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   public ConservationThread(AlignViewportI alignViewport,
  42           AlignmentViewPanel alignPanel)
  43   {
  44     super(alignViewport, alignPanel);
  45     ConsPercGaps = alignViewport.getConsPercGaps();
  46   }
  47
  48   private Conservation cons;
  49
  50   AlignmentAnnotation conservation, quality;
  51
  52         @Override
  53         protected void run1(int state) {
  54                 while (!interrupted()) {
  55                         try {
  56                                 switch (state) {
  57                                 case INIT:
  58                                         if (calcMan.isPending(this))
  59                                                 return;
  60                                         calcMan.notifyStart(this);
  61                                         state = LOOP_STANDBY;
  62                                         break;
  63                                 case LOOP_STANDBY:
  64                                         while (!calcMan.notifyWorking(this)) {
  65                                                 if (ap != null) {
  66                                                         ap.paintAlignment(false);
  67                                                 }
  68                                                 try {
  69                                                         if (sleepAndReturn(200, state))
  70                                                                 return;
  71                                                 } catch (InterruptedException e) {
  72                                                         state = DONE;
  73                                                         break;
  74                                                 }
  75                                         }
  76                                         if (alignViewport.isClosed()) {
  77                                                 abortAndDestroy();
  78                                                 state = DONE;
  79                                                 break;
  80                                         }
  81                       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
  82                       alignment = alignViewport.getAlignment();
  83                       conservation = alignViewport.getAlignmentConservationAnnotation();
  84                       quality = alignViewport.getAlignmentQualityAnnot();
  85                       ourAnnot.add(conservation);
  86                       ourAnnot.add(quality);
  87                       ourAnnots = ourAnnot;
  88                       ConsPercGaps = alignViewport.getConsPercGaps();
  89                       // AlignViewport.UPDATING_CONSERVATION = true;
  90
  91                       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
  92                       {
  93                         calcMan.workerComplete(this);
  94                         // .updatingConservation = false;
  95                         // AlignViewport.UPDATING_CONSERVATION = false;
  96
  97                         return;
  98                       }
  99                                         state = LOOP_CALCULATE;
 100                                         break;
 101                                 case LOOP_CALCULATE:
 102                                         iFirst = iLast;
 103                                         nPer = aWidth  + 1; // for now - one big chunk
 104                                         iLast = Math.min(iLast + nPer, aWidth);
 105                                         if (iLast == iFirst) {
 106                                                 state = DONE;
 107                                         } else {
 108                                                 computeConsensus();
 109                                                 if (sleepAndReturn(0, state))
 110                                                         return;
 111                                         }
 112                                         break;
 113                                 case DONE:
 114                       updateResultAnnotation(true);
 115                                         return;
 116                                 }
 117                         } catch (OutOfMemoryError error) {
 118                                 calcMan.workerCannotRun(this);
 119               ap.raiseOOMWarning("calculating conservation", error);
 120                         } catch (Throwable e) {
 121                                 System.out.println("Error in ConsensusThread: " + e);
 122                                 e.printStackTrace();
 123                                 calcMan.workerComplete(this);
 124                         }
 125                 }
 126         }
 127
 128         private void computeConsensus() {
 129     cons = Conservation.calculateConservation("All",
 130         ResidueProperties.propHash, 3,
 131         alignment.getSequences(), 0, aWidth - 1, false,
 132         ConsPercGaps, quality != null);
 133         }
 134
 135
 136   private void updateResultAnnotation(boolean b)
 137   {
 138     if (b || !calcMan.isWorking(this) && cons != null
 139             && conservation != null && quality != null)
 140     {
 141       alignViewport.setConservation(cons);
 142       cons.completeAnnotations(conservation, quality, 0, aWidth);
 143     }
 144   }
 145
 146   @Override
 147   public void updateAnnotation()
 148   {
 149     updateResultAnnotation(false);
 150
 151   }
 152
 153 }