+++ /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;
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff