src/jalview/workers/ConservationThread.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ 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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.workers;
  22
  23 import jalview.analysis.Conservation;
  24 import jalview.api.AlignCalcWorkerI;
  25 import jalview.api.AlignViewportI;
  26 import jalview.api.AlignmentViewPanel;
  27 import jalview.datamodel.AlignmentAnnotation;
  28 import jalview.datamodel.AlignmentI;
  29 import jalview.schemes.ResidueProperties;
  30
  31 import java.util.ArrayList;
  32 import java.util.List;
  33
  34 public class ConservationThread extends AlignCalcWorker implements
  35         AlignCalcWorkerI
  36 {
  37
  38   private int ConsPercGaps = 25; // JBPNote : This should be a configurable
  39                                  // property!
  40
  41         @Override
  42         public AlignCalcWorkerI getNewWorker() {
  43                 return new ConservationThread(alignViewport, ap);
  44         }
  45
  46   public ConservationThread(AlignViewportI alignViewport,
  47           AlignmentViewPanel alignPanel)
  48   {
  49     super(alignViewport, alignPanel);
  50     ConsPercGaps = alignViewport.getConsPercGaps();
  51   }
  52
  53   private Conservation cons;
  54
  55   AlignmentAnnotation conservation, quality;
  56
  57         @Override
  58         protected void run1(int state) {
  59                 while (!interrupted()) {
  60                         try {
  61                                 switch (state) {
  62                                 case INIT:
  63                                         if (calcMan.isPending(this))
  64                                                 return;
  65                                         calcMan.notifyStart(this);
  66                                         state = LOOP_STANDBY;
  67                                         break;
  68                                 case LOOP_STANDBY:
  69                                         while (!calcMan.notifyWorking(this)) {
  70                                                 if (ap != null) {
  71                                                         ap.paintAlignment(false);
  72                                                 }
  73                                                 try {
  74                                                         if (sleepAndReturn(200, state))
  75                                                                 return;
  76                                                 } catch (InterruptedException e) {
  77                                                         state = DONE;
  78                                                         break;
  79                                                 }
  80                                         }
  81                                         if (alignViewport.isClosed()) {
  82                                                 abortAndDestroy();
  83                                                 state = DONE;
  84                                                 break;
  85                                         }
  86                       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
  87                       alignment = alignViewport.getAlignment();
  88                       conservation = alignViewport.getAlignmentConservationAnnotation();
  89                       quality = alignViewport.getAlignmentQualityAnnot();
  90                       ourAnnot.add(conservation);
  91                       ourAnnot.add(quality);
  92                       ourAnnots = ourAnnot;
  93                       ConsPercGaps = alignViewport.getConsPercGaps();
  94                       // AlignViewport.UPDATING_CONSERVATION = true;
  95
  96                       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  97                       {
  98                         calcMan.workerComplete(this);
  99                         // .updatingConservation = false;
 100                         // AlignViewport.UPDATING_CONSERVATION = false;
 101
 102                         return;
 103                       }
 104                                         state = LOOP_CALCULATE;
 105                                         break;
 106                                 case LOOP_CALCULATE:
 107                                         iFirst = iLast;
 108                                         nPer = aWidth  + 1; // for now - one big chunk
 109                                         iLast = Math.min(iLast + nPer, aWidth);
 110                                         if (iLast == iFirst) {
 111                                                 state = DONE;
 112                                         } else {
 113                                                 computeConsensus();
 114                                                 if (sleepAndReturn(0, state))
 115                                                         return;
 116                                         }
 117                                         break;
 118                                 case DONE:
 119                       updateResultAnnotation(true);
 120                                         notifyDone();
 121                                         return;
 122                                 }
 123                         } catch (OutOfMemoryError error) {
 124                                 calcMan.workerCannotRun(this);
 125               ap.raiseOOMWarning("calculating conservation", error);
 126                         } catch (Throwable e) {
 127                                 System.out.println("Error in ConsensusThread: " + e);
 128                                 e.printStackTrace();
 129                                 calcMan.workerComplete(this);
 130                         }
 131                 }
 132         }
 133
 134         private void computeConsensus() {
 135     cons = Conservation.calculateConservation("All",
 136         ResidueProperties.propHash, 3,
 137         alignment.getSequences(), 0, aWidth - 1, false,
 138         ConsPercGaps, quality != null);
 139         }
 140
 141
 142   private void updateResultAnnotation(boolean b)
 143   {
 144     if (b || !calcMan.isWorking(this) && cons != null
 145             && conservation != null && quality != null)
 146     {
 147       alignViewport.setConservation(cons);
 148       cons.completeAnnotations(conservation, quality, 0, aWidth);
 149     }
 150   }
 151
 152   @Override
 153   public void updateAnnotation()
 154   {
 155     updateResultAnnotation(false);
 156
 157   }
 158
 159 }