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package jalview.ws.jws2; |
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import jalview.api.FeatureColourI; |
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import jalview.bin.Cache; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.GraphLine; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.schemes.FeatureColour; |
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import jalview.util.ColorUtils; |
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import jalview.ws.jws2.jabaws2.Jws2Instance; |
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import jalview.ws.params.WsParamSetI; |
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import java.awt.Color; |
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import java.util.ArrayList; |
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import java.util.HashMap; |
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import java.util.Hashtable; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Map; |
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import compbio.data.sequence.FastaSequence; |
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import compbio.data.sequence.Range; |
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import compbio.data.sequence.Score; |
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import compbio.data.sequence.ScoreManager.ScoreHolder; |
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import compbio.metadata.Argument; |
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| 0% |
Uncovered Elements: 200 (200) |
Complexity: 38 |
Complexity Density: 0.26 |
|
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public class AADisorderClient extends JabawsCalcWorker |
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{ |
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private static final String THRESHOLD = "THRESHOLD"; |
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private static final String RANGE = "RANGE"; |
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String typeName; |
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String methodName; |
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String groupName; |
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AlignFrame af; |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
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public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,... |
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WsParamSetI thePreset, List<Argument> paramset) |
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{ |
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super(sh, alignFrame, thePreset, paramset); |
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af = alignFrame; |
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typeName = sh.action; |
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methodName = sh.serviceType; |
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|
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submitGaps = false; |
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alignedSeqs = false; |
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nucleotidesAllowed = false; |
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proteinAllowed = true; |
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bySequence = true; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public String getServiceActionText() |
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{ |
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return "Submitting amino acid sequences for disorder prediction."; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs) |
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{ |
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return (seqs.size() > 0); |
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} |
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private static Map<String, Map<String, String[]>> featureMap; |
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private static Map<String, Map<String, Map<String, Object>>> annotMap; |
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private static String DONTCOMBINE = "DONTCOMBINE"; |
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private static String INVISIBLE = "INVISIBLE"; |
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| 0% |
Uncovered Elements: 44 (44) |
Complexity: 1 |
Complexity Density: 0.02 |
|
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static... |
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{ |
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featureMap = new HashMap<>(); |
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Map<String, String[]> fmap; |
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featureMap.put(compbio.ws.client.Services.IUPredWS.toString(), |
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fmap = new HashMap<>()); |
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fmap.put("Glob", |
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new String[] |
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{ "Globular Domain", "Predicted globular domain" }); |
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featureMap.put(compbio.ws.client.Services.JronnWS.toString(), |
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fmap = new HashMap<>()); |
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featureMap.put(compbio.ws.client.Services.DisemblWS.toString(), |
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fmap = new HashMap<>()); |
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fmap.put("REM465", new String[] { "REM465", "Missing density" }); |
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fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" }); |
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fmap.put("COILS", new String[] { "COILS", "Random coil" }); |
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featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(), |
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fmap = new HashMap<>()); |
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fmap.put("GlobDoms", |
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new String[] |
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{ "Globular Domain", "Predicted globular domain" }); |
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fmap.put("Disorder", |
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new String[] |
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{ "Protein Disorder", "Probable unstructured peptide region" }); |
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Map<String, Map<String, Object>> amap; |
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annotMap = new HashMap<>(); |
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annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(), |
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amap = new HashMap<>()); |
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amap.put("Dydx", new HashMap<String, Object>()); |
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amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE); |
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amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 }); |
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amap.get("Dydx").put(RANGE, new float[] { -1, +1 }); |
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amap.put("SmoothedScore", new HashMap<String, Object>()); |
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amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE); |
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amap.put("RawScore", new HashMap<String, Object>()); |
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amap.get("RawScore").put(INVISIBLE, INVISIBLE); |
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annotMap.put(compbio.ws.client.Services.DisemblWS.toString(), |
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amap = new HashMap<>()); |
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amap.put("COILS", new HashMap<String, Object>()); |
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amap.put("HOTLOOPS", new HashMap<String, Object>()); |
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amap.put("REM465", new HashMap<String, Object>()); |
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amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 }); |
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amap.get("COILS").put(RANGE, new float[] { 0, 1 }); |
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amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 }); |
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amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 }); |
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amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 }); |
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amap.get("REM465").put(RANGE, new float[] { 0, 1 }); |
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annotMap.put(compbio.ws.client.Services.IUPredWS.toString(), |
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amap = new HashMap<>()); |
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amap.put("Long", new HashMap<String, Object>()); |
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amap.put("Short", new HashMap<String, Object>()); |
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amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 }); |
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amap.get("Long").put(RANGE, new float[] { 0, 1 }); |
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amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 }); |
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amap.get("Short").put(RANGE, new float[] { 0, 1 }); |
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annotMap.put(compbio.ws.client.Services.JronnWS.toString(), |
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amap = new HashMap<>()); |
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amap.put("JRonn", new HashMap<String, Object>()); |
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amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 }); |
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amap.get("JRonn").put(RANGE, new float[] { 0, 1 }); |
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} |
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| 0% |
Uncovered Elements: 138 (138) |
Complexity: 33 |
Complexity Density: 0.38 |
|
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@Override... |
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public void updateResultAnnotation(boolean immediate) |
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{ |
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if (immediate || !calcMan.isWorking(this) && scoremanager != null) |
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{ |
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Map<String, String[]> featureTypeMap = featureMap |
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.get(service.serviceType); |
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Map<String, Map<String, Object>> annotTypeMap = annotMap |
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.get(service.serviceType); |
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boolean dispFeatures = false; |
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Map<String, Object> fc = new Hashtable<>(); |
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List<AlignmentAnnotation> ourAnnot = new ArrayList<>(); |
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int graphGroup = 1; |
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if (alignViewport.getAlignment().getAlignmentAnnotation() != null) |
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{ |
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for (AlignmentAnnotation ala : alignViewport.getAlignment() |
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.getAlignmentAnnotation()) |
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{ |
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if (ala.graphGroup > graphGroup) |
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{ |
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graphGroup = ala.graphGroup; |
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} |
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} |
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} |
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for (String seqId : seqNames.keySet()) |
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{ |
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boolean sameGroup = false; |
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SequenceI dseq, aseq, seq = seqNames.get(seqId); |
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int base = seq.findPosition(start) - 1; |
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aseq = seq; |
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while ((dseq = seq).getDatasetSequence() != null) |
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{ |
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seq = seq.getDatasetSequence(); |
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} |
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ScoreHolder scores = null; |
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try |
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{ |
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scores = scoremanager.getAnnotationForSequence(seqId); |
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} catch (Exception q) |
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{ |
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Cache.log |
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.info("Couldn't recover disorder prediction for sequence " |
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+ seq.getName() + "(Prediction name was " + seqId |
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+ ")" |
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+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail."); |
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} |
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float last = Float.NaN, val = Float.NaN; |
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int lastAnnot = ourAnnot.size(); |
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if (scores != null && scores.scores != null) |
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{ |
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for (Score scr : scores.scores) |
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{ |
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if (scr.getRanges() != null && scr.getRanges().size() > 0) |
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{ |
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Iterator<Float> vals = scr.getScores().iterator(); |
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for (Range rn : scr.getRanges()) |
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{ |
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SequenceFeature sf; |
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String[] type = featureTypeMap.get(scr.getMethod()); |
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0 |
if (type == null) |
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{ |
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type = new String[] { |
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typeName + " (" + scr.getMethod() + ")", |
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service.getActionText() }; |
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} |
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if (vals.hasNext()) |
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{ |
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val = vals.next().floatValue(); |
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sf = new SequenceFeature(type[0], type[1], |
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base + rn.from, base + rn.to, val, methodName); |
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} |
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else |
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{ |
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sf = new SequenceFeature(type[0], type[1], |
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base + rn.from, base + rn.to, methodName); |
249 |
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} |
250 |
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dseq.addSequenceFeature(sf); |
251 |
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if (last != val && !Float.isNaN(last)) |
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{ |
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fc.put(sf.getType(), sf); |
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} |
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last = val; |
256 |
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dispFeatures = true; |
257 |
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} |
258 |
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} |
259 |
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else |
260 |
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{ |
261 |
0 |
if (scr.getScores().size() == 0) |
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{ |
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continue; |
264 |
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} |
265 |
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String typename, calcName; |
266 |
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AlignmentAnnotation annot = createAnnotationRowsForScores( |
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ourAnnot, |
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typename = service.serviceType + " (" |
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+ scr.getMethod() + ")", |
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calcName = service.getServiceTypeURI() + "/" |
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+ scr.getMethod(), |
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aseq, base + 1, scr); |
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annot.graph = AlignmentAnnotation.LINE_GRAPH; |
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Map<String, Object> styleMap = (annotTypeMap == null) ? null |
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: annotTypeMap.get(scr.getMethod()); |
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annot.visible = (styleMap == null |
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|| styleMap.get(INVISIBLE) == null); |
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double[] thrsh = (styleMap == null) ? null |
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: (double[]) styleMap.get(THRESHOLD); |
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float[] range = (styleMap == null) ? null |
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: (float[]) styleMap.get(RANGE); |
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if (range != null) |
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{ |
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annot.graphMin = range[0]; |
287 |
0 |
annot.graphMax = range[1]; |
288 |
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} |
289 |
0 |
if (styleMap == null || styleMap.get(DONTCOMBINE) == null) |
290 |
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{ |
291 |
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{ |
292 |
0 |
if (!sameGroup) |
293 |
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{ |
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0 |
graphGroup++; |
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0 |
sameGroup = true; |
296 |
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} |
297 |
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0 |
annot.graphGroup = graphGroup; |
299 |
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} |
300 |
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} |
301 |
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annot.description = "<html>" + service.getActionText() |
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+ " - raw scores"; |
304 |
0 |
if (thrsh != null) |
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{ |
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String threshNote = (thrsh[0] > 0 ? "Above " : "Below ") |
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+ thrsh[1] + " indicates disorder"; |
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annot.threshold = new GraphLine((float) thrsh[1], |
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threshNote, Color.red); |
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annot.description += "<br/>" + threshNote; |
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} |
312 |
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annot.description += "</html>"; |
313 |
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Color col = ColorUtils |
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.createColourFromName(typeName + scr.getMethod()); |
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for (int p = 0, ps = annot.annotations.length; p < ps; p++) |
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{ |
317 |
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if (annot.annotations[p] != null) |
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{ |
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annot.annotations[p].colour = col; |
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} |
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} |
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annot._linecolour = col; |
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replaceAnnotationOnAlignmentWith(annot, typename, calcName, |
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aseq); |
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} |
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} |
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} |
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if (lastAnnot + 1 == ourAnnot.size()) |
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{ |
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ourAnnot.get(lastAnnot).graphGroup = -1; |
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} |
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} |
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{ |
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if (dispFeatures) |
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{ |
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jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap) |
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.cloneFeatureRenderer(); |
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for (String ft : fc.keySet()) |
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{ |
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FeatureColourI gc = fr.getFeatureStyle(ft); |
343 |
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if (gc.isSimpleColour()) |
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{ |
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|
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FeatureColourI ggc = new FeatureColour(gc.getColour(), |
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Color.white, gc.getColour(), Color.white, |
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Float.MIN_VALUE, Float.MAX_VALUE); |
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0 |
ggc.setAutoScaled(true); |
351 |
0 |
fr.setColour(ft, ggc); |
352 |
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} |
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} |
354 |
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|
355 |
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|
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0 |
((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr); |
357 |
0 |
if (af.alignPanel == ap) |
358 |
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{ |
359 |
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|
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0 |
af.setShowSeqFeatures(true); |
361 |
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} |
362 |
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} |
363 |
0 |
if (ourAnnot.size() > 0) |
364 |
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{ |
365 |
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|
366 |
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|
367 |
0 |
updateOurAnnots(ourAnnot); |
368 |
0 |
ap.adjustAnnotationHeight(); |
369 |
0 |
ap.paintAlignment(true, true); |
370 |
|
} |
371 |
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} |
372 |
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} |
373 |
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} |
374 |
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|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
375 |
0 |
@Override... |
376 |
|
public String getCalcId() |
377 |
|
{ |
378 |
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|
379 |
0 |
return null; |
380 |
|
} |
381 |
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|
382 |
|
} |