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 JabawsCalcWorker implements
  46         AlignCalcWorkerI
  47 {
  48
  49   private static final String THRESHOLD = "THRESHOLD";
  50   private static final String RANGE = "RANGE";
  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.get("Dydx").put(RANGE, new float[]
 123             { -1, +1 });
 124
 125     amap.put("SmoothedScore", new HashMap<String, Object>());
 126     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 127     amap.put("RawScore", new HashMap<String, Object>());
 128     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 129     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 130             amap = new HashMap<String, Map<String, Object>>());
 131     amap.put("COILS", new HashMap<String, Object>());
 132     amap.put("HOTLOOPS", new HashMap<String, Object>());
 133     amap.put("REM465", new HashMap<String, Object>());
 134     amap.get("COILS").put(THRESHOLD, new double[]
 135     { 1, 0.516 });
 136     amap.get("COILS").put(RANGE, new float[]
 137             { 0, 1 });
 138
 139     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 140     { 1, 0.6 });
 141     amap.get("HOTLOOPS").put(RANGE, new float[]
 142             { 0, 1 });
 143     amap.get("REM465").put(THRESHOLD, new double[]
 144     { 1, 0.1204 });
 145     amap.get("REM465").put(RANGE, new float[]
 146             { 0, 1 });
 147
 148
 149     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 150             amap = new HashMap<String, Map<String, Object>>());
 151     amap.put("Long", new HashMap<String, Object>());
 152     amap.put("Short", new HashMap<String, Object>());
 153     amap.get("Long").put(THRESHOLD, new double[]
 154     { 1, 0.5 });
 155     amap.get("Long").put(RANGE, new float[]
 156             { 0, 1 });
 157     amap.get("Short").put(THRESHOLD, new double[]
 158     { 1, 0.5 });
 159     amap.get("Short").put(RANGE, new float[]
 160             { 0, 1 });
 161     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 162             amap = new HashMap<String, Map<String, Object>>());
 163     amap.put("JRonn", new HashMap<String, Object>());
 164     amap.get("JRonn").put(THRESHOLD, new double[]
 165     { 1, 0.5 });
 166     amap.get("JRonn").put(RANGE, new float[]
 167             { 0, 1 });
 168   }
 169
 170   @Override
 171   public void updateResultAnnotation(boolean immediate)
 172   {
 173
 174     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 175     {
 176       Map<String, String[]> featureTypeMap = featureMap
 177               .get(service.serviceType);
 178       Map<String, Map<String, Object>> annotTypeMap = annotMap
 179               .get(service.serviceType);
 180       boolean dispFeatures = false;
 181       Map<String, Object> fc = new Hashtable<String, Object>();
 182       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 183       /**
 184        * grouping for any annotation rows created
 185        */
 186       int graphGroup = 1;
 187       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 188       {
 189         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 190                 .getAlignmentAnnotation())
 191         {
 192           if (ala.graphGroup > graphGroup)
 193           {
 194             graphGroup = ala.graphGroup;
 195           }
 196         }
 197       }
 198
 199       for (String seqId : seqNames.keySet())
 200       {
 201         boolean sameGroup = false;
 202         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 203         int base = seq.findPosition(start)-1;
 204         aseq = seq;
 205         while ((dseq = seq).getDatasetSequence() != null)
 206         {
 207           seq = seq.getDatasetSequence();
 208         }
 209         ;
 210         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
 211         float last = Float.NaN, val = Float.NaN;
 212         int lastAnnot = ourAnnot.size();
 213         if (scores!=null && scores.scores!=null) {
 214           for (Score scr : scores.scores)
 215           {
 216
 217             if (scr.getRanges() != null && scr.getRanges().size() > 0)
 218             {
 219               Iterator<Float> vals = scr.getScores().iterator();
 220               // make features on sequence
 221               for (Range rn : scr.getRanges())
 222               {
 223
 224                 SequenceFeature sf;
 225                 String[] type = featureTypeMap.get(scr.getMethod());
 226                 if (type == null)
 227                 {
 228                   // create a default type for this feature
 229                   type = new String[]
 230                   { typeName + " (" + scr.getMethod() + ")",
 231                       service.getActionText() };
 232                 }
 233                 if (vals.hasNext())
 234                 {
 235                   sf = new SequenceFeature(type[0], type[1],
 236                           base + rn.from, base + rn.to, val = vals.next()
 237                                   .floatValue(), methodName);
 238                 }
 239                 else
 240                 {
 241                   sf = new SequenceFeature(type[0], type[1], null, base
 242                           + rn.from, base + rn.to, methodName);
 243                 }
 244                 dseq.addSequenceFeature(sf);
 245                 if (last != val && last != Float.NaN)
 246                 {
 247                   fc.put(sf.getType(), sf);
 248                 }
 249                 last = val;
 250                 dispFeatures = true;
 251               }
 252             }
 253             else
 254             {
 255               if (scr.getScores().size() == 0)
 256               {
 257                 continue;
 258               }
 259               AlignmentAnnotation annot = createAnnotationRowsForScores(
 260                       ourAnnot,
 261                       service.serviceType + " (" + scr.getMethod() + ")",
 262                       service.getServiceTypeURI() + "/" + scr.getMethod(),
 263                       aseq, base + 1, scr);
 264               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 265
 266               Map<String,Object> styleMap = (annotTypeMap == null) ? null : annotTypeMap.get(scr.getMethod());
 267
 268               annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
 269               double[] thrsh = (styleMap==null) ? null
 270                       : (double[]) styleMap.get(
 271                               THRESHOLD);
 272               float[] range = (styleMap==null) ? null : (float[]) styleMap.get(
 273                       RANGE);
 274               if (range!=null)
 275               {
 276                 annot.graphMin = range[0];
 277                 annot.graphMax = range[1];
 278               }
 279               if (styleMap==null || styleMap.get(DONTCOMBINE) == null)
 280               {
 281                 {
 282                   if (!sameGroup)
 283                   {
 284                     graphGroup++;
 285                     sameGroup = true;
 286                   }
 287
 288                   annot.graphGroup = graphGroup;
 289                 }
 290               }
 291
 292               annot.description = "<html>" + service.getActionText()
 293                       + " - raw scores";
 294               if (thrsh != null)
 295               {
 296                 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 297                         + thrsh[1] + " indicates disorder";
 298                 annot.threshold = new GraphLine((float) thrsh[1],
 299                         threshNote, Color.red);
 300                 annot.description += "<br/>" + threshNote;
 301               }
 302               annot.description += "</html>";
 303               Color col = new UserColourScheme(typeName)
 304                       .createColourFromName(typeName + scr.getMethod());
 305               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 306               {
 307                 if (annot.annotations[p] != null)
 308                 {
 309                   annot.annotations[p].colour = col;
 310                 }
 311               }
 312               annot._linecolour = col;
 313             }
 314           }
 315         }
 316         if (lastAnnot + 1 == ourAnnot.size())
 317         {
 318           // remove singleton alignment annotation row
 319           ourAnnot.get(lastAnnot).graphGroup = -1;
 320         }
 321       }
 322       {
 323         if (dispFeatures)
 324         {
 325           jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 326                   .cloneFeatureRenderer();
 327           for (String ft : fc.keySet())
 328           {
 329             Object gc = fr.getFeatureStyle(ft);
 330             if (gc instanceof Color)
 331             {
 332               // set graduated color as fading to white for minimum, and
 333               // autoscaling to values on alignment
 334               GraduatedColor ggc = new GraduatedColor(Color.white,
 335                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 336               ggc.setAutoScaled(true);
 337               fr.setColour(ft, ggc);
 338             }
 339           }
 340           // TODO: JAL-1150 - create sequence feature settings API for defining
 341           // styles and enabling/disabling feature overlay on alignment panel
 342           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 343           if (af.alignPanel == ap)
 344           {
 345             // only do this if the alignFrame is currently showing this view.
 346             af.setShowSeqFeatures(true);
 347           }
 348           ap.paintAlignment(true);
 349         }
 350         if (ourAnnot.size() > 0)
 351         {
 352           // Modify the visible annotation on the alignment viewport with the
 353           // new alignment annotation rows created.
 354           updateOurAnnots(ourAnnot);
 355           ap.adjustAnnotationHeight();
 356         }
 357       }
 358     }
 359   }
 360
 361 }