/*
* 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.jabaws2;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
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 annotationFromScoreManager(AlignmentI seqs,
Map featureColours,
Map featureFilters)
{
Map featureTypeMap = featureMap.get(our.getName());
Map> annotTypeMap = annotMap
.get(our.getName());
boolean dispFeatures = false;
Map fc = new Hashtable<>(),
fex = new Hashtable();
List ourAnnot = new ArrayList<>();
int graphGroup = 1, lastAnnot = 0;
for (SequenceI seq : seqs.getSequences())
{
String seqId = seq.getName();
boolean sameGroup = false;
SequenceI dseq, aseq;
int base = seq.findPosition(0) - 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.",
q);
}
float last = Float.NaN, val = Float.NaN;
if (scores != null && scores.scores != null)
{
for (Score scr : scores.scores)
{
if (scr.getRanges() != null && scr.getRanges().size() > 0)
{
Iterator vals = scr.getScores().iterator();
// make features on sequence
for (Range rn : scr.getRanges())
{
// TODO: Create virtual feature settings
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);
// mark feature as requiring a graduated colourscheme if has
// variable scores
if (!Float.isNaN(last) && !Float.isNaN(val) && last != val)
{
fc.put(sf.getType(), sf);
} else
{
fex.put(sf.getType(), sf);
}
last = val;
dispFeatures = true;
}
}
else
{
if (scr.getScores().size() == 0)
{
continue;
}
String typename, calcName;
AlignmentAnnotation annot = createAnnotationRowsForScores(
seqs, null, ourAnnot,
typename = our.getName() + " (" + scr.getMethod() + ")",
calcName = our.getNameURI() + "/" + 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)
{
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 = "" + 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 += "
" + threshNote;
}
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
AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(annot,
typename, calcName);
}
}
}
if (lastAnnot + 1 == ourAnnot.size())
{
// remove singleton alignment annotation row
ourAnnot.get(lastAnnot).graphGroup = -1;
}
}
{
if (dispFeatures)
{
// TODO: virtual feature settings
// feature colours need to merged with current viewport's colours
// simple feature colours promoted to colour-by-score ranges using
// currently assigned or created feature colour
for (String ft : fex.keySet())
{
Color col = ColorUtils.createColourFromName(ft);
// set graduated color as fading to white for minimum, and
// autoscaling to values on alignment
FeatureColourI ggc;
if (fc.get(ft) != null)
{
ggc = new FeatureColour(col, Color.white, col,
Color.white, Float.MIN_VALUE, Float.MAX_VALUE);
ggc.setAutoScaled(true);
}
else
{
ggc = new FeatureColour(col);
}
featureColours.put(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> 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 });
}
}