src/jalview/ws/jws2/AADisorderClient.java

   1 package jalview.ws.jws2;
   2
   3 import jalview.api.AlignCalcWorkerI;
   4 import jalview.bin.Cache;
   5 import jalview.datamodel.AlignmentAnnotation;
   6
   7 import jalview.datamodel.SequenceFeature;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.gui.AlignFrame;
  10 import jalview.schemes.GraduatedColor;
  11 import jalview.schemes.UserColourScheme;
  12 import jalview.ws.jws2.jabaws2.Jws2Instance;
  13 import jalview.ws.params.WsParamSetI;
  14
  15 import java.awt.Color;
  16 import java.util.ArrayList;
  17 import java.util.HashMap;
  18 import java.util.Hashtable;
  19 import java.util.Iterator;
  20 import java.util.List;
  21 import java.util.Map;
  22 import compbio.data.sequence.Range;
  23 import compbio.data.sequence.Score;
  24 import compbio.data.sequence.ScoreManager.ScoreHolder;
  25 import compbio.metadata.Argument;
  26 import compbio.ws.client.Services;
  27
  28 public class AADisorderClient extends JabawsAlignCalcWorker implements
  29         AlignCalcWorkerI
  30 {
  31
  32   String typeName;
  33
  34   String methodName;
  35
  36   String groupName;
  37
  38   AlignFrame af;
  39
  40   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  41           WsParamSetI preset, List<Argument> paramset)
  42   {
  43     super(sh, alignFrame, preset, paramset);
  44     af = alignFrame;
  45     typeName = sh.action;
  46     methodName = sh.serviceType;
  47
  48     submitGaps = false;
  49     alignedSeqs = false;
  50     nucleotidesAllowed = false;
  51     proteinAllowed = true;
  52     bySequence = true;
  53   }
  54
  55   @Override
  56   public String getServiceActionText()
  57   {
  58     return "Submitting amino acid sequences for disorder prediction.";
  59   }
  60
  61   private static Map<String, Map<String, String[]>> featureMap;
  62
  63   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  64
  65   private static String DONTCOMBINE = "DONTCOMBINE";
  66   private static String INVISIBLE = "INVISIBLE";
  67   static
  68   {
  69     featureMap = new HashMap<String, Map<String, String[]>>();
  70     Map<String, String[]> fmap;
  71     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  72             fmap = new HashMap<String, String[]>());
  73     fmap.put("Glob", new String[]
  74     { "Globular Domain", "Predicted globular domain" });
  75     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
  76             fmap = new HashMap<String, String[]>());
  77     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
  78             fmap = new HashMap<String, String[]>());
  79     fmap.put("REM465", new String[]
  80     { "REM465", "Missing density" });
  81     fmap.put("HOTLOOPS", new String[]
  82     { "HOTLOOPS", "Flexible loops" });
  83     fmap.put("COILS", new String[]
  84     { "COILS", "Random coil" });
  85     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
  86             fmap = new HashMap<String, String[]>());
  87     fmap.put("GlobDoms", new String[]
  88     { "Globular Domain", "Predicted globular domain" });
  89     fmap.put("Disorder", new String[]
  90     { "Protein Disorder", "Probable unstructured peptide region" });
  91     Map<String, Map<String, Object>> amap;
  92     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
  93     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
  94             amap = new HashMap<String, Map<String, Object>>());
  95     amap.put("Dydx", new HashMap<String, Object>());
  96     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
  97     amap.put("SmoothedScore", new HashMap<String, Object>());
  98     amap.get("SmoothedScore").put(INVISIBLE,INVISIBLE);
  99     amap.put("RawScore", new HashMap<String, Object>());
 100     amap.get("RawScore").put(INVISIBLE,INVISIBLE);
 101     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 102             amap = new HashMap<String, Map<String, Object>>());
 103
 104   }
 105
 106   @Override
 107   public void updateResultAnnotation(boolean immediate)
 108   {
 109
 110     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 111     {
 112       Map<String, String[]> featureTypeMap = featureMap
 113               .get(service.serviceType);
 114       Map<String, Map<String, Object>> annotTypeMap = annotMap
 115               .get(service.serviceType);
 116       boolean dispFeatures = false;
 117       Map<String, Object> fc = new Hashtable<String, Object>();
 118       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 119       /**
 120        * grouping for any annotation rows created
 121        */
 122       int graphGroup = 1, iGraphGroup = 1;
 123       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 124       {
 125         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 126                 .getAlignmentAnnotation())
 127         {
 128           if (ala.graphGroup > graphGroup)
 129           {
 130             graphGroup = ala.graphGroup;
 131           }
 132         }
 133       }
 134
 135       for (String seqId : seqNames.keySet())
 136       {
 137         boolean sameGroup = false;
 138         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 139         int base = seq.getStart() - 1;
 140         aseq = seq;
 141         while ((dseq = seq).getDatasetSequence() != null)
 142         {
 143           seq = seq.getDatasetSequence();
 144         }
 145         ;
 146         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
 147         float last = Float.NaN, val = Float.NaN;
 148         int lastAnnot = ourAnnot.size();
 149         for (Score scr : scores.scores)
 150         {
 151
 152           if (scr.getRanges() != null && scr.getRanges().size() > 0)
 153           {
 154             Iterator<Float> vals = scr.getScores().iterator();
 155             // make features on sequence
 156             for (Range rn : scr.getRanges())
 157             {
 158
 159               SequenceFeature sf;
 160               String[] type = featureTypeMap.get(scr.getMethod());
 161               if (type == null)
 162               {
 163                 // create a default type for this feature
 164                 type = new String[]
 165                 { typeName + " (" + scr.getMethod() + ")",
 166                     service.getActionText() };
 167               }
 168               if (vals.hasNext())
 169               {
 170                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 171                         base + rn.to, val = vals.next().floatValue(),
 172                         methodName);
 173               }
 174               else
 175               {
 176                 sf = new SequenceFeature(type[0], type[1], null, base
 177                         + rn.from, base + rn.to, methodName);
 178               }
 179               dseq.addSequenceFeature(sf);
 180               if (last != val && last != Float.NaN)
 181               {
 182                 fc.put(sf.getType(), sf);
 183               }
 184               last = val;
 185               dispFeatures = true;
 186             }
 187           }
 188           else
 189           {
 190             if (scr.getScores().size()==0)
 191             {
 192               continue;
 193             }
 194             AlignmentAnnotation annot = createAnnotationRowsForScores(
 195                     ourAnnot, service.serviceType + " (" + scr.getMethod()
 196                             + ")", service.getServiceTypeURI()+"/"+ scr.getMethod(), aseq,
 197                     base, scr);
 198             annot.graph = AlignmentAnnotation.LINE_GRAPH;
 199             annot.visible = (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(INVISIBLE) == null);
 200
 201             if (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
 202             {
 203               {
 204                 if (!sameGroup)
 205                 {
 206                   graphGroup++;
 207                   sameGroup = true;
 208                 }
 209
 210                 annot.graphGroup = graphGroup;
 211               }
 212             }
 213
 214             annot.description = service.getActionText() + " - raw scores";
 215             Color col = new UserColourScheme(typeName)
 216                     .createColourFromName(typeName + scr.getMethod());
 217             for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 218             {
 219               if (annot.annotations[p] != null)
 220               {
 221                 annot.annotations[p].colour = col;
 222               }
 223             }
 224             annot._linecolour=col;
 225           }
 226         }
 227         if (lastAnnot + 1 == ourAnnot.size())
 228         {
 229           // remove singleton alignment annotation row
 230           ourAnnot.get(lastAnnot).graphGroup = -1;
 231         }
 232       }
 233       {
 234         if (dispFeatures)
 235         {
 236           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 237                   .cloneFeatureRenderer();
 238           for (String ft : fc.keySet())
 239           {
 240             Object gc = fr.getFeatureStyle(ft);
 241             if (gc instanceof Color)
 242             {
 243               // set graduated color as fading to white for minimum, and
 244               // autoscaling to values on alignment
 245               GraduatedColor ggc = new GraduatedColor(Color.white,
 246                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 247               ggc.setAutoScaled(true);
 248               fr.setColour(ft, ggc);
 249             }
 250           }
 251           // TODO: JAL-1150 - create sequence feature settings API for defining styles and enabling/disabling feature overlay on alignment panel
 252           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 253           if (af.alignPanel==ap)
 254           {
 255             // only do this if the alignFrame is currently showing this view.
 256             af.setShowSeqFeatures(true);
 257           }
 258           ap.paintAlignment(true);
 259         }
 260         if (ourAnnot.size() > 0)
 261         {
 262           // Modify the visible annotation on the alignment viewport with the
 263           // new alignment annotation rows created.
 264           updateOurAnnots(ourAnnot);
 265           ap.adjustAnnotationHeight();
 266         }
 267       }
 268     }
 269   }
 270
 271 }