src/jalview/ws/jws2/AADisorderClient.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.ws.jws2;
  19
  20 import jalview.api.AlignCalcWorkerI;
  21 import jalview.bin.Cache;
  22 import jalview.datamodel.AlignmentAnnotation;
  23
  24 import jalview.datamodel.GraphLine;
  25 import jalview.datamodel.SequenceFeature;
  26 import jalview.datamodel.SequenceI;
  27 import jalview.gui.AlignFrame;
  28 import jalview.schemes.GraduatedColor;
  29 import jalview.schemes.UserColourScheme;
  30 import jalview.ws.jws2.jabaws2.Jws2Instance;
  31 import jalview.ws.params.WsParamSetI;
  32
  33 import java.awt.Color;
  34 import java.util.ArrayList;
  35 import java.util.HashMap;
  36 import java.util.Hashtable;
  37 import java.util.Iterator;
  38 import java.util.List;
  39 import java.util.Map;
  40 import compbio.data.sequence.Range;
  41 import compbio.data.sequence.Score;
  42 import compbio.data.sequence.ScoreManager.ScoreHolder;
  43 import compbio.metadata.Argument;
  44 import compbio.ws.client.Services;
  45
  46 public class AADisorderClient extends JabawsAlignCalcWorker implements
  47         AlignCalcWorkerI
  48 {
  49
  50   private static final String THRESHOLD = "THRESHOLD";
  51
  52   String typeName;
  53
  54   String methodName;
  55
  56   String groupName;
  57
  58   AlignFrame af;
  59
  60   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  61           WsParamSetI preset, List<Argument> paramset)
  62   {
  63     super(sh, alignFrame, preset, paramset);
  64     af = alignFrame;
  65     typeName = sh.action;
  66     methodName = sh.serviceType;
  67
  68     submitGaps = false;
  69     alignedSeqs = false;
  70     nucleotidesAllowed = false;
  71     proteinAllowed = true;
  72     bySequence = true;
  73   }
  74
  75   @Override
  76   public String getServiceActionText()
  77   {
  78     return "Submitting amino acid sequences for disorder prediction.";
  79   }
  80
  81   private static Map<String, Map<String, String[]>> featureMap;
  82
  83   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  84
  85   private static String DONTCOMBINE = "DONTCOMBINE";
  86
  87   private static String INVISIBLE = "INVISIBLE";
  88   static
  89   {
  90     // TODO: turn this into some kind of configuration file that's a bit easier
  91     // to edit
  92     featureMap = new HashMap<String, Map<String, String[]>>();
  93     Map<String, String[]> fmap;
  94     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  95             fmap = new HashMap<String, String[]>());
  96     fmap.put("Glob", new String[]
  97     { "Globular Domain", "Predicted globular domain" });
  98     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
  99             fmap = new HashMap<String, String[]>());
 100     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 101             fmap = new HashMap<String, String[]>());
 102     fmap.put("REM465", new String[]
 103     { "REM465", "Missing density" });
 104     fmap.put("HOTLOOPS", new String[]
 105     { "HOTLOOPS", "Flexible loops" });
 106     fmap.put("COILS", new String[]
 107     { "COILS", "Random coil" });
 108     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 109             fmap = new HashMap<String, String[]>());
 110     fmap.put("GlobDoms", new String[]
 111     { "Globular Domain", "Predicted globular domain" });
 112     fmap.put("Disorder", new String[]
 113     { "Protein Disorder", "Probable unstructured peptide region" });
 114     Map<String, Map<String, Object>> amap;
 115     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 116     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 117             amap = new HashMap<String, Map<String, Object>>());
 118     amap.put("Dydx", new HashMap<String, Object>());
 119     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 120     amap.get("Dydx").put(THRESHOLD, new double[]
 121     { 1, 0 });
 122     amap.put("SmoothedScore", new HashMap<String, Object>());
 123     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 124     amap.put("RawScore", new HashMap<String, Object>());
 125     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 126     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 127             amap = new HashMap<String, Map<String, Object>>());
 128     amap.put("COILS", new HashMap<String, Object>());
 129     amap.put("HOTLOOPS", new HashMap<String, Object>());
 130     amap.put("REM465", new HashMap<String, Object>());
 131     amap.get("COILS").put(THRESHOLD, new double[]
 132     { 1, 0.516 });
 133     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 134     { 1, 0.6 });
 135     amap.get("REM465").put(THRESHOLD, new double[]
 136     { 1, 0.1204 });
 137
 138     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 139             amap = new HashMap<String, Map<String, Object>>());
 140     amap.put("Long", new HashMap<String, Object>());
 141     amap.put("Short", new HashMap<String, Object>());
 142     amap.get("Long").put(THRESHOLD, new double[]
 143     { 1, 0.5 });
 144     amap.get("Short").put(THRESHOLD, new double[]
 145     { 1, 0.5 });
 146     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 147             amap = new HashMap<String, Map<String, Object>>());
 148     amap.put("JRonn", new HashMap<String, Object>());
 149     amap.get("JRonn").put(THRESHOLD, new double[]
 150     { 1, 0.5 });
 151   }
 152
 153   @Override
 154   public void updateResultAnnotation(boolean immediate)
 155   {
 156
 157     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 158     {
 159       Map<String, String[]> featureTypeMap = featureMap
 160               .get(service.serviceType);
 161       Map<String, Map<String, Object>> annotTypeMap = annotMap
 162               .get(service.serviceType);
 163       boolean dispFeatures = false;
 164       Map<String, Object> fc = new Hashtable<String, Object>();
 165       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 166       /**
 167        * grouping for any annotation rows created
 168        */
 169       int graphGroup = 1;
 170       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 171       {
 172         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 173                 .getAlignmentAnnotation())
 174         {
 175           if (ala.graphGroup > graphGroup)
 176           {
 177             graphGroup = ala.graphGroup;
 178           }
 179         }
 180       }
 181
 182       for (String seqId : seqNames.keySet())
 183       {
 184         boolean sameGroup = false;
 185         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 186         int base = seq.getStart() - 1;
 187         aseq = seq;
 188         while ((dseq = seq).getDatasetSequence() != null)
 189         {
 190           seq = seq.getDatasetSequence();
 191         }
 192         ;
 193         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
 194         float last = Float.NaN, val = Float.NaN;
 195         int lastAnnot = ourAnnot.size();
 196         for (Score scr : scores.scores)
 197         {
 198
 199           if (scr.getRanges() != null && scr.getRanges().size() > 0)
 200           {
 201             Iterator<Float> vals = scr.getScores().iterator();
 202             // make features on sequence
 203             for (Range rn : scr.getRanges())
 204             {
 205
 206               SequenceFeature sf;
 207               String[] type = featureTypeMap.get(scr.getMethod());
 208               if (type == null)
 209               {
 210                 // create a default type for this feature
 211                 type = new String[]
 212                 { typeName + " (" + scr.getMethod() + ")",
 213                     service.getActionText() };
 214               }
 215               if (vals.hasNext())
 216               {
 217                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 218                         base + rn.to, val = vals.next().floatValue(),
 219                         methodName);
 220               }
 221               else
 222               {
 223                 sf = new SequenceFeature(type[0], type[1], null, base
 224                         + rn.from, base + rn.to, methodName);
 225               }
 226               dseq.addSequenceFeature(sf);
 227               if (last != val && last != Float.NaN)
 228               {
 229                 fc.put(sf.getType(), sf);
 230               }
 231               last = val;
 232               dispFeatures = true;
 233             }
 234           }
 235           else
 236           {
 237             if (scr.getScores().size() == 0)
 238             {
 239               continue;
 240             }
 241             AlignmentAnnotation annot = createAnnotationRowsForScores(
 242                     ourAnnot, service.serviceType + " (" + scr.getMethod()
 243                             + ")",
 244                     service.getServiceTypeURI() + "/" + scr.getMethod(),
 245                     aseq, base + 1, scr);
 246             annot.graph = AlignmentAnnotation.LINE_GRAPH;
 247             annot.visible = (annotTypeMap == null
 248                     || annotTypeMap.get(scr.getMethod()) == null || annotTypeMap
 249                     .get(scr.getMethod()).get(INVISIBLE) == null);
 250             double[] thrsh = (annotTypeMap == null || annotTypeMap.get(scr
 251                     .getMethod()) == null) ? null : (double[]) annotTypeMap
 252                     .get(scr.getMethod()).get(THRESHOLD);
 253             if (annotTypeMap == null
 254                     || annotTypeMap.get(scr.getMethod()) == null
 255                     || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
 256             {
 257               {
 258                 if (!sameGroup)
 259                 {
 260                   graphGroup++;
 261                   sameGroup = true;
 262                 }
 263
 264                 annot.graphGroup = graphGroup;
 265               }
 266             }
 267
 268             annot.description = "<html>" + service.getActionText()
 269                     + " - raw scores";
 270             if (thrsh != null)
 271             {
 272               String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 273                       + thrsh[1] + " indicates disorder";
 274               annot.threshold = new GraphLine((float) thrsh[1], threshNote,
 275                       Color.red);
 276               annot.description += "<br/>" + threshNote;
 277             }
 278             annot.description += "</html>";
 279             Color col = new UserColourScheme(typeName)
 280                     .createColourFromName(typeName + scr.getMethod());
 281             for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 282             {
 283               if (annot.annotations[p] != null)
 284               {
 285                 annot.annotations[p].colour = col;
 286               }
 287             }
 288             annot._linecolour = col;
 289           }
 290         }
 291         if (lastAnnot + 1 == ourAnnot.size())
 292         {
 293           // remove singleton alignment annotation row
 294           ourAnnot.get(lastAnnot).graphGroup = -1;
 295         }
 296       }
 297       {
 298         if (dispFeatures)
 299         {
 300           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 301                   .cloneFeatureRenderer();
 302           for (String ft : fc.keySet())
 303           {
 304             Object gc = fr.getFeatureStyle(ft);
 305             if (gc instanceof Color)
 306             {
 307               // set graduated color as fading to white for minimum, and
 308               // autoscaling to values on alignment
 309               GraduatedColor ggc = new GraduatedColor(Color.white,
 310                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 311               ggc.setAutoScaled(true);
 312               fr.setColour(ft, ggc);
 313             }
 314           }
 315           // TODO: JAL-1150 - create sequence feature settings API for defining
 316           // styles and enabling/disabling feature overlay on alignment panel
 317           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 318           if (af.alignPanel == ap)
 319           {
 320             // only do this if the alignFrame is currently showing this view.
 321             af.setShowSeqFeatures(true);
 322           }
 323           ap.paintAlignment(true);
 324         }
 325         if (ourAnnot.size() > 0)
 326         {
 327           // Modify the visible annotation on the alignment viewport with the
 328           // new alignment annotation rows created.
 329           updateOurAnnots(ourAnnot);
 330           ap.adjustAnnotationHeight();
 331         }
 332       }
 333     }
 334   }
 335
 336 }