src/jalview/ws/jws2/AADisorderClient.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 The Jalview Authors
   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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.ws.jws2;
  20
  21 import jalview.api.AlignCalcWorkerI;
  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
  45 public class AADisorderClient extends JabawsAlignCalcWorker implements
  46         AlignCalcWorkerI
  47 {
  48
  49   private static final String THRESHOLD = "THRESHOLD";
  50
  51   String typeName;
  52
  53   String methodName;
  54
  55   String groupName;
  56
  57   AlignFrame af;
  58
  59   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  60           WsParamSetI preset, List<Argument> paramset)
  61   {
  62     super(sh, alignFrame, preset, paramset);
  63     af = alignFrame;
  64     typeName = sh.action;
  65     methodName = sh.serviceType;
  66
  67     submitGaps = false;
  68     alignedSeqs = false;
  69     nucleotidesAllowed = false;
  70     proteinAllowed = true;
  71     bySequence = true;
  72   }
  73
  74   @Override
  75   public String getServiceActionText()
  76   {
  77     return "Submitting amino acid sequences for disorder prediction.";
  78   }
  79
  80   private static Map<String, Map<String, String[]>> featureMap;
  81
  82   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  83
  84   private static String DONTCOMBINE = "DONTCOMBINE";
  85
  86   private static String INVISIBLE = "INVISIBLE";
  87   static
  88   {
  89     // TODO: turn this into some kind of configuration file that's a bit easier
  90     // to edit
  91     featureMap = new HashMap<String, Map<String, String[]>>();
  92     Map<String, String[]> fmap;
  93     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  94             fmap = new HashMap<String, String[]>());
  95     fmap.put("Glob", new String[]
  96     { "Globular Domain", "Predicted globular domain" });
  97     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
  98             fmap = new HashMap<String, String[]>());
  99     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 100             fmap = new HashMap<String, String[]>());
 101     fmap.put("REM465", new String[]
 102     { "REM465", "Missing density" });
 103     fmap.put("HOTLOOPS", new String[]
 104     { "HOTLOOPS", "Flexible loops" });
 105     fmap.put("COILS", new String[]
 106     { "COILS", "Random coil" });
 107     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 108             fmap = new HashMap<String, String[]>());
 109     fmap.put("GlobDoms", new String[]
 110     { "Globular Domain", "Predicted globular domain" });
 111     fmap.put("Disorder", new String[]
 112     { "Protein Disorder", "Probable unstructured peptide region" });
 113     Map<String, Map<String, Object>> amap;
 114     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 115     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 116             amap = new HashMap<String, Map<String, Object>>());
 117     amap.put("Dydx", new HashMap<String, Object>());
 118     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 119     amap.get("Dydx").put(THRESHOLD, new double[]
 120     { 1, 0 });
 121     amap.put("SmoothedScore", new HashMap<String, Object>());
 122     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 123     amap.put("RawScore", new HashMap<String, Object>());
 124     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 125     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 126             amap = new HashMap<String, Map<String, Object>>());
 127     amap.put("COILS", new HashMap<String, Object>());
 128     amap.put("HOTLOOPS", new HashMap<String, Object>());
 129     amap.put("REM465", new HashMap<String, Object>());
 130     amap.get("COILS").put(THRESHOLD, new double[]
 131     { 1, 0.516 });
 132     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 133     { 1, 0.6 });
 134     amap.get("REM465").put(THRESHOLD, new double[]
 135     { 1, 0.1204 });
 136
 137     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 138             amap = new HashMap<String, Map<String, Object>>());
 139     amap.put("Long", new HashMap<String, Object>());
 140     amap.put("Short", new HashMap<String, Object>());
 141     amap.get("Long").put(THRESHOLD, new double[]
 142     { 1, 0.5 });
 143     amap.get("Short").put(THRESHOLD, new double[]
 144     { 1, 0.5 });
 145     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 146             amap = new HashMap<String, Map<String, Object>>());
 147     amap.put("JRonn", new HashMap<String, Object>());
 148     amap.get("JRonn").put(THRESHOLD, new double[]
 149     { 1, 0.5 });
 150   }
 151
 152   @Override
 153   public void updateResultAnnotation(boolean immediate)
 154   {
 155
 156     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 157     {
 158       Map<String, String[]> featureTypeMap = featureMap
 159               .get(service.serviceType);
 160       Map<String, Map<String, Object>> annotTypeMap = annotMap
 161               .get(service.serviceType);
 162       boolean dispFeatures = false;
 163       Map<String, Object> fc = new Hashtable<String, Object>();
 164       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 165       /**
 166        * grouping for any annotation rows created
 167        */
 168       int graphGroup = 1;
 169       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 170       {
 171         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 172                 .getAlignmentAnnotation())
 173         {
 174           if (ala.graphGroup > graphGroup)
 175           {
 176             graphGroup = ala.graphGroup;
 177           }
 178         }
 179       }
 180
 181       for (String seqId : seqNames.keySet())
 182       {
 183         boolean sameGroup = false;
 184         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 185         int base = seq.findPosition(start)-1;
 186         aseq = seq;
 187         while ((dseq = seq).getDatasetSequence() != null)
 188         {
 189           seq = seq.getDatasetSequence();
 190         }
 191         ;
 192         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
 193         float last = Float.NaN, val = Float.NaN;
 194         int lastAnnot = ourAnnot.size();
 195         if (scores!=null && scores.scores!=null) {
 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],
 218                           base + rn.from, base + rn.to, val = vals.next()
 219                                   .floatValue(), 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,
 243                       service.serviceType + " (" + scr.getMethod() + ")",
 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
 251                       .get(scr.getMethod()) == null) ? null
 252                       : (double[]) annotTypeMap.get(scr.getMethod()).get(
 253                               THRESHOLD);
 254               if (annotTypeMap == null
 255                       || annotTypeMap.get(scr.getMethod()) == null
 256                       || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
 257               {
 258                 {
 259                   if (!sameGroup)
 260                   {
 261                     graphGroup++;
 262                     sameGroup = true;
 263                   }
 264
 265                   annot.graphGroup = graphGroup;
 266                 }
 267               }
 268
 269               annot.description = "<html>" + service.getActionText()
 270                       + " - raw scores";
 271               if (thrsh != null)
 272               {
 273                 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 274                         + thrsh[1] + " indicates disorder";
 275                 annot.threshold = new GraphLine((float) thrsh[1],
 276                         threshNote, Color.red);
 277                 annot.description += "<br/>" + threshNote;
 278               }
 279               annot.description += "</html>";
 280               Color col = new UserColourScheme(typeName)
 281                       .createColourFromName(typeName + scr.getMethod());
 282               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 283               {
 284                 if (annot.annotations[p] != null)
 285                 {
 286                   annot.annotations[p].colour = col;
 287                 }
 288               }
 289               annot._linecolour = col;
 290             }
 291           }
 292         }
 293         if (lastAnnot + 1 == ourAnnot.size())
 294         {
 295           // remove singleton alignment annotation row
 296           ourAnnot.get(lastAnnot).graphGroup = -1;
 297         }
 298       }
 299       {
 300         if (dispFeatures)
 301         {
 302           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 303                   .cloneFeatureRenderer();
 304           for (String ft : fc.keySet())
 305           {
 306             Object gc = fr.getFeatureStyle(ft);
 307             if (gc instanceof Color)
 308             {
 309               // set graduated color as fading to white for minimum, and
 310               // autoscaling to values on alignment
 311               GraduatedColor ggc = new GraduatedColor(Color.white,
 312                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 313               ggc.setAutoScaled(true);
 314               fr.setColour(ft, ggc);
 315             }
 316           }
 317           // TODO: JAL-1150 - create sequence feature settings API for defining
 318           // styles and enabling/disabling feature overlay on alignment panel
 319           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 320           if (af.alignPanel == ap)
 321           {
 322             // only do this if the alignFrame is currently showing this view.
 323             af.setShowSeqFeatures(true);
 324           }
 325           ap.paintAlignment(true);
 326         }
 327         if (ourAnnot.size() > 0)
 328         {
 329           // Modify the visible annotation on the alignment viewport with the
 330           // new alignment annotation rows created.
 331           updateOurAnnots(ourAnnot);
 332           ap.adjustAnnotationHeight();
 333         }
 334       }
 335     }
 336   }
 337
 338 }