X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=9a2316c47b8d479e78dee9a43e2c9de1a79c8162;hb=36067eda8f713ab855b839fd4cc9af5cf36854a4;hp=c5c7a1378b57f1de3c380bd51b35cdc70a5bec67;hpb=04f45d8c1e6e2c9e6f0ce9887402262102a56191;p=jalview.git
diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index c5c7a13..9a2316c 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,29 +1,58 @@
+/*
+ * 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 .
+ * 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.FeatureColour;
+import jalview.util.ColorUtils;
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
- AlignCalcWorkerI
+public class AADisorderClient extends JabawsCalcWorker
{
+ private static final String THRESHOLD = "THRESHOLD";
+
+ private static final String RANGE = "RANGE";
+
String typeName;
String methodName;
@@ -33,9 +62,9 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
AlignFrame af;
public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
- WsParamSetI preset, List paramset)
+ WsParamSetI thePreset, List paramset)
{
- super(sh, alignFrame, preset, paramset);
+ super(sh, alignFrame, thePreset, paramset);
af = alignFrame;
typeName = sh.action;
methodName = sh.serviceType;
@@ -54,98 +83,299 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
}
@Override
+ boolean checkValidInputSeqs(boolean dynamic, List seqs)
+ {
+ return (seqs.size() > 0);
+ }
+
+ private static Map> featureMap;
+
+ private static Map>> 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 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> amap;
+ annotMap = new HashMap<>();
+ annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
+ amap = new HashMap<>());
+ amap.put("Dydx", new HashMap());
+ 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());
+ amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
+ amap.put("RawScore", new HashMap());
+ amap.get("RawScore").put(INVISIBLE, INVISIBLE);
+ annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
+ amap = new HashMap<>());
+ amap.put("COILS", new HashMap());
+ amap.put("HOTLOOPS", new HashMap());
+ amap.put("REM465", new HashMap());
+ 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());
+ amap.put("Short", new HashMap());
+ 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());
+ 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 featureTypeMap = featureMap
+ .get(service.serviceType);
+ Map> annotTypeMap = annotMap
+ .get(service.serviceType);
boolean dispFeatures = false;
- Map fc=new Hashtable();
+ Map fc = new Hashtable<>();
+ List 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())
{
- 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);
- float last=Float.NaN,val=Float.NaN;
- 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 vals = scr.getScores().iterator();
- // make features on sequence
- for (Range rn : scr.getRanges())
+
+ if (scr.getRanges() != null && scr.getRanges().size() > 0)
{
+ Iterator vals = scr.getScores().iterator();
+ // make features on sequence
+ for (Range rn : scr.getRanges())
+ {
- SequenceFeature sf;
- if (vals.hasNext())
+ 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)
{
- sf = new SequenceFeature(typeName + "(" + scr.getMethod()
- + ")", "Disordered Region", base + rn.from, base
- + rn.to, val=vals.next().floatValue(), methodName);
+ continue;
}
- else
+ 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 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)
{
- sf = new SequenceFeature(typeName + "(" + scr.getMethod()
- + ")", "Disordered Region", null, base + rn.from,
- base + rn.to, methodName);
+ annot.graphMin = range[0];
+ annot.graphMax = range[1];
}
- dseq.addSequenceFeature(sf);
- if (last!=val && last!=Float.NaN)
+ if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
{
- fc.put(sf.getType(),sf);
+ {
+ if (!sameGroup)
+ {
+ graphGroup++;
+ sameGroup = true;
+ }
+
+ annot.graphGroup = graphGroup;
+ }
}
- last=val;
- dispFeatures = true;
- }
- }
- else
- {
- Iterator vals = scr.getScores().iterator();
- for (int start = base + 1; vals.hasNext(); start++)
- {
- SequenceFeature sf = new SequenceFeature(typeName + "("
- + scr.getMethod() + ")", "Disordered Region", start,
- start, val=vals.next().floatValue(), methodName);
- if (last!=val && last!=Float.NaN)
+
+ annot.description = "" + service.getActionText()
+ + " - raw scores";
+ if (thrsh != null)
{
- fc.put(sf.getType(),sf);
+ String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
+ + thrsh[1] + " indicates disorder";
+ annot.threshold = new GraphLine((float) thrsh[1],
+ threshNote, Color.red);
+ annot.description += "
" + threshNote;
}
- last=val;
- dseq.addSequenceFeature(sf);
- dispFeatures = true;
+ annot.description += "";
+ 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.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer();
- // TODO: configure feature display settings for added types if they don't already exist
- for (String ft:fc.keySet())
+ jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+ .cloneFeatureRenderer();
+ for (String ft : fc.keySet())
{
- Cache.log.debug("Set graduated feature for new type:"+ft);
- 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);
+ // set graduated color as fading to white for minimum, and
+ // autoscaling to values on alignment
+ FeatureColourI ggc = new FeatureColour(Color.white,
+ gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
ggc.setAutoScaled(true);
fr.setColour(ft, ggc);
}
}
- af.alignPanel.updateFeatureRendererFrom(fr);
- af.alignPanel.av.setShowSequenceFeatures(true);
- ap.paintAlignment(true);
+ // 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;
+ }
+
}