/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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.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.GraduatedColor;
-import jalview.schemes.UserColourScheme;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
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
- AlignCalcWorkerI
+public class AADisorderClient extends JabawsCalcWorker
{
private static final String THRESHOLD = "THRESHOLD";
+ private static final String RANGE = "RANGE";
+
String typeName;
String methodName;
AlignFrame af;
public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ WsParamSetI thePreset, List<Argument> paramset)
{
- super(sh, alignFrame, preset, paramset);
+ super(sh, alignFrame, thePreset, paramset);
af = alignFrame;
typeName = sh.action;
methodName = sh.serviceType;
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;
{
// TODO: turn this into some kind of configuration file that's a bit easier
// to edit
- featureMap = new HashMap<String, Map<String, String[]>>();
+ featureMap = new HashMap<>();
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" });
+ fmap = new HashMap<>());
+ fmap.put("Glob",
+ new String[]
+ { "Globular Domain", "Predicted globular domain" });
featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
- fmap = new HashMap<String, String[]>());
+ fmap = new HashMap<>());
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" });
+ 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<String, String[]>());
- fmap.put("GlobDoms", new String[]
- { "Globular Domain", "Predicted globular domain" });
- fmap.put("Disorder", new String[]
- { "Protein Disorder", "Probable unstructured peptide region" });
+ 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<String, Map<String, Map<String, Object>>>();
+ annotMap = new HashMap<>();
annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
- amap = new HashMap<String, Map<String, Object>>());
+ 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(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 = 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("HOTLOOPS").put(THRESHOLD, new double[]
- { 1, 0.6 });
- amap.get("REM465").put(THRESHOLD, new double[]
- { 1, 0.1204 });
+ 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 = 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("Short").put(THRESHOLD, new double[]
- { 1, 0.5 });
+ 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 = new HashMap<>());
amap.put("JRonn", new HashMap<String, Object>());
- amap.get("JRonn").put(THRESHOLD, new double[]
- { 1, 0.5 });
+ amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
}
@Override
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>();
+ Map<String, Object> fc = new Hashtable<>();
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
/**
* grouping for any annotation rows created
*/
{
boolean sameGroup = false;
SequenceI dseq, aseq, seq = seqNames.get(seqId);
- int base = seq.getStart() - 1;
+ int base = seq.findPosition(start) - 1;
aseq = seq;
while ((dseq = seq).getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
}
- ;
- ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
+ ScoreHolder scores = null;
+ try
+ {
+ scores = scoremanager.getAnnotationForSequence(seqId);
+ } catch (Exception q)
+ {
+ Cache.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();
- for (Score scr : scores.scores)
+ if (scores != null && scores.scores != null)
{
-
- if (scr.getRanges() != null && scr.getRanges().size() > 0)
+ for (Score scr : scores.scores)
{
- 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())
+ if (scr.getRanges() != null && scr.getRanges().size() > 0)
+ {
+ Iterator<Float> vals = scr.getScores().iterator();
+ // make features on sequence
+ for (Range rn : scr.getRanges())
{
- sf = new SequenceFeature(type[0], type[1], base + rn.from,
- base + rn.to, val = vals.next().floatValue(),
- methodName);
+
+ 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
+ }
+ else
+ {
+ if (scr.getScores().size() == 0)
{
- sf = new SequenceFeature(type[0], type[1], null, base
- + rn.from, base + rn.to, methodName);
+ continue;
}
- dseq.addSequenceFeature(sf);
- if (last != val && last != Float.NaN)
+ 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());
+
+ 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)
{
- fc.put(sf.getType(), sf);
+ annot.graphMin = range[0];
+ annot.graphMax = range[1];
}
- last = val;
- dispFeatures = true;
- }
- }
- else
- {
- if (scr.getScores().size() == 0)
- {
- continue;
- }
- AlignmentAnnotation annot = createAnnotationRowsForScores(
- ourAnnot, service.serviceType + " (" + scr.getMethod()
- + ")",
- service.getServiceTypeURI() + "/" + scr.getMethod(),
- aseq, base + 1, scr);
- annot.graph = AlignmentAnnotation.LINE_GRAPH;
- annot.visible = (annotTypeMap == null
- || annotTypeMap.get(scr.getMethod()) == null || annotTypeMap
- .get(scr.getMethod()).get(INVISIBLE) == null);
- double[] thrsh = (annotTypeMap == null || annotTypeMap.get(scr
- .getMethod()) == null) ? null : (double[]) annotTypeMap
- .get(scr.getMethod()).get(THRESHOLD);
- if (annotTypeMap == null
- || annotTypeMap.get(scr.getMethod()) == null
- || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
- {
+ if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
{
- if (!sameGroup)
{
- graphGroup++;
- sameGroup = true;
- }
+ if (!sameGroup)
+ {
+ graphGroup++;
+ sameGroup = true;
+ }
- annot.graphGroup = graphGroup;
+ 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 = new UserColourScheme(typeName)
- .createColourFromName(typeName + scr.getMethod());
- for (int p = 0, ps = annot.annotations.length; p < ps; p++)
- {
- if (annot.annotations[p] != null)
+ 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++)
{
- annot.annotations[p].colour = col;
+ if (annot.annotations[p] != null)
+ {
+ annot.annotations[p].colour = col;
+ }
}
+ annot._linecolour = col;
+ // finally, update any dataset annotation
+ replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+ aseq);
}
- annot._linecolour = col;
}
}
if (lastAnnot + 1 == ourAnnot.size())
{
if (dispFeatures)
{
- jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+ jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
.cloneFeatureRenderer();
for (String ft : fc.keySet())
{
- Object gc = fr.getFeatureStyle(ft);
- if (gc instanceof Color)
+ FeatureColourI gc = fr.getFeatureStyle(ft);
+ if (gc.isSimpleColour())
{
// 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);
+ 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);
}
// only do this if the alignFrame is currently showing this view.
af.setShowSeqFeatures(true);
}
- ap.paintAlignment(true);
}
if (ourAnnot.size() > 0)
{
// 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