed ?
+ this.alignFrame = alignFrame;
this.guiProgress = alignFrame;
this.preset = preset;
this.arguments = paramset;
this.service = service;
+ try
+ {
+ annotService = (jalview.ws.api.SequenceAnnotationServiceI) service
+ .getEndpoint();
+ } catch (ClassCastException cce)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.service_called_is_not_an_annotation_service",
+ new String[]
+ { service.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ // configure submission flags
+ if (service.getAlignAnalysisUI() != null)
+ {
+ // instantaneous calculation. Right now that's either AACons or RNAAliFold
+ proteinAllowed = service.getAlignAnalysisUI().isPr();
+ nucleotidesAllowed = service.getAlignAnalysisUI().isNa();
+ alignedSeqs = service.getAlignAnalysisUI().isNeedsAlignedSeqs();
+ bySequence = !service.getAlignAnalysisUI().isAA();
+ filterNonStandardResidues = service.getAlignAnalysisUI()
+ .isFilterSymbols();
+ min_valid_seqs = service.getAlignAnalysisUI().getMinimumSequences();
+ initViewportParams();
+ }
+ else
+ {
+ // assume disorder prediction : per-sequence protein only no gaps
+ // analysis.
+ // TODO - move configuration to UIInfo base class for all these flags !
+ alignedSeqs = false;
+ bySequence = true;
+ filterNonStandardResidues = true;
+ nucleotidesAllowed = false;
+ proteinAllowed = true;
+ submitGaps = false;
+ min_valid_seqs = 1;
+ }
}
/**
*
* @return true if the submission thread should attempt to submit data
*/
- abstract boolean hasService();
+ public boolean hasService()
+ {
+ return annotService != null;
+ }
+
+ protected jalview.ws.api.SequenceAnnotationServiceI annotService = null;
+
+ volatile JobId rslt = null;
- volatile String rslt = "JOB NOT DEFINED";
+ AnnotationWsJob running = null;
+
+ private int min_valid_seqs;
@Override
public void run()
{
return;
}
+
long progressId = -1;
int serverErrorsLeft = 3;
-
+ final boolean cancellable = CancellableI.class
+ .isAssignableFrom(annotService.getClass());
StringBuffer msg = new StringBuffer();
try
{
{
return;
}
- List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(
+ List<SequenceI> seqs = getInputSequences(
alignViewport.getAlignment(),
bySequence ? alignViewport.getSelectionGroup() : null);
- if (seqs == null || !checkValidInputSeqs(true, seqs))
+ if (seqs == null || !checkValidInputSeqs(seqs))
{
+ jalview.bin.Cache.log.debug(
+ "Sequences for analysis service were null or not valid");
calcMan.workerComplete(this);
return;
}
.getAlignmentAnnotation();
if (guiProgress != null)
{
- guiProgress.setProgressBar("JABA " + getServiceActionText(),
+ guiProgress.setProgressBar(service.getActionText(),
progressId = System.currentTimeMillis());
}
- rslt = submitToService(seqs);
+ jalview.bin.Cache.log.debug("submitted " + seqs.size()
+ + " sequences to " + service.getActionText());
+
+ rslt = annotService.submitToService(seqs, getPreset(),
+ getArguments());
+ if (rslt == null)
+ {
+ return;
+ }
+ // TODO: handle job submission error reporting here.
+
+ // ///
+ // otherwise, construct WsJob and any UI handlers
+ running = new AnnotationWsJob();
+ running.setJobHandle(rslt);
+ running.setSeqNames(seqNames);
+ running.setStartPos(start);
+ running.setSeqs(seqs);
+
if (guiProgress != null)
{
guiProgress.registerHandler(progressId,
@Override
public boolean cancelActivity(long id)
{
- cancelCurrentJob();
+ ((CancellableI) annotService).cancel(running);
return true;
}
@Override
public boolean canCancel()
{
- return true;
+ return cancellable;
}
});
}
+
+ // ///
+ // and poll for updates until job finishes, fails or becomes stale
+
boolean finished = false;
long rpos = 0;
do
{
- JobStatus status = getJobStatus(rslt);
- if (status.equals(JobStatus.FINISHED))
+ Cache.log.debug("Updating status for annotation service.");
+ annotService.updateStatus(running);
+
+ if (running.isFinished())
{
+ Cache.log.debug("Analysis service job reported finished.");
finished = true;
}
- if (calcMan.isPending(this) && isInteractiveUpdate())
+ else
{
- finished = true;
- // cancel this job and yield to the new job
- try
- {
- if (cancelJob(rslt))
- {
- System.err.println("Cancelled AACon job: " + rslt);
- }
- else
- {
- System.err.println("FAILED TO CANCEL AACon job: " + rslt);
- }
-
- } catch (Exception x)
- {
-
- }
- rslt = "CANCELLED JOB";
- return;
+ Cache.log.debug("Status now " + running.getState());
}
- long cpos;
- ChunkHolder stats = null;
- do
+
+ if (calcMan.isPending(this) && isInteractiveUpdate())
{
- cpos = rpos;
- boolean retry = false;
- do
- {
+ Cache.log.debug("Analysis service job is stale. aborting.");
+ // job has become stale.
+ if (!finished) {
+ finished = true;
+ // cancel this job and yield to the new job
try
{
- stats = pullExecStatistics(rslt, rpos);
- } catch (Exception x)
- {
-
- if (x.getMessage().contains(
- "Position in a file could not be negative!"))
+ if (cancellable
+ && ((CancellableI) annotService).cancel(running))
{
- // squash index out of bounds exception- seems to happen for
- // disorder predictors which don't (apparently) produce any
- // progress information and JABA server throws an exception
- // because progress length is -1.
- stats = null;
+ System.err.println("Cancelled AACon job: " + rslt);
}
else
{
- if (--serverErrorsLeft > 0)
- {
- retry = true;
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException q)
- {
- }
- ;
- }
- else
- {
- throw x;
- }
+ System.err.println("FAILED TO CANCEL AACon job: " + rslt);
}
+
+ } catch (Exception x)
+ {
+
}
- } while (retry);
- if (stats != null)
- {
- System.out.print(stats.getChunk());
- msg.append(stats);
- rpos = stats.getNextPosition();
}
- } while (stats != null && rpos > cpos);
+ rslt = running.getJobHandle();
+ return;
+ }
+
+ // pull any stats - some services need to flush log output before
+ // results are available
+ Cache.log.debug("Updating progress log for annotation service.");
+
+ try
+ {
+ annotService.updateJobProgress(running);
+ } catch (Throwable thr)
+ {
+ Cache.log.debug("Ignoring exception during progress update.",
+ thr);
+ }
+ Cache.log.trace("Result of poll: " + running.getStatus());
- if (!finished && status.equals(JobStatus.FAILED))
+ if (!finished && !running.isFailed())
{
try
{
+ Cache.log.debug("Analysis service job thread sleeping.");
Thread.sleep(200);
+ Cache.log.debug("Analysis service job thread woke.");
} catch (InterruptedException x)
{
}
;
}
} while (!finished);
+
+ // TODO: need to poll/retry
if (serverErrorsLeft > 0)
{
try
} catch (InterruptedException x)
{
}
- if (collectAnnotationResultsFor(rslt))
+ }
+ // configure job with the associated view's feature renderer, if one
+ // exists.
+ // TODO: here one would also grab the 'master feature renderer' in order
+ // to enable/disable
+ // features automatically according to user preferences
+ running.setFeatureRenderer(
+ ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
+ Cache.log.debug("retrieving job results.");
+ List<AlignmentAnnotation> returnedAnnot = annotService
+ .getAlignmentAnnotation(running, this);
+ Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
+ : ("" + returnedAnnot.size())));
+ running.setAnnotation(returnedAnnot);
+
+ if (running.hasResults())
+ {
+ jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ + rslt + " at " + service.getUri());
+ updateResultAnnotation(true);
+ if (running.isTransferSequenceFeatures())
{
- jalview.bin.Cache.log.debug("Updating result annotation from Job "
- + rslt + " at " + service.getUri());
- updateResultAnnotation(true);
- ap.adjustAnnotationHeight();
+ jalview.bin.Cache.log.debug(
+ "Updating feature display settings and transferring features from Job "
+ + rslt + " at " + service.getUri());
+ ((jalview.gui.AlignmentPanel) ap)
+ .updateFeatureRendererFrom(running.getFeatureRenderer());
+ // TODO: JAL-1150 - create sequence feature settings API for defining
+ // styles and enabling/disabling feature overlay on alignment panel
+
+ if (alignFrame.alignPanel == ap)
+ {
+ // only do this if the alignFrame is currently showing this view.
+ Desktop.getAlignFrameFor(alignViewport)
+ .setShowSeqFeatures(true);
+ }
}
+ ap.adjustAnnotationHeight();
}
+ Cache.log.debug("Annotation Service Worker thread finished.");
}
-
- catch (JobSubmissionException x)
- {
-
- System.err.println(
- "submission error with " + getServiceActionText() + " :");
- x.printStackTrace();
- calcMan.disableWorker(this);
- } catch (ResultNotAvailableException x)
- {
- System.err.println("collection error:\nJob ID: " + rslt);
- x.printStackTrace();
- calcMan.disableWorker(this);
-
- } catch (OutOfMemoryError error)
- {
- calcMan.disableWorker(this);
-
- // consensus = null;
- // hconsensus = null;
- ap.raiseOOMWarning(getServiceActionText(), error);
- } catch (Exception x)
+// TODO: use service specitic exception handlers
+// catch (JobSubmissionException x)
+// {
+//
+// System.err.println(
+// "submission error with " + getServiceActionText() + " :");
+// x.printStackTrace();
+// calcMan.disableWorker(this);
+// } catch (ResultNotAvailableException x)
+// {
+// System.err.println("collection error:\nJob ID: " + rslt);
+// x.printStackTrace();
+// calcMan.disableWorker(this);
+//
+// } catch (OutOfMemoryError error)
+// {
+// calcMan.disableWorker(this);
+//
+// ap.raiseOOMWarning(getServiceActionText(), error);
+// }
+ catch (Throwable x)
{
calcMan.disableWorker(this);
- // consensus = null;
- // hconsensus = null;
System.err
.println("Blacklisting worker due to unexpected exception:");
x.printStackTrace();
}
/**
- * validate input for dynamic/non-dynamic update context
- *
- * @param dynamic
+ * validate input for dynamic/non-dynamic update context TODO: move to
+ * analysis interface ?
* @param seqs
+ *
* @return true if input is valid
*/
- abstract boolean checkValidInputSeqs(boolean dynamic,
- List<FastaSequence> seqs);
-
- abstract String submitToService(
- List<compbio.data.sequence.FastaSequence> seqs)
- throws JobSubmissionException;
-
- abstract boolean cancelJob(String rslt) throws Exception;
-
- abstract JobStatus getJobStatus(String rslt) throws Exception;
-
- abstract ChunkHolder pullExecStatistics(String rslt, long rpos);
-
- abstract boolean collectAnnotationResultsFor(String rslt)
- throws ResultNotAvailableException;
+ boolean checkValidInputSeqs(List<SequenceI> seqs)
+ {
+ int nvalid = 0;
+ for (SequenceI sq : seqs)
+ {
+ if (sq.getStart() <= sq.getEnd()
+ && (sq.isProtein() ? proteinAllowed : nucleotidesAllowed))
+ {
+ if (submitGaps
+ || sq.getLength() == (sq.getEnd() - sq.getStart() + 1))
+ {
+ nvalid++;
+ }
+ }
+ }
+ return nvalid >= min_valid_seqs;
+ }
public void cancelCurrentJob()
{
try
{
- String id = rslt;
- if (cancelJob(rslt))
+ String id = running.getJobId();
+ if (((CancellableI) annotService).cancel(running))
{
System.err.println("Cancelled job " + id);
}
* @return true if a running job should be cancelled because new input data is
* available for analysis
*/
- abstract boolean isInteractiveUpdate();
+ boolean isInteractiveUpdate()
+ {
+ return service.isInteractiveUpdate();
+ }
- public List<FastaSequence> getInputSequences(AlignmentI alignment,
+ /**
+ * decide what sequences will be analysed TODO: refactor to generate
+ * List<SequenceI> for submission to service interface
+ *
+ * @param alignment
+ * @param inputSeqs
+ * @return
+ */
+ public List<SequenceI> getInputSequences(AlignmentI alignment,
AnnotatedCollectionI inputSeqs)
{
if (alignment == null || alignment.getWidth() <= 0
inputSeqs = alignment;
}
- List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
+ List<SequenceI> seqs = new ArrayList<>();
int minlen = 10;
int ln = -1;
gapMap = new boolean[0];
start = inputSeqs.getStartRes();
end = inputSeqs.getEndRes();
-
+ // TODO: URGENT! unify with JPred / MSA code to handle hidden regions
+ // correctly
+ // TODO: push attributes into WsJob instance (so they can be safely
+ // persisted/restored
for (SequenceI sq : (inputSeqs.getSequences()))
{
if (bySequence
{
seqNames.put(newname, sq);
}
- FastaSequence seq;
+ SequenceI seq;
if (submitGaps)
{
- seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+ seqs.add(seq = new jalview.datamodel.Sequence(newname,
sq.getSequenceAsString()));
- if (gapMap == null || gapMap.length < seq.getSequence().length())
+ if (gapMap == null || gapMap.length < seq.getLength())
{
boolean[] tg = gapMap;
gapMap = new boolean[seq.getLength()];
}
else
{
- seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+ // TODO: add ability to exclude hidden regions
+ seqs.add(seq = new jalview.datamodel.Sequence(newname,
AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
sq.getSequenceAsString(start, end + 1))));
+ // for annotation need to also record map to sequence start/end
+ // position in range
+ // then transfer back to original sequence on return.
}
- if (seq.getSequence().length() > ln)
+ if (seq.getLength() > ln)
{
- ln = seq.getSequence().length();
+ ln = seq.getLength();
}
}
}
// acids at each position, and AAcon doesn't gracefully degrade.
for (int p = 0; p < seqs.size(); p++)
{
- FastaSequence sq = seqs.get(p);
- int l = sq.getSequence().length();
+ SequenceI sq = seqs.get(p);
// strip gapped columns
char[] padded = new char[realw],
- orig = sq.getSequence().toCharArray();
+ orig = sq.getSequence();
for (int i = 0, pp = 0; i < realw; pp++)
{
if (gapMap[pp])
}
}
}
- seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
+ seqs.set(p, new jalview.datamodel.Sequence(sq.getName(),
new String(padded)));
}
}
updateResultAnnotation(false);
}
- public abstract void updateResultAnnotation(boolean immediate);
-
- public abstract String getServiceActionText();
+ public void updateResultAnnotation(boolean immediate)
+ {
+ if ((immediate || !calcMan.isWorking(this)) && running != null
+ && running.hasResults())
+ {
+ List<AlignmentAnnotation> ourAnnot = running.getAnnotation();
+ updateOurAnnots(ourAnnot);
+ }
+ }
/**
* notify manager that we have started, and wait for a free calculation slot
}
}
our.clear();
-
+ // validate rows and update Alignmment state
+ for (AlignmentAnnotation an : ourAnnots)
+ {
+ alignViewport.getAlignment().validateAnnotation(an);
+ }
+ // TODO: may need a menu refresh after this
+ // af.setMenusForViewport();
ap.adjustAnnotationHeight();
}
}
*/
package jalview.ws.jws2;
-import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
import jalview.gui.AlignFrame;
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
import jalview.ws.api.ServiceWithParameters;
-import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
-import jalview.ws.uimodel.AlignAnalysisUIText;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
import java.util.List;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
/**
* provides metadata for a jabaws2 service instance - resolves names, etc.
*/
public abstract class Jws2Client extends jalview.ws.WSClient
{
+ /**
+ * instantiate a new service client. preset and arguments are assumed to be
+ * valid for the service
+ *
+ * @param _alignFrame
+ * @param preset
+ * @param arguments
+ */
public Jws2Client(AlignFrame _alignFrame, WsParamSetI preset,
List<ArgumentI> arguments)
{
super(_alignFrame, preset, arguments);
- if (preset != null)
- {
-// if (!((preset instanceof JabaPreset)
-// || preset instanceof JabaWsParamSet))
-// {
-// /*
-// * { this.preset = ((JabaPreset) preset).p; } else if (preset instanceof
-// * JabaWsParamSet) { List<Argument> newargs = new ArrayList<Argument>();
-// * JabaWsParamSet pset = ((JabaWsParamSet) preset); for (Option opt :
-// * pset.getjabaArguments()) { newargs.add(opt); } if (arguments != null
-// * && arguments.size() > 0) { // merge arguments with preset's own
-// * arguments. for (Argument opt : arguments) { newargs.add(opt); } }
-// * paramset = newargs; } else {
-// */
-// throw new Error(MessageManager.getString(
-// "error.implementation_error_can_only_instantiate_jaba_param_sets"));
-// }
- }
- else
- {
- // TODO: verify that paramset is compatible with the service being
- // contacted
- }
}
public Jws2Client()
abstract void attachWSMenuEntry(JMenu wsmenu,
final ServiceWithParameters service,
final AlignFrame alignFrame);
-
- static boolean registerAAConWSInstance(final JMenu wsmenu,
- final ServiceWithParameters service, final AlignFrame alignFrame)
- {
- Jws2Instance jaba_service = (Jws2Instance) service;
- final AlignAnalysisUIText aaui = jaba_service.getAlignAnalysisUI(); // null ; //
- // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
- if (aaui == null)
- {
- // not an instantaneous calculation GUI type service
- return false;
- }
- // create the instaneous calculation GUI bits and update state if existing
- // GUI elements already present
-
- JCheckBoxMenuItem _aaConEnabled = null;
- for (int i = 0; i < wsmenu.getItemCount(); i++)
- {
- JMenuItem item = wsmenu.getItem(i);
- if (item instanceof JCheckBoxMenuItem
- && item.getText().equals(aaui.getAAconToggle()))
- {
- _aaConEnabled = (JCheckBoxMenuItem) item;
- }
- }
- // is there an aaCon worker already present - if so, set it to use the
- // given service handle
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) aaconClient
- .get(0);
- if (!worker.service.getHostURL().equals(service.getHostURL()))
- {
- // javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- // @Override
- // public void run()
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- buildCurrentAAConWorkerFor(aaui, alignFrame, jaba_service);
- }
- } // );
- }
- }
- }
-
- // is there a service already registered ? there shouldn't be if we are
- // being called correctly
- if (_aaConEnabled == null)
- {
- final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
- aaui.getAAconToggle());
-
- aaConEnabled.setToolTipText(
- JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
- aaConEnabled.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- }
- else
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame);
-
- }
- }
-
- });
- wsmenu.add(aaConEnabled);
- final JMenuItem modifyParams = new JMenuItem(
- aaui.getAAeditSettings());
- modifyParams.setToolTipText(JvSwingUtils.wrapTooltip(true,
- aaui.getAAeditSettingsTooltip()));
- modifyParams.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- showAAConAnnotationSettingsFor(aaui, alignFrame);
- }
- });
- wsmenu.add(modifyParams);
- wsmenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent arg0)
- {
- // TODO: refactor to the implementing class.
- if (alignFrame.getViewport().getAlignment().isNucleotide()
- ? aaui.isNa()
- : aaui.isPr())
- {
- aaConEnabled.setEnabled(true);
- modifyParams.setEnabled(true);
- }
- else
- {
- aaConEnabled.setEnabled(false);
- modifyParams.setEnabled(false);
- }
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- aaConEnabled.setSelected(true);
- }
- else
- {
- aaConEnabled.setSelected(false);
- }
- }
-
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
- });
-
- }
- return true;
- }
-
- private static void showAAConAnnotationSettingsFor(
- final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- // could actually do a class search for this too
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui);
- }
- new SequenceAnnotationWSClient(fave, alignFrame, true);
-
- }
-
- private static void buildCurrentAAConWorkerFor(
- final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame, null);
- }
-
- private static void buildCurrentAAConWorkerFor(
- final AlignAnalysisUIText aaui, AlignFrame alignFrame,
- Jws2Instance service)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui, service);
- }
- else
- {
- if (service != null
- && !fave.getService().getHostURL()
- .equals(service.getHostURL()))
- {
- Cache.log.debug("Changing AACon service to " + service.getHostURL()
- + " from " + fave.getService().getHostURL());
- fave.setService(service);
- }
- }
- new SequenceAnnotationWSClient(fave, alignFrame, false);
- }
-
- private static AAConSettings createDefaultAAConSettings(
- AlignAnalysisUIText aaui)
- {
- return createDefaultAAConSettings(aaui, null);
- }
-
- private static AAConSettings createDefaultAAConSettings(
- AlignAnalysisUIText aaui, Jws2Instance service)
- {
- if (service != null)
- {
- if (!service.getServiceType()
- .equals(compbio.ws.client.Services.AAConWS.toString()))
- {
- Cache.log.warn(
- "Ignoring invalid preferred service for AACon calculations (service type was "
- + service.getServiceType() + ")");
- service = null;
- }
- else
- {
- // check service is actually in the list of currently avaialable
- // services
- if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
- {
- // it isn't ..
- service = null;
- }
- }
- }
- if (service == null)
- {
- // get the default service for AACon
- service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
- aaui.getServiceType());
- }
- if (service == null)
- {
- // TODO raise dialog box explaining error, and/or open the JABA
- // preferences menu.
- throw new Error(
- MessageManager.getString("error.no_aacon_service_found"));
- }
- return new AAConSettings(true, service, null, null);
- }
-
- private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui,
- AlignFrame alignFrame)
- {
- alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(aaui.getClient());
- }
-
}
--- /dev/null
+package jalview.ws.jws2;
+
+import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+public class Jws2ClientFactory
+{
+ static boolean registerAAConWSInstance(final JMenu wsmenu,
+ final ServiceWithParameters service, final AlignFrame alignFrame)
+ {
+ Jws2Instance jaba_service = (Jws2Instance) service;
+ final AlignAnalysisUIText aaui = jaba_service.getAlignAnalysisUI(); // null
+ // ; //
+ // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
+ if (aaui == null)
+ {
+ // not an instantaneous calculation GUI type service
+ return false;
+ }
+ // create the instaneous calculation GUI bits and update state if existing
+ // GUI elements already present
+
+ JCheckBoxMenuItem _aaConEnabled = null;
+ for (int i = 0; i < wsmenu.getItemCount(); i++)
+ {
+ JMenuItem item = wsmenu.getItem(i);
+ if (item instanceof JCheckBoxMenuItem
+ && item.getText().equals(aaui.getAAconToggle()))
+ {
+ _aaConEnabled = (JCheckBoxMenuItem) item;
+ }
+ }
+ // is there an aaCon worker already present - if so, set it to use the
+ // given service handle
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) aaconClient
+ .get(0);
+ if (!worker.service.getHostURL().equals(service.getHostURL()))
+ {
+ // javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ // @Override
+ // public void run()
+ {
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ buildCurrentAAConWorkerFor(aaui, alignFrame, jaba_service);
+ }
+ } // );
+ }
+ }
+ }
+
+ // is there a service already registered ? there shouldn't be if we are
+ // being called correctly
+ if (_aaConEnabled == null)
+ {
+ final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
+ aaui.getAAconToggle());
+
+ aaConEnabled.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
+ aaConEnabled.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ }
+ else
+ {
+ buildCurrentAAConWorkerFor(aaui, alignFrame);
+
+ }
+ }
+
+ });
+ wsmenu.add(aaConEnabled);
+ final JMenuItem modifyParams = new JMenuItem(
+ aaui.getAAeditSettings());
+ modifyParams.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ aaui.getAAeditSettingsTooltip()));
+ modifyParams.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ showAAConAnnotationSettingsFor(aaui, alignFrame);
+ }
+ });
+ wsmenu.add(modifyParams);
+ wsmenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent arg0)
+ {
+ // TODO: refactor to the implementing class.
+ if (alignFrame.getViewport().getAlignment().isNucleotide()
+ ? aaui.isNa()
+ : aaui.isPr())
+ {
+ aaConEnabled.setEnabled(true);
+ modifyParams.setEnabled(true);
+ }
+ else
+ {
+ aaConEnabled.setEnabled(false);
+ modifyParams.setEnabled(false);
+ }
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ aaConEnabled.setSelected(true);
+ }
+ else
+ {
+ aaConEnabled.setSelected(false);
+ }
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
+
+ }
+ return true;
+ }
+
+ private static void showAAConAnnotationSettingsFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ /*
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
+ */
+ // could actually do a class search for this too
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui);
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, true);
+
+ }
+
+ private static void buildCurrentAAConWorkerFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ buildCurrentAAConWorkerFor(aaui, alignFrame, null);
+ }
+
+ private static void buildCurrentAAConWorkerFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame,
+ Jws2Instance service)
+ {
+ /*
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
+ */
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui, service);
+ }
+ else
+ {
+ if (service != null && !fave.getService().getHostURL()
+ .equals(service.getHostURL()))
+ {
+ Cache.log.debug("Changing AACon service to " + service.getHostURL()
+ + " from " + fave.getService().getHostURL());
+ fave.setService(service);
+ }
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, false);
+ }
+
+ private static AAConSettings createDefaultAAConSettings(
+ AlignAnalysisUIText aaui)
+ {
+ return createDefaultAAConSettings(aaui, null);
+ }
+
+ private static AAConSettings createDefaultAAConSettings(
+ AlignAnalysisUIText aaui, Jws2Instance service)
+ {
+ if (service != null)
+ {
+ if (!service.getServiceType()
+ .equals(compbio.ws.client.Services.AAConWS.toString()))
+ {
+ Cache.log.warn(
+ "Ignoring invalid preferred service for AACon calculations (service type was "
+ + service.getServiceType() + ")");
+ service = null;
+ }
+ else
+ {
+ // check service is actually in the list of currently avaialable
+ // services
+ if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
+ {
+ // it isn't ..
+ service = null;
+ }
+ }
+ }
+ if (service == null)
+ {
+ // get the default service for AACon
+ service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+ aaui.getServiceType());
+ }
+ if (service == null)
+ {
+ // TODO raise dialog box explaining error, and/or open the JABA
+ // preferences menu.
+ throw new Error(
+ MessageManager.getString("error.no_aacon_service_found"));
+ }
+ return new AAConSettings(true, service, null, null);
+ }
+
+ private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui,
+ AlignFrame alignFrame)
+ {
+ alignFrame.getViewport().getCalcManager()
+ .removeRegisteredWorkersOfClass(aaui.getClient());
+ }
+}
\ No newline at end of file
public void attachWSMenuEntry(JMenu rmsawsmenu,
final ServiceWithParameters service, final AlignFrame alignFrame)
{
- if (registerAAConWSInstance(rmsawsmenu, service,
+ if (Jws2ClientFactory.registerAAConWSInstance(rmsawsmenu, service,
alignFrame))
{
// Alignment dependent analysis calculation WS gui
}
try
{
- worker = (AbstractJabaCalcWorker) (clientClass
- .getConstructor(new Class[]
- { Jws2Instance.class, AlignFrame.class, WsParamSetI.class,
- List.class })
- .newInstance(new Object[]
- { sh, alignFrame, this.preset, paramset }));
+ worker = new AbstractJabaCalcWorker(sh, alignFrame, this.preset,
+ paramset);
} catch (Exception x)
{
x.printStackTrace();
}
alignFrame.getViewport().getCalcManager().startWorker(
- new AADisorderClient(sh, alignFrame, preset, paramset));
+ new AbstractJabaCalcWorker(sh, alignFrame, preset, paramset));
}
}
final ServiceWithParameters service,
final AlignFrame alignFrame)
{
- if (registerAAConWSInstance(wsmenu, service, alignFrame))
+ if (Jws2ClientFactory.registerAAConWSInstance(wsmenu, service,
+ alignFrame))
{
// Alignment dependent analysis calculation WS gui
return;
--- /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.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.util.MessageManager;
+import jalview.ws.gui.AnnotationWsJob;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import compbio.data.sequence.Score;
+
+public class AAConClient extends JabawsAnnotationInstance
+{
+ // configuration for factory
+ public static String getServiceActionText()
+ {
+ return "calculating Amino acid consensus using AACon service";
+ }
+
+
+
+ private static String CALC_ID = "jabaws2.AACon";
+
+ public static AlignAnalysisUIText getAlignAnalysisUIText()
+ {
+ return new AlignAnalysisUIText(
+ compbio.ws.client.Services.AAConWS.toString(),
+ AAConClient.class, CALC_ID, false, true, true, true,
+ true, 2, MessageManager.getString("label.aacon_calculations"),
+ MessageManager.getString("tooltip.aacon_calculations"),
+ MessageManager.getString("label.aacon_settings"),
+ MessageManager.getString("tooltip.aacon_settings"));
+ }
+
+ // instance
+ public AAConClient(Jws2Instance handle)
+ {
+ super(handle);
+ }
+
+ @Override
+ List<AlignmentAnnotation> annotationFromScoreManager(
+ AnnotationWsJob running, AlignViewportI alignViewport,
+ boolean[] gapMap)
+ {
+
+ Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
+ int alWidth = alignViewport.getAlignment().getWidth();
+ ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
+ for (String score : scoremap.keySet())
+ {
+ Set<Score> scores = scoremap.get(score);
+ for (Score scr : scores)
+ {
+ if (scr.getRanges() != null && scr.getRanges().size() > 0)
+ {
+ /**
+ * annotation in range annotation = findOrCreate(scr.getMethod(),
+ * true, null, null); Annotation[] elm = new Annotation[alWidth];
+ * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng :
+ * scr.getRanges()) { float val = vals.next().floatValue(); for (int i
+ * = rng.from; i <= rng.to; i++) { elm[i] = new Annotation("", "", '
+ * ', val); } } annotation.annotations = elm;
+ * annotation.validateRangeAndDisplay();
+ */
+ }
+ else
+ {
+ createAnnotationRowsForScores(alignViewport, gapMap, ourAnnot,
+ getCalcId(), alWidth, scr);
+ }
+ }
+ }
+ return ourAnnot;
+ }
+
+}
--- /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.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
+import jalview.ws.gui.AnnotationWsJob;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import compbio.data.sequence.Range;
+import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager.ScoreHolder;
+
+public class AADisorderClient extends JabawsAnnotationInstance
+{
+ // static configuration
+ public static String getServiceActionText()
+ {
+ return "Submitting amino acid sequences for disorder prediction.";
+ }
+
+ // minSeq = 1; protein only, no gaps
+
+ // instance
+ public AADisorderClient(Jws2Instance handle)
+ {
+ super(handle);
+
+ }
+
+ @Override
+ List<AlignmentAnnotation> annotationFromScoreManager(
+ AnnotationWsJob running, AlignViewportI alignViewport,
+ boolean[] gapMap)
+ {
+
+ Map<String, String[]> featureTypeMap = featureMap.get(our.getName());
+ Map<String, Map<String, Object>> annotTypeMap = annotMap
+ .get(our.getName());
+ boolean dispFeatures = false;
+ Map<String, Object> fc = new Hashtable<>();
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
+ /**
+ * grouping for any annotation rows created
+ */
+ int graphGroup = 1;
+ if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation ala : alignViewport.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (ala.graphGroup > graphGroup)
+ {
+ graphGroup = ala.graphGroup;
+ }
+ }
+ }
+
+ // TODO: downgrade code below so we don't annotate sequences directly
+ Map<String, SequenceI> seqNames = running.getSeqNames();
+ int start = running.getStartPos();
+ for (String seqId : seqNames.keySet())
+ {
+ boolean sameGroup = false;
+ SequenceI dseq, aseq, seq = seqNames.get(seqId);
+ int base = seq.findPosition(start) - 1;
+ aseq = seq;
+ while ((dseq = seq).getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ ScoreHolder scores = null;
+ try
+ {
+ scores = scoremanager.getAnnotationForSequence(seqId);
+ } catch (Exception q)
+ {
+ Cache.log.info("Couldn't recover disorder prediction for sequence "
+ + seq.getName() + "(Prediction name was " + seqId + ")"
+ + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
+ }
+ float last = Float.NaN, val = Float.NaN;
+ int lastAnnot = ourAnnot.size();
+ if (scores != null && scores.scores != null)
+ {
+ for (Score scr : scores.scores)
+ {
+
+ if (scr.getRanges() != null && scr.getRanges().size() > 0)
+ {
+ Iterator<Float> vals = scr.getScores().iterator();
+ // make features on sequence
+ for (Range rn : scr.getRanges())
+ {
+
+ SequenceFeature sf;
+ String[] type = featureTypeMap.get(scr.getMethod());
+ if (type == null)
+ {
+ // create a default type for this feature
+ type = new String[] {
+ typeName + " (" + scr.getMethod() + ")",
+ our.getActionText() };
+ }
+ if (vals.hasNext())
+ {
+ val = vals.next().floatValue();
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, val, methodName);
+ }
+ else
+ {
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, methodName);
+ }
+ dseq.addSequenceFeature(sf);
+ if (last != val && !Float.isNaN(last))
+ {
+ fc.put(sf.getType(), sf);
+ }
+ last = val;
+ running.setTransferSequenceFeatures(true);
+ dispFeatures = true;
+ }
+ }
+ else
+ {
+ if (scr.getScores().size() == 0)
+ {
+ continue;
+ }
+ String typename, calcName;
+ AlignmentAnnotation annot = createAnnotationRowsForScores(
+ alignViewport, gapMap, ourAnnot,
+ typename = our.getName() + " (" + scr.getMethod() + ")",
+ calcName = our.getNameURI() + "/" + scr.getMethod(),
+ aseq, base + 1, scr);
+ annot.graph = AlignmentAnnotation.LINE_GRAPH;
+
+ Map<String, Object> styleMap = (annotTypeMap == null) ? null
+ : annotTypeMap.get(scr.getMethod());
+
+ annot.visible = (styleMap == null
+ || styleMap.get(INVISIBLE) == null);
+ double[] thrsh = (styleMap == null) ? null
+ : (double[]) styleMap.get(THRESHOLD);
+ float[] range = (styleMap == null) ? null
+ : (float[]) styleMap.get(RANGE);
+ if (range != null)
+ {
+ annot.graphMin = range[0];
+ annot.graphMax = range[1];
+ }
+ if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
+ {
+ {
+ if (!sameGroup)
+ {
+ graphGroup++;
+ sameGroup = true;
+ }
+
+ annot.graphGroup = graphGroup;
+ }
+ }
+
+ annot.description = "<html>" + our.getActionText()
+ + " - raw scores";
+ if (thrsh != null)
+ {
+ String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
+ + thrsh[1] + " indicates disorder";
+ annot.threshold = new GraphLine((float) thrsh[1], threshNote,
+ Color.red);
+ annot.description += "<br/>" + threshNote;
+ }
+ annot.description += "</html>";
+ Color col = ColorUtils
+ .createColourFromName(typeName + scr.getMethod());
+ for (int p = 0, ps = annot.annotations.length; p < ps; p++)
+ {
+ if (annot.annotations[p] != null)
+ {
+ annot.annotations[p].colour = col;
+ }
+ }
+ annot._linecolour = col;
+ // finally, update any dataset annotation
+ replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+ aseq);
+ }
+ }
+ }
+ if (lastAnnot + 1 == ourAnnot.size())
+ {
+ // remove singleton alignment annotation row
+ ourAnnot.get(lastAnnot).graphGroup = -1;
+ }
+ }
+ {
+ if (dispFeatures)
+ {
+ jalview.api.FeatureRenderer fr = running.getFeatureRenderer();
+ for (String ft : fc.keySet())
+ {
+ FeatureColourI gc = fr.getFeatureStyle(ft);
+ if (gc.isSimpleColour())
+ {
+ // set graduated color as fading to white for minimum, and
+ // autoscaling to values on alignment
+ FeatureColourI ggc = new FeatureColour(gc.getColour(),
+ Color.white, gc.getColour(), Color.white,
+ Float.MIN_VALUE, Float.MAX_VALUE);
+ ggc.setAutoScaled(true);
+ fr.setColour(ft, ggc);
+ }
+ }
+
+ }
+ return ourAnnot;
+ }
+ }
+
+ private static final String THRESHOLD = "THRESHOLD";
+
+ private static final String RANGE = "RANGE";
+
+ String typeName;
+
+ String methodName;
+
+ String groupName;
+
+ private static Map<String, Map<String, String[]>> featureMap;
+
+ private static Map<String, Map<String, Map<String, Object>>> annotMap;
+
+ private static String DONTCOMBINE = "DONTCOMBINE";
+
+ private static String INVISIBLE = "INVISIBLE";
+ static
+ {
+ // TODO: turn this into some kind of configuration file that's a bit easier
+ // to edit
+ featureMap = new HashMap<>();
+ Map<String, String[]> fmap;
+ featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
+ fmap = new HashMap<>());
+ fmap.put("Glob",
+ new String[]
+ { "Globular Domain", "Predicted globular domain" });
+ featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
+ fmap = new HashMap<>());
+ featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
+ fmap = new HashMap<>());
+ fmap.put("REM465", new String[] { "REM465", "Missing density" });
+ fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
+ fmap.put("COILS", new String[] { "COILS", "Random coil" });
+ featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
+ fmap = new HashMap<>());
+ fmap.put("GlobDoms",
+ new String[]
+ { "Globular Domain", "Predicted globular domain" });
+ fmap.put("Disorder",
+ new String[]
+ { "Protein Disorder", "Probable unstructured peptide region" });
+ Map<String, Map<String, Object>> amap;
+ annotMap = new HashMap<>();
+ annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
+ amap = new HashMap<>());
+ amap.put("Dydx", new HashMap<String, Object>());
+ amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
+ amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
+ amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
+
+ amap.put("SmoothedScore", new HashMap<String, Object>());
+ amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
+ amap.put("RawScore", new HashMap<String, Object>());
+ amap.get("RawScore").put(INVISIBLE, INVISIBLE);
+ annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
+ amap = new HashMap<>());
+ amap.put("COILS", new HashMap<String, Object>());
+ amap.put("HOTLOOPS", new HashMap<String, Object>());
+ amap.put("REM465", new HashMap<String, Object>());
+ amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
+ amap.get("COILS").put(RANGE, new float[] { 0, 1 });
+
+ amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
+ amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
+ amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
+ amap.get("REM465").put(RANGE, new float[] { 0, 1 });
+
+ annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
+ amap = new HashMap<>());
+ amap.put("Long", new HashMap<String, Object>());
+ amap.put("Short", new HashMap<String, Object>());
+ amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("Long").put(RANGE, new float[] { 0, 1 });
+ amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("Short").put(RANGE, new float[] { 0, 1 });
+ annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
+ amap = new HashMap<>());
+ amap.put("JRonn", new HashMap<String, Object>());
+ amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
+ }
+
+}
-/*
- * 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;
+package jalview.ws.jws2.jabaws2;
+import jalview.api.AlignViewportI;
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.api.JobId;
+import jalview.ws.api.SequenceAnnotationServiceI;
+import jalview.ws.gui.AnnotationWsJob;
+import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
+import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
import compbio.metadata.JobSubmissionException;
-import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.WrongParameterException;
-public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
+public abstract class JabawsAnnotationInstance
+ extends JabawsServiceInstance<SequenceAnnotation>
+ implements SequenceAnnotationServiceI
{
- @SuppressWarnings("unchecked")
- protected SequenceAnnotation aaservice;
+ /**
+ * holds last results obtained when non-null. TODO: remove this as a field ?
+ */
+ protected ScoreManager scoremanager = null;
- protected ScoreManager scoremanager;
-
- public JabawsCalcWorker(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<ArgumentI> paramset)
+ public JabawsAnnotationInstance(Jws2Instance handle)
{
- super(service, alignFrame, preset, paramset);
- aaservice = (SequenceAnnotation) service.service;
+ super(handle);
}
- @Override
- ChunkHolder pullExecStatistics(String rslt, long rpos)
+
+ /**
+ *
+ * @return the calcId for this Jabaws Service (convenience method).
+ *
+ * TODO: decide if this is really convenient since manager and
+ * instance have same method !
+ */
+ public String getCalcId()
{
- return aaservice.pullExecStatistics(rslt, rpos);
+ return our.aaui == null ? null : our.aaui.getCalcId();
}
@Override
- boolean collectAnnotationResultsFor(String rslt)
- throws ResultNotAvailableException
+ public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset,
+ List<ArgumentI> arguments) throws Throwable
{
- scoremanager = aaservice.getAnnotation(rslt);
- if (scoremanager != null)
+ String rslt = null;
+ scoremanager = null;
+ List<FastaSequence> jabaseqs = new ArrayList(seqs.size());
+ for (SequenceI seq : seqs)
{
- return true;
+ jabaseqs.add(
+ new FastaSequence(seq.getName(), seq.getSequenceAsString()));
}
- return false;
- }
-
- @Override
- boolean cancelJob(String rslt) throws Exception
- {
- return aaservice.cancelJob(rslt);
- }
-
- @Override
- protected JobStatus getJobStatus(String rslt) throws Exception
- {
- return aaservice.getJobStatus(rslt);
- }
-
- @Override
- boolean hasService()
- {
- return aaservice != null;
- }
-
- @Override
- protected boolean isInteractiveUpdate()
- {
- return this instanceof AAConClient;
- }
-
- @Override
- protected String submitToService(
- List<compbio.data.sequence.FastaSequence> seqs)
- throws JobSubmissionException
- {
- String rslt;
if (preset == null && arguments == null)
{
- rslt = aaservice.analize(seqs);
+ rslt = service.analize(jabaseqs);
}
- else
+ if (preset != null)
+ {
+ if (preset instanceof JabaPreset)
+ {
+ // TODO: verify behaviour is really the same, since preset analyze was
+ // never called in Jalview 2.11.x
+ rslt = service.presetAnalize(jabaseqs,
+ ((JabaPreset) preset).getJabaPreset());
+ }
+ else
+ {
+ rslt = service.customAnalize(jabaseqs,
+ JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
+ }
+ }
+ else if (arguments != null && arguments.size() > 0)
{
try
{
- rslt = aaservice.customAnalize(seqs, getJabaArguments());
+ rslt = service.customAnalize(jabaseqs,
+ JabaParamStore.getJabafromJwsArgs(arguments));
} catch (WrongParameterException x)
{
throw new JobSubmissionException(MessageManager.getString(
}
}
- return rslt;
+
+ if (rslt == null)
+ {
+ return null;
+ }
+ return new JobId(our.getServiceType(), our.getName(), rslt);
}
- protected void createAnnotationRowsForScores(
- List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
- Score scr)
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotation(
+ AnnotationWsJob running,
+ AbstractJabaCalcWorker abstractJabaCalcWorker) throws Throwable
+ {
+ if (scoremanager == null)
+ {
+ // TODO: raise annotation unavailable exception ?
+ scoremanager = service.getAnnotation(running.getJobId());
+ }
+ if (scoremanager == null)
+ {
+ return List.of();
+ }
+
+ return annotationFromScoreManager(running,
+ abstractJabaCalcWorker.getAlignViewport(),
+ abstractJabaCalcWorker.getGapMap());
+ }
+
+ abstract List<AlignmentAnnotation> annotationFromScoreManager(
+ AnnotationWsJob running,
+ AlignViewportI alignViewport, boolean[] gapMap);
+
+ // From JabawsCalcWorker
+
+ protected void createAnnotationRowsForScores(AlignViewportI alignViewport,
+ boolean[] gapMap, List<AlignmentAnnotation> ourAnnot,
+ String calcId,
+ int alWidth, Score scr)
{
// simple annotation row
AlignmentAnnotation annotation = alignViewport.getAlignment()
null);
if (alWidth == gapMap.length) // scr.getScores().size())
{
- constructAnnotationFromScore(annotation, 0, alWidth, scr);
+ constructAnnotationFromScore(gapMap, annotation, 0,
+ alWidth, scr);
ourAnnot.add(annotation);
}
}
protected AlignmentAnnotation createAnnotationRowsForScores(
+ AlignViewportI alignViewport, boolean[] gapMap,
List<AlignmentAnnotation> ourAnnot, String typeName,
String calcId, SequenceI dseq, int base, Score scr)
{
// annotation.setCalcId(calcId);
AlignmentAnnotation annotation = alignViewport.getAlignment()
.findOrCreateAnnotation(typeName, calcId, false, dseq, null);
- constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
+ constructAnnotationFromScore(gapMap, annotation, 0, dseq.getLength(),
+ scr);
annotation.createSequenceMapping(dseq, base, false);
annotation.adjustForAlignment();
dseq.addAlignmentAnnotation(annotation);
dssan.adjustForAlignment();
}
- private void constructAnnotationFromScore(AlignmentAnnotation annotation,
+ protected void constructAnnotationFromScore(boolean[] gapMap,
+ AlignmentAnnotation annotation,
int base, int alWidth, Score scr)
{
Annotation[] elm = new Annotation[alWidth];
// if we're at a gapped column then skip to next ungapped position
if (gapMap != null && gapMap.length > 0)
{
- while (!gapMap[i])
+ // if gapMap is a different length to the result then it may be out of
+ // sync with the job.
+ while (i < gapMap.length && !gapMap[i])
{
elm[i++] = new Annotation("", "", ' ', Float.NaN);
}
package jalview.ws.jws2.jabaws2;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.gui.WebserviceInfo;
-import jalview.util.MessageManager;
import jalview.ws.api.CancellableI;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
-import jalview.ws.gui.WsJob;
-import jalview.ws.gui.WsJob.JobState;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;
import java.io.IOError;
import java.rmi.ServerError;
import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
-import compbio.data.msa.MsaWS;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.FastaSequence;
-import compbio.metadata.Argument;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.Preset;
import compbio.metadata.ResultNotAvailableException;
public class JabawsMsaInstance
+ extends JabawsServiceInstance<compbio.data.msa.MsaWS>
implements MultipleSequenceAlignmentI, CancellableI
{
- /**
- * our service instance handler generated by the discoverer
- */
- Jws2Instance our;
-
- MsaWS<?> service;
-
@Override
public JobId align(List<SequenceI> toalign, WsParamSetI parameters,
List<ArgumentI> arguments) throws Throwable
public JabawsMsaInstance(Jws2Instance handle)
{
- our = handle;
- service = (MsaWS<?>) our.service;
- }
-
- @Override
- public boolean cancel(WsJob job)
- {
- service.cancelJob(job.getJobId());
- // if the Jaba server indicates the job can't be cancelled, its
- // because its running on the server's local execution engine
- // so we just close the window anyway.
-
- return true;
- }
-
- Map<JobStatus, JobState> jwsState = new HashMap<>();
- {
- jwsState.put(JobStatus.CANCELLED, JobState.CANCELLED);
- jwsState.put(JobStatus.COLLECTED, JobState.FINISHED);
- jwsState.put(JobStatus.FAILED, JobState.FAILED);
- jwsState.put(JobStatus.FINISHED, JobState.FINISHED);
- jwsState.put(JobStatus.PENDING, JobState.QUEUED);
- jwsState.put(JobStatus.RUNNING, JobState.RUNNING);
- jwsState.put(JobStatus.STARTED, JobState.RUNNING);
- jwsState.put(JobStatus.SUBMITTED, JobState.SUBMITTED);
- jwsState.put(JobStatus.UNDEFINED, JobState.UNKNOWN);
- }
- @Override
- public void updateStatus(WsJob job)
- {
- JobStatus jwsstatus = service.getJobStatus(job.getJobId());
- job.setState(jwsState.get(jwsstatus));
- }
-
- @Override
- public boolean updateJobProgress(WsJob job) throws Exception
- {
- StringBuilder response = new StringBuilder(job.getStatus());
- long lastchunk = job.getNextChunk();
- boolean changed = false;
- do
- {
- ChunkHolder chunk = service.pullExecStatistics(job.getJobId(),
- lastchunk);
- if (chunk != null)
- {
- changed |= chunk.getChunk().length() > 0;
- response.append(chunk.getChunk());
- lastchunk = chunk.getNextPosition();
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException x)
- {
- }
- ;
- }
- ;
- job.setnextChunk(lastchunk);
- } while (lastchunk >= 0 && job.getNextChunk() != lastchunk);
- if (job instanceof WsJob)
- {
- // TODO decide if WsJob will be the bean for all ng-webservices
- job.setStatus(response.toString());
- }
- return changed;
- }
-
- public boolean isPresetJob(WsJob job)
- {
- return job.getPreset() != null && job.getPreset() instanceof JabaPreset;
- }
-
- public Preset getServerPreset(WsJob job)
- {
- return (isPresetJob(job))
- ? ((JabaPreset) job.getPreset()).getJabaPreset()
- : null;
- }
-
- public List<Argument> getJabaArguments(WsParamSetI preset)
- {
- List<Argument> newargs = new ArrayList<>();
- if (preset != null)
- {
- if (preset instanceof JabaWsParamSet)
- {
- newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
- }
- else
- {
- newargs.addAll(
- JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
- }
- }
- return newargs;
+ super(handle);
}
- @Override
- public boolean handleSubmitError(Throwable _lex, WsJob j,
- WebserviceInfo wsInfo) throws Exception, Error
- {
- if (_lex instanceof compbio.metadata.UnsupportedRuntimeException)
- {
- wsInfo.appendProgressText(MessageManager.formatMessage(
- "info.job_couldnt_be_run_server_doesnt_support_program",
- new String[]
- { _lex.getMessage() }));
- wsInfo.warnUser(_lex.getMessage(),
- MessageManager.getString("warn.service_not_supported"));
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setStatus(j.getJobnum(),
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- return true;
- }
- if (_lex instanceof compbio.metadata.LimitExceededException)
- {
- wsInfo.appendProgressText(MessageManager.formatMessage(
- "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
- { _lex.getMessage() }));
- wsInfo.warnUser(_lex.getMessage(),
- MessageManager.getString("warn.input_is_too_big"));
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
- return true;
- }
- if (_lex instanceof compbio.metadata.WrongParameterException)
- {
- wsInfo.warnUser(_lex.getMessage(),
- MessageManager.getString("warn.invalid_job_param_set"));
- wsInfo.appendProgressText(MessageManager.formatMessage(
- "info.job_couldnt_be_run_incorrect_param_setting",
- new String[]
- { _lex.getMessage() }));
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
- return true;
- }
- // pass on to generic error handler
- return false;
- }
-
- @Override
- public boolean handleCollectionException(Exception ex, WsJob msjob,
- WebserviceInfo wsInfo)
- {
- if (ex instanceof compbio.metadata.ResultNotAvailableException)
- {
- // job has failed for some reason - probably due to invalid
- // parameters
- Cache.log.debug(
- "Results not available for finished job - marking as broken job.",
- ex);
- String status = msjob.getStatus();
-
- msjob.setStatus(status
- +
- "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
- + ex.getLocalizedMessage());
- msjob.setState(WsJob.JobState.BROKEN);
- return true;
- }
- return false;
- }
}
* 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();
+ * }
+ ***/
}
--- /dev/null
+package jalview.ws.jws2.jabaws2;
+
+import jalview.bin.Cache;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.gui.WsJob;
+import jalview.ws.gui.WsJob.JobState;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import compbio.metadata.Argument;
+import compbio.metadata.ChunkHolder;
+import compbio.metadata.JobStatus;
+import compbio.metadata.Preset;
+
+/**
+ * Base class for JABAWS service instances. Provides helper methods for
+ * interfacing with Jalview.
+ *
+ * @author jprocter
+ *
+ */
+public class JabawsServiceInstance<T extends compbio.data.msa.JManagement>
+ implements
+ jalview.ws.api.JalviewWebServiceI, jalview.ws.api.CancellableI
+{
+ /**
+ * our service instance handler generated by the discoverer
+ */
+ Jws2Instance our;
+ protected T service;
+ protected Map<JobStatus, JobState> jwsState = new HashMap<>();
+
+ @Override
+ public boolean cancel(WsJob job)
+ {
+ service.cancelJob(job.getJobId());
+ // if the Jaba server indicates the job can't be cancelled, its
+ // because its running on the server's local execution engine
+ // so we just close the window anyway.
+
+ return true;
+ }
+
+
+ public JabawsServiceInstance(Jws2Instance handle)
+ {
+ our = handle;
+ service = (T) handle.service;
+ }
+
+ @Override
+ public void updateStatus(WsJob job)
+ {
+ JobStatus jwsstatus = service.getJobStatus(job.getJobId());
+ job.setState(jwsState.get(jwsstatus));
+ }
+
+ @Override
+ public boolean updateJobProgress(WsJob job) throws Exception
+ {
+ StringBuilder response = new StringBuilder(job.getStatus());
+ long lastchunk = job.getNextChunk();
+ if (lastchunk == -1)
+ {
+ Cache.log.debug("No more status messages for job " + job.getJobId());
+ return false;
+ }
+ boolean changed = false;
+ do
+ {
+ ChunkHolder chunk = service.pullExecStatistics(job.getJobId(),
+ lastchunk);
+ if (chunk != null)
+ {
+ changed |= chunk.getChunk().length() > 0;
+ response.append(chunk.getChunk());
+ lastchunk = chunk.getNextPosition();
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ }
+ ;
+ job.setnextChunk(lastchunk);
+ } while (lastchunk >= 0 && job.getNextChunk() != lastchunk);
+ if (job instanceof WsJob)
+ {
+ // TODO decide if WsJob will be the bean for all ng-webservices
+ job.setStatus(response.toString());
+ }
+ return changed;
+ }
+
+ {
+ jwsState.put(JobStatus.CANCELLED, JobState.CANCELLED);
+ jwsState.put(JobStatus.COLLECTED, JobState.FINISHED);
+ jwsState.put(JobStatus.FAILED, JobState.FAILED);
+ jwsState.put(JobStatus.FINISHED, JobState.FINISHED);
+ jwsState.put(JobStatus.PENDING, JobState.QUEUED);
+ jwsState.put(JobStatus.RUNNING, JobState.RUNNING);
+ jwsState.put(JobStatus.STARTED, JobState.RUNNING);
+ jwsState.put(JobStatus.SUBMITTED, JobState.SUBMITTED);
+ jwsState.put(JobStatus.UNDEFINED, JobState.UNKNOWN);
+ }
+
+ public boolean isPresetJob(WsJob job)
+ {
+ return job.getPreset() != null && job.getPreset() instanceof JabaPreset;
+ }
+
+ public Preset getServerPreset(WsJob job)
+ {
+ return (isPresetJob(job))
+ ? ((JabaPreset) job.getPreset()).getJabaPreset()
+ : null;
+ }
+
+ public List<Argument> getJabaArguments(WsParamSetI preset)
+ {
+ List<Argument> newargs = new ArrayList<>();
+ if (preset != null)
+ {
+ if (preset instanceof JabaWsParamSet)
+ {
+ newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
+ }
+ else
+ {
+ newargs.addAll(
+ JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
+ }
+ }
+ return newargs;
+ }
+
+ @Override
+ public boolean handleSubmitError(Throwable _lex, WsJob j,
+ WebserviceInfo wsInfo) throws Exception, Error
+ {
+ if (_lex instanceof compbio.metadata.UnsupportedRuntimeException)
+ {
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_server_doesnt_support_program",
+ new String[]
+ { _lex.getMessage() }));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.service_not_supported"));
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ return true;
+ }
+ if (_lex instanceof compbio.metadata.LimitExceededException)
+ {
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
+ { _lex.getMessage() }));
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.input_is_too_big"));
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
+ return true;
+ }
+ if (_lex instanceof compbio.metadata.WrongParameterException)
+ {
+ wsInfo.warnUser(_lex.getMessage(),
+ MessageManager.getString("warn.invalid_job_param_set"));
+ wsInfo.appendProgressText(MessageManager.formatMessage(
+ "info.job_couldnt_be_run_incorrect_param_setting",
+ new String[]
+ { _lex.getMessage() }));
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
+ return true;
+ }
+ // pass on to generic error handler
+ return false;
+ }
+
+ @Override
+ public boolean handleCollectionException(Exception ex, WsJob msjob,
+ WebserviceInfo wsInfo)
+ {
+ if (ex instanceof compbio.metadata.ResultNotAvailableException)
+ {
+ // job has failed for some reason - probably due to invalid
+ // parameters
+ Cache.log.debug(
+ "Results not available for finished job - marking as broken job.",
+ ex);
+ String status = msjob.getStatus();
+
+ msjob.setStatus(status
+ + "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ + ex.getLocalizedMessage());
+ msjob.setState(WsJob.JobState.BROKEN);
+ return true;
+ }
+ return false;
+ }
+}
@Override
public Object getEndpoint()
{
- if (aaui!=null) {
- // TODO complete
- return null;
- } else {
- if (service instanceof MsaWS<?>)
+ if (service instanceof MsaWS<?>)
+ {
+ if (aaui != null)
+ {
+ throw new Error(
+ "JABAWS MsaWS based instant calculation not implemented.");
+
+ }
+ else
{
- return new JabawsMsaInstance(this);
- } else {
- // TODO complete
- // service is for sequence analysis
- return null;
+ return new JabawsMsaInstance(this);
+ }
+ }
+ else
+ {
+ if (service instanceof compbio.data.msa.SequenceAnnotation)
+ {
+ if (aaui != null)
+ {
+ try
+ {
+ // probably a factory would be nicer but..
+ return aaui.getClient().getConstructor(getClass())
+ .newInstance(this);
+ } catch (Throwable t)
+ {
+ throw new Error("Implementation Error in web service framework",
+ t);
+ }
+ }
+ return new AADisorderClient(this);
+ }
+ return null;
}
}
-}
+
+ public boolean isInteractiveUpdate()
+ {
+ return aaui != null && aaui.isAA();
+ }
}
*/
package jalview.ws.jws2.jabaws2;
-import jalview.ws.jws2.AAConClient;
-import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.uimodel.AlignAnalysisUIText;
import java.util.HashMap;
{
if (aaConGUI == null)
{
- aaConGUI = new HashMap<String, AlignAnalysisUIText>();
+ aaConGUI = new HashMap<>();
aaConGUI.put(compbio.ws.client.Services.AAConWS.toString(),
- AAConClient.getAlignAnalysisUITest());
+ AAConClient.getAlignAnalysisUIText());
aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
- RNAalifoldClient.getAlignAnalysisUITest());
+ RNAalifoldClient.getAlignAnalysisUIText());
// ignore list for JABAWS services not supported in jalview ...
- ignoreGUI = new HashSet<String>();
+ ignoreGUI = new HashSet<>();
}
}
* 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.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
-import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.WsParamSetI;
+import jalview.ws.gui.AnnotationWsJob;
import jalview.ws.uimodel.AlignAnalysisUIText;
import java.text.MessageFormat;
import java.util.TreeSet;
import java.util.regex.Pattern;
-import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructReader.AlifoldResult;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
*
*/
-public class RNAalifoldClient extends JabawsCalcWorker
+public class RNAalifoldClient extends JabawsAnnotationInstance
{
- String methodName;
-
- AlignFrame af;
-
- // keeps track of whether the RNAalifold result includes base contact
- // probabilities
- boolean bpScores;
-
- public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
- WsParamSetI preset, List<ArgumentI> paramset)
- {
- super(sh, alignFrame, preset, paramset);
- af = alignFrame;
- methodName = sh.getName();
- alignedSeqs = true;
- submitGaps = true;
- nucleotidesAllowed = true;
- proteinAllowed = false;
- initViewportParams();
- }
+ // configuration
@Override
public String getCalcId()
private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
- public static AlignAnalysisUIText getAlignAnalysisUITest()
+
+ public static AlignAnalysisUIText getAlignAnalysisUIText()
{
return new AlignAnalysisUIText(
compbio.ws.client.Services.RNAalifoldWS.toString(),
- jalview.ws.jws2.RNAalifoldClient.class, CALC_ID, true, false,
- true, MessageManager.getString("label.rnalifold_calculations"),
+ jalview.ws.jws2.jabaws2.RNAalifoldClient.class, CALC_ID, true,
+ false,
+ true, true, false, 2,
+ MessageManager.getString("label.rnalifold_calculations"),
MessageManager.getString("tooltip.rnalifold_calculations"),
MessageManager.getString("label.rnalifold_settings"),
MessageManager.getString("tooltip.rnalifold_settings"));
}
- @Override
- public String getServiceActionText()
+ public static String getServiceActionText()
{
return "Submitting RNA alignment for Secondary Structure prediction using "
+ "RNAalifold Service";
}
- @Override
- boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+
+ // instance
+
+ public RNAalifoldClient(Jws2Instance handle)
{
- return (seqs.size() > 1);
+ super(handle);
}
@Override
- public void updateResultAnnotation(boolean immediate)
+ List<AlignmentAnnotation> annotationFromScoreManager(
+ AnnotationWsJob running, AlignViewportI alignViewport,
+ boolean[] gapMap)
{
-
- if (immediate || !calcMan.isWorking(this) && scoremanager != null)
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
+
+ // Unpack the ScoreManager
+ List<String> structs = ((RNAStructScoreManager) scoremanager)
+ .getStructs();
+ List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager)
+ .getData();
+
+ // test to see if this data object contains base pair contacts
+ Score fscore = data.get(0).first();
+ boolean bpScores = (fscore.getMethod()
+ .equals(AlifoldResult.contactProbabilities.toString()));
+
+ // add annotation for the consensus sequence alignment
+ createAnnotationRowforScoreHolder(alignViewport, gapMap, ourAnnot,
+ getCalcId(), structs.get(0), null, null);
+
+ // Add annotations for the mfe Structure
+ createAnnotationRowforScoreHolder(alignViewport, gapMap, ourAnnot,
+ getCalcId(), structs.get(1), data.get(1), null);
+
+ // decide whether to add base pair contact probability histogram
+ int count = 2;
+ if (bpScores)
{
+ createAnnotationRowforScoreHolder(alignViewport, gapMap, ourAnnot,
+ getCalcId(), structs.get(2), data.get(0), data.get(2));
+ count++;
+ }
- List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
-
- // Unpack the ScoreManager
- List<String> structs = ((RNAStructScoreManager) scoremanager)
- .getStructs();
- List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager)
- .getData();
-
- // test to see if this data object contains base pair contacts
- Score fscore = data.get(0).first();
- this.bpScores = (fscore.getMethod()
- .equals(AlifoldResult.contactProbabilities.toString()));
-
- // add annotation for the consensus sequence alignment
- createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
- structs.get(0), null, null);
-
- // Add annotations for the mfe Structure
- createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
- structs.get(1), data.get(1), null);
-
- // decide whether to add base pair contact probability histogram
- int count = 2;
- if (bpScores)
- {
- createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
- structs.get(2), data.get(0), data.get(2));
- count++;
- }
-
- // Now loop for the rest of the Annotations (if there it isn't stochastic
- // output
- // only the centroid and MEA structures remain anyway)
- for (int i = count; i < structs.size(); i++)
- {
- // The ensemble values should be displayed in the description of the
- // first (or all?) Stochastic Backtrack Structures.
- if (!data.get(i).first().getMethod()
- .equals(AlifoldResult.ensembleValues.toString()))
- {
-
- createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
- structs.get(i), data.get(i), null);
- }
- }
-
- if (ourAnnot.size() > 0)
+ // Now loop for the rest of the Annotations (if there it isn't stochastic
+ // output
+ // only the centroid and MEA structures remain anyway)
+ for (int i = count; i < structs.size(); i++)
+ {
+ // The ensemble values should be displayed in the description of the
+ // first (or all?) Stochastic Backtrack Structures.
+ if (!data.get(i).first().getMethod()
+ .equals(AlifoldResult.ensembleValues.toString()))
{
- updateOurAnnots(ourAnnot);
- ap.adjustAnnotationHeight();
+ createAnnotationRowforScoreHolder(alignViewport, gapMap, ourAnnot,
+ getCalcId(), structs.get(i), data.get(i), null);
}
}
+ return ourAnnot;
}
- protected void createAnnotationRowforScoreHolder(
+ private static void createAnnotationRowforScoreHolder(
+ AlignViewportI alignViewport, boolean[] gapMap,
List<AlignmentAnnotation> ourAnnot, String calcId, String struct,
TreeSet<Score> data, TreeSet<Score> descriptionData)
{
AlignmentAnnotation annotation = alignViewport.getAlignment()
.findOrCreateAnnotation(typename, calcId, false, null, null);
- constructAnnotationFromScoreHolder(annotation, struct, data);
+ constructAnnotationFromScoreHolder(gapMap, annotation, struct, data);
/*
* update annotation description with the free Energy, frequency in ensemble
annotation.belowAlignment = false;
// annotation.showAllColLabels = true;
- alignViewport.getAlignment().validateAnnotation(annotation);
- af.setMenusForViewport();
-
ourAnnot.add(annotation);
}
- private AlignmentAnnotation constructAnnotationFromScoreHolder(
- AlignmentAnnotation annotation, String struct,
+ private static AlignmentAnnotation constructAnnotationFromScoreHolder(
+ boolean[] gapMap, AlignmentAnnotation annotation, String struct,
TreeSet<Score> data)
{
Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
return annotation;
}
- private String[] constructTypenameAndDescription(Score score)
+ private static String[] constructTypenameAndDescription(Score score)
{
String description = "";
String typename = "";
// Check whether, at position i there is a base contact and return all the
// contacts at this position. Should be in order of descending probability.
- private LinkedHashMap<Range, Float> isContact(
+ private static LinkedHashMap<Range, Float> isContact(
LinkedHashMap<Range, Float> basePairs, int i)
{
LinkedHashMap<Range, Float> contacts = new LinkedHashMap<>();
return contacts;
}
- private char isSS(char chr)
+ private static char isSS(char chr)
{
String regex = "\\(|\\)|\\{|\\}|\\[|\\]";
char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
return ss;
}
-}
+
+ }
*/
package jalview.ws.uimodel;
+/**
+ * configures annotation worker style web service clients
+ *
+ * @author jprocter
+ *
+ */
public class AlignAnalysisUIText
{
return isPr;
}
+ /**
+ * @return true if service can accept sequences with gaps
+ */
public boolean isAA()
{
return isAA;
private boolean isAA;
+ private boolean filterSymbols;
+
+
+ private boolean needsAlignedSeqs;
+
+ private int min_valid_seqs;
+
+
public AlignAnalysisUIText(String serviceType, Class<?> client,
String calcId, boolean acceptNucl, boolean acceptProt,
- boolean acceptGaps, String toggle, String toggleTooltip,
+ boolean acceptGaps, boolean alignedSeq,
+ boolean filterNonStandardSymbols, int minSeq, String toggle,
+ String toggleTooltip,
String settings, String settingsTooltip)
{
this.serviceType = serviceType;
isNa = acceptNucl;
isPr = acceptProt;
isAA = acceptGaps;
+ this.needsAlignedSeqs = alignedSeq;
+ this.filterSymbols = filterNonStandardSymbols;
this.client = client;
this.AAconToggle = toggle;
this.AAconToggleTooltip = toggleTooltip;
this.AAeditSettings = settings;
this.AAeditSettingsTooltip = settingsTooltip;
+ this.min_valid_seqs = minSeq;
+ }
+
+ /**
+ *
+ * @return true if non-standard nucleotides and amino acids should be replaced
+ * or omitted
+ *
+ */
+ public boolean isFilterSymbols()
+ {
+ return filterSymbols;
+ }
+
+ /**
+ *
+ * @return true if service needs sequences all the same length (ie padded with
+ * gaps if necessary)
+ */
+ public boolean isNeedsAlignedSeqs()
+ {
+ return needsAlignedSeqs;
}
public Class getClient()
AAeditSettingsTooltip = aAeditSettingsTooltip;
}
+ public int getMinimumSequences()
+ {
+ return min_valid_seqs;
+ }
+
}
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.AADisorderClient;
+import jalview.ws.jws2.AbstractJabaCalcWorker;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
public static List<Jws2Instance> iupreds;
- jalview.ws.jws2.AADisorderClient disorderClient;
+ jalview.ws.jws2.AbstractJabaCalcWorker disorderClient;
public static jalview.gui.AlignFrame af = null;
@Test(groups = { "External", "Network" })
public void testDisorderAnnotExport()
{
- disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
+ disorderClient = new AbstractJabaCalcWorker(iupreds.get(0), af, null,
+ null);
af.getViewport().getCalcManager().startWorker(disorderClient);
do
{
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.project.Jalview2XML;
+import jalview.ws.jws2.AbstractJabaCalcWorker;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.AutoCalcSetting;
public static Jws2Instance rnaalifoldws;
- jalview.ws.jws2.RNAalifoldClient alifoldClient;
+ AbstractJabaCalcWorker alifoldClient;
public static jalview.gui.AlignFrame af = null;
public void testRNAAliFoldValidStructure()
{
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+ alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+ null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
public void testRNAStructExport()
{
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+ alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+ null);
af.getViewport().getCalcManager().startWorker(alifoldClient);
AlignmentI orig_alig = af.getViewport().getAlignment();
// JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
// annotation is mistakenly recognised as an RNA annotation row when read in
- // as an annotation file.
+ // as an annotation file. bug is JAL-3122
verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
opts.add(rg);
}
}
- alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null,
+ alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
JabaParamStore.getJwsArgsfromJaba(opts));
af.getViewport().getCalcManager().startWorker(alifoldClient);
git://source.jalview.org / jalview.git / commitdiff