/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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;
{
private static final String THRESHOLD = "THRESHOLD";
+
private static final String RANGE = "RANGE";
String typeName;
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;
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.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" });
+ 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.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.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("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 });
+ 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 });
+ 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 });
+ amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
}
@Override
{
boolean sameGroup = false;
SequenceI dseq, aseq, seq = seqNames.get(seqId);
- int base = seq.findPosition(start)-1;
+ int base = seq.findPosition(start) - 1;
aseq = seq;
while ((dseq = seq).getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
}
ScoreHolder scores = null;
- try {
+ try
+ {
scores = scoremanager.getAnnotationForSequence(seqId);
} catch (Exception q)
{
.info("Couldn't recover disorder prediction for sequence "
+ seq.getName()
+ "(Prediction name was "
- + seqId+")"
+ + 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) {
+ if (scores != null && scores.scores != null)
+ {
for (Score scr : scores.scores)
{
if (type == null)
{
// create a default type for this feature
- type = new String[]
- { typeName + " (" + scr.getMethod() + ")",
+ type = new String[] {
+ typeName + " (" + scr.getMethod() + ")",
service.getActionText() };
}
if (vals.hasNext())
+ rn.from, base + rn.to, methodName);
}
dseq.addSequenceFeature(sf);
- if (last != val && last != Float.NaN)
+ if (last != val && !Float.isNaN(last))
{
fc.put(sf.getType(), sf);
}
{
continue;
}
+ String typename, calcName;
AlignmentAnnotation annot = createAnnotationRowsForScores(
ourAnnot,
- service.serviceType + " (" + scr.getMethod() + ")",
- service.getServiceTypeURI() + "/" + scr.getMethod(),
- aseq, base + 1, scr);
+ 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());
-
+
+ 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)
+ 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 (styleMap == null || styleMap.get(DONTCOMBINE) == null)
{
{
if (!sameGroup)
}
}
annot._linecolour = col;
+ // finally, update any dataset annotation
+ replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+ aseq);
}
}
}
{
if (dispFeatures)
{
- jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+ jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
.cloneFeatureRenderer();
for (String ft : fc.keySet())
{
}
}
+ @Override
+ public String getCalcId()
+ {
+ // Disorder predictions are not dynamically updated so we return null
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff