+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.AlignCalcWorkerI;
+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.GraduatedColor;
+import jalview.schemes.UserColourScheme;
import jalview.ws.jws2.jabaws2.Jws2Instance;
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;
import compbio.metadata.Argument;
-public class AADisorderClient extends JabawsAlignCalcWorker implements
+public class AADisorderClient extends JabawsCalcWorker implements
AlignCalcWorkerI
{
+ private static final String THRESHOLD = "THRESHOLD";
+
+ private static final String RANGE = "RANGE";
+
String typeName;
String methodName;
}
@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<String, Map<String, String[]>>();
+ Map<String, String[]> fmap;
+ featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
+ fmap = new HashMap<String, String[]>());
+ fmap.put("Glob", new String[] { "Globular Domain",
+ "Predicted globular domain" });
+ featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
+ fmap = new HashMap<String, String[]>());
+ featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
+ fmap = new HashMap<String, String[]>());
+ 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<String, String[]>());
+ 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<String, Map<String, Map<String, Object>>>();
+ annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
+ amap = new HashMap<String, Map<String, Object>>());
+ 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<String, Map<String, Object>>());
+ 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<String, Map<String, Object>>());
+ 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<String, Map<String, Object>>());
+ 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.serviceType);
+ Map<String, Map<String, Object>> annotTypeMap = annotMap
+ .get(service.serviceType);
boolean dispFeatures = false;
+ Map<String, Object> fc = new Hashtable<String, Object>();
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+ /**
+ * 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())
{
- SequenceI dseq, seq = seqNames.get(seqId);
- int base = seq.getStart() - 1;
+ 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 = scoremanager.getAnnotationForSequence(seqId);
-
- for (Score scr : scores.scores)
+ ScoreHolder scores = null;
+ try
{
-
- if (scr.getRanges() != null && scr.getRanges().size() > 0)
+ 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)
{
- Iterator<Float> vals = scr.getScores().iterator();
- // make features on sequence
- for (Range rn : scr.getRanges())
+
+ 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())
+ {
+ sf = new SequenceFeature(type[0], type[1],
+ base + rn.from, base + rn.to, val = vals.next()
+ .floatValue(), methodName);
+ }
+ else
+ {
+ sf = new SequenceFeature(type[0], type[1], null, 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.serviceType + " ("
+ + scr.getMethod() + ")",
+ calcName = service.getServiceTypeURI() + "/"
+ + scr.getMethod(), aseq, base + 1, scr);
+ annot.graph = AlignmentAnnotation.LINE_GRAPH;
+
+ Map<String, Object> styleMap = (annotTypeMap == null) ? null
+ : annotTypeMap.get(scr.getMethod());
- SequenceFeature sf;
- if (vals.hasNext())
+ 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)
{
- sf = new SequenceFeature(typeName + "(" + scr.getMethod()
- + ")", "Disordered Region", base + rn.from, base
- + rn.to, vals.next().floatValue(), methodName);
+ annot.graphMin = range[0];
+ annot.graphMax = range[1];
}
- else
+ if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
{
- sf = new SequenceFeature(typeName + "(" + scr.getMethod()
- + ")", "Disordered Region", null, base + rn.from,
- base + rn.to, methodName);
+ {
+ if (!sameGroup)
+ {
+ graphGroup++;
+ sameGroup = true;
+ }
+
+ annot.graphGroup = graphGroup;
+ }
}
- dseq.addSequenceFeature(sf);
- dispFeatures = true;
- }
- }
- else
- {
- Iterator<Float> vals = scr.getScores().iterator();
- for (int start = base + 1; vals.hasNext(); start++)
- {
- SequenceFeature sf = new SequenceFeature(typeName + "("
- + scr.getMethod() + ")", "Disordered Region", start,
- start, vals.next().floatValue(), methodName);
- dseq.addSequenceFeature(sf);
- dispFeatures = true;
+
+ 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 = new UserColourScheme(typeName)
+ .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)
{
- // TODO: configure feature display settings for added types if they don't already exist
-
- af.alignPanel.av.setShowSequenceFeatures(true);
+ jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+ .cloneFeatureRenderer();
+ for (String ft : fc.keySet())
+ {
+ Object gc = fr.getFeatureStyle(ft);
+ if (gc instanceof Color)
+ {
+ // set graduated color as fading to white for minimum, and
+ // autoscaling to values on alignment
+ GraduatedColor ggc = new GraduatedColor(Color.white,
+ (Color) gc, 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);
+ }
ap.paintAlignment(true);
}
+ if (ourAnnot.size() > 0)
+ {
+ // Modify the visible annotation on the alignment viewport with the
+ // new alignment annotation rows created.
+ updateOurAnnots(ourAnnot);
+ ap.adjustAnnotationHeight();
+ }
}
- /*
- * else { ap.paintAlignment(true); }
- */
}
}
+ @Override
+ public String getCalcId()
+ {
+ // Disorder predictions are not dynamically updated so we return null
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff