--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
+ Map<String, FeatureColourI> featureColours,
+ Map<String, FeatureMatcherSetI> featureFilters)
+ {
+
+ Map<String, String[]> featureTypeMap = featureMap.get(our.getName());
+ Map<String, Map<String, Object>> annotTypeMap = annotMap
+ .get(our.getName());
+ boolean dispFeatures = false;
+ Map<String, SequenceFeature> fc = new Hashtable<>(),
+ fex = new Hashtable();
+ List<AlignmentAnnotation> 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<Float> 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<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)
+ {
+ 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 = "<html>" + 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 += "<br/>" + threshNote;
+ }
+ annot.description += "</html>";
+ 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<String, Map<String, String[]>> featureMap;
+
+ private static Map<String, Map<String, Map<String, Object>>> 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<String, String[]> 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<String, Map<String, Object>> amap;
+ annotMap = new HashMap<>();
+ annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
+ 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(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<>());
+ 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 });
+
+ annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
+ 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("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<String, Object>());
+ amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff