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.datamodel.AlignmentAnnotation;
  22
  23 import jalview.datamodel.GraphLine;
  24 import jalview.datamodel.SequenceFeature;
  25 import jalview.datamodel.SequenceI;
  26 import jalview.gui.AlignFrame;
  27 import jalview.schemes.GraduatedColor;
  28 import jalview.schemes.UserColourScheme;
  29 import jalview.ws.jws2.jabaws2.Jws2Instance;
  30 import jalview.ws.params.WsParamSetI;
  31
  32 import java.awt.Color;
  33 import java.util.ArrayList;
  34 import java.util.HashMap;
  35 import java.util.Hashtable;
  36 import java.util.Iterator;
  37 import java.util.List;
  38 import java.util.Map;
  39 import compbio.data.sequence.Range;
  40 import compbio.data.sequence.Score;
  41 import compbio.data.sequence.ScoreManager.ScoreHolder;
  42 import compbio.metadata.Argument;
  43
  44 public class AADisorderClient extends JabawsAlignCalcWorker implements
  45         AlignCalcWorkerI
  46 {
  47
  48   private static final String THRESHOLD = "THRESHOLD";
  49
  50   String typeName;
  51
  52   String methodName;
  53
  54   String groupName;
  55
  56   AlignFrame af;
  57
  58   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  59           WsParamSetI preset, List<Argument> paramset)
  60   {
  61     super(sh, alignFrame, preset, paramset);
  62     af = alignFrame;
  63     typeName = sh.action;
  64     methodName = sh.serviceType;
  65
  66     submitGaps = false;
  67     alignedSeqs = false;
  68     nucleotidesAllowed = false;
  69     proteinAllowed = true;
  70     bySequence = true;
  71   }
  72
  73   @Override
  74   public String getServiceActionText()
  75   {
  76     return "Submitting amino acid sequences for disorder prediction.";
  77   }
  78
  79   private static Map<String, Map<String, String[]>> featureMap;
  80
  81   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  82
  83   private static String DONTCOMBINE = "DONTCOMBINE";
  84
  85   private static String INVISIBLE = "INVISIBLE";
  86   static
  87   {
  88     // TODO: turn this into some kind of configuration file that's a bit easier
  89     // to edit
  90     featureMap = new HashMap<String, Map<String, String[]>>();
  91     Map<String, String[]> fmap;
  92     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  93             fmap = new HashMap<String, String[]>());
  94     fmap.put("Glob", new String[]
  95     { "Globular Domain", "Predicted globular domain" });
  96     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
  97             fmap = new HashMap<String, String[]>());
  98     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
  99             fmap = new HashMap<String, String[]>());
 100     fmap.put("REM465", new String[]
 101     { "REM465", "Missing density" });
 102     fmap.put("HOTLOOPS", new String[]
 103     { "HOTLOOPS", "Flexible loops" });
 104     fmap.put("COILS", new String[]
 105     { "COILS", "Random coil" });
 106     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 107             fmap = new HashMap<String, String[]>());
 108     fmap.put("GlobDoms", new String[]
 109     { "Globular Domain", "Predicted globular domain" });
 110     fmap.put("Disorder", new String[]
 111     { "Protein Disorder", "Probable unstructured peptide region" });
 112     Map<String, Map<String, Object>> amap;
 113     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 114     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 115             amap = new HashMap<String, Map<String, Object>>());
 116     amap.put("Dydx", new HashMap<String, Object>());
 117     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 118     amap.get("Dydx").put(THRESHOLD, new double[]
 119     { 1, 0 });
 120     amap.put("SmoothedScore", new HashMap<String, Object>());
 121     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 122     amap.put("RawScore", new HashMap<String, Object>());
 123     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 124     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 125             amap = new HashMap<String, Map<String, Object>>());
 126     amap.put("COILS", new HashMap<String, Object>());
 127     amap.put("HOTLOOPS", new HashMap<String, Object>());
 128     amap.put("REM465", new HashMap<String, Object>());
 129     amap.get("COILS").put(THRESHOLD, new double[]
 130     { 1, 0.516 });
 131     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 132     { 1, 0.6 });
 133     amap.get("REM465").put(THRESHOLD, new double[]
 134     { 1, 0.1204 });
 135
 136     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 137             amap = new HashMap<String, Map<String, Object>>());
 138     amap.put("Long", new HashMap<String, Object>());
 139     amap.put("Short", new HashMap<String, Object>());
 140     amap.get("Long").put(THRESHOLD, new double[]
 141     { 1, 0.5 });
 142     amap.get("Short").put(THRESHOLD, new double[]
 143     { 1, 0.5 });
 144     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 145             amap = new HashMap<String, Map<String, Object>>());
 146     amap.put("JRonn", new HashMap<String, Object>());
 147     amap.get("JRonn").put(THRESHOLD, new double[]
 148     { 1, 0.5 });
 149   }
 150
 151   @Override
 152   public void updateResultAnnotation(boolean immediate)
 153   {
 154
 155     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 156     {
 157       Map<String, String[]> featureTypeMap = featureMap
 158               .get(service.serviceType);
 159       Map<String, Map<String, Object>> annotTypeMap = annotMap
 160               .get(service.serviceType);
 161       boolean dispFeatures = false;
 162       Map<String, Object> fc = new Hashtable<String, Object>();
 163       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 164       /**
 165        * grouping for any annotation rows created
 166        */
 167       int graphGroup = 1;
 168       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 169       {
 170         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 171                 .getAlignmentAnnotation())
 172         {
 173           if (ala.graphGroup > graphGroup)
 174           {
 175             graphGroup = ala.graphGroup;
 176           }
 177         }
 178       }
 179
 180       for (String seqId : seqNames.keySet())
 181       {
 182         boolean sameGroup = false;
 183         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 184         int base = seq.findPosition(start)-1;
 185         aseq = seq;
 186         while ((dseq = seq).getDatasetSequence() != null)
 187         {
 188           seq = seq.getDatasetSequence();
 189         }
 190         ;
 191         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
 192         float last = Float.NaN, val = Float.NaN;
 193         int lastAnnot = ourAnnot.size();
 194         if (scores!=null && scores.scores!=null) {
 195           for (Score scr : scores.scores)
 196           {
 197
 198             if (scr.getRanges() != null && scr.getRanges().size() > 0)
 199             {
 200               Iterator<Float> vals = scr.getScores().iterator();
 201               // make features on sequence
 202               for (Range rn : scr.getRanges())
 203               {
 204
 205                 SequenceFeature sf;
 206                 String[] type = featureTypeMap.get(scr.getMethod());
 207                 if (type == null)
 208                 {
 209                   // create a default type for this feature
 210                   type = new String[]
 211                   { typeName + " (" + scr.getMethod() + ")",
 212                       service.getActionText() };
 213                 }
 214                 if (vals.hasNext())
 215                 {
 216                   sf = new SequenceFeature(type[0], type[1],
 217                           base + rn.from, base + rn.to, val = vals.next()
 218                                   .floatValue(), methodName);
 219                 }
 220                 else
 221                 {
 222                   sf = new SequenceFeature(type[0], type[1], null, base
 223                           + rn.from, base + rn.to, methodName);
 224                 }
 225                 dseq.addSequenceFeature(sf);
 226                 if (last != val && last != Float.NaN)
 227                 {
 228                   fc.put(sf.getType(), sf);
 229                 }
 230                 last = val;
 231                 dispFeatures = true;
 232               }
 233             }
 234             else
 235             {
 236               if (scr.getScores().size() == 0)
 237               {
 238                 continue;
 239               }
 240               AlignmentAnnotation annot = createAnnotationRowsForScores(
 241                       ourAnnot,
 242                       service.serviceType + " (" + scr.getMethod() + ")",
 243                       service.getServiceTypeURI() + "/" + scr.getMethod(),
 244                       aseq, base + 1, scr);
 245               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 246               annot.visible = (annotTypeMap == null
 247                       || annotTypeMap.get(scr.getMethod()) == null || annotTypeMap
 248                       .get(scr.getMethod()).get(INVISIBLE) == null);
 249               double[] thrsh = (annotTypeMap == null || annotTypeMap
 250                       .get(scr.getMethod()) == null) ? null
 251                       : (double[]) annotTypeMap.get(scr.getMethod()).get(
 252                               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],
 275                         threshNote, 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         }
 292         if (lastAnnot + 1 == ourAnnot.size())
 293         {
 294           // remove singleton alignment annotation row
 295           ourAnnot.get(lastAnnot).graphGroup = -1;
 296         }
 297       }
 298       {
 299         if (dispFeatures)
 300         {
 301           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 302                   .cloneFeatureRenderer();
 303           for (String ft : fc.keySet())
 304           {
 305             Object gc = fr.getFeatureStyle(ft);
 306             if (gc instanceof Color)
 307             {
 308               // set graduated color as fading to white for minimum, and
 309               // autoscaling to values on alignment
 310               GraduatedColor ggc = new GraduatedColor(Color.white,
 311                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 312               ggc.setAutoScaled(true);
 313               fr.setColour(ft, ggc);
 314             }
 315           }
 316           // TODO: JAL-1150 - create sequence feature settings API for defining
 317           // styles and enabling/disabling feature overlay on alignment panel
 318           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 319           if (af.alignPanel == ap)
 320           {
 321             // only do this if the alignFrame is currently showing this view.
 322             af.setShowSeqFeatures(true);
 323           }
 324           ap.paintAlignment(true);
 325         }
 326         if (ourAnnot.size() > 0)
 327         {
 328           // Modify the visible annotation on the alignment viewport with the
 329           // new alignment annotation rows created.
 330           updateOurAnnots(ourAnnot);
 331           ap.adjustAnnotationHeight();
 332         }
 333       }
 334     }
 335   }
 336
 337 }