src/jalview/controller/AlignViewController.java

   1 package jalview.controller;
   2
   3 import java.awt.Color;
   4 import java.util.BitSet;
   5 import java.util.List;
   6
   7 import jalview.api.AlignViewControllerGuiI;
   8 import jalview.api.AlignViewControllerI;
   9 import jalview.api.AlignViewportI;
  10 import jalview.api.AlignmentViewPanel;
  11 import jalview.datamodel.ColumnSelection;
  12 import jalview.datamodel.SequenceFeature;
  13 import jalview.datamodel.SequenceGroup;
  14 import jalview.datamodel.SequenceI;
  15
  16 public class AlignViewController implements AlignViewControllerI
  17 {
  18   AlignViewportI viewport=null;
  19   AlignmentViewPanel alignPanel=null;
  20   /**
  21    * the GUI container that is handling interactions with the user
  22    */
  23   private AlignViewControllerGuiI avcg;
  24   @Override
  25   protected void finalize() throws Throwable {
  26     viewport = null;
  27     alignPanel = null;
  28     avcg = null;
  29   };
  30
  31   public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
  32           AlignmentViewPanel alignPanel)
  33   {
  34     this.avcg = alignFrame;
  35     this.viewport=viewport;
  36     this.alignPanel = alignPanel;
  37   }
  38   @Override
  39   public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
  40   {
  41     this.alignPanel = alignPanel;
  42     this.viewport = viewport;
  43
  44   }
  45   @Override
  46   public boolean makeGroupsFromSelection()
  47   {
  48
  49     if (viewport.getSelectionGroup() != null)
  50     {
  51       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
  52               viewport.getSequenceSelection(),
  53               viewport.getAlignmentView(true).getSequenceStrings(
  54                       viewport.getGapCharacter()), viewport.getAlignment()
  55                       .getGroups());
  56       viewport.getAlignment().deleteAllGroups();
  57       viewport.clearSequenceColours();
  58       viewport.setSelectionGroup(null);
  59       // set view properties for each group
  60       for (int g = 0; g < gps.length; g++)
  61       {
  62         // gps[g].setShowunconserved(viewport.getShowUnconserved());
  63         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
  64         viewport.getAlignment().addGroup(gps[g]);
  65         Color col = new Color((int) (Math.random() * 255),
  66                 (int) (Math.random() * 255), (int) (Math.random() * 255));
  67         col = col.brighter();
  68         for (SequenceI sq : gps[g].getSequences(null))
  69           viewport.setSequenceColour(sq, col);
  70       }
  71       return true;
  72     }
  73     return false;
  74 }
  75   @Override
  76   public boolean createGroup()
  77   {
  78
  79     SequenceGroup sg = viewport.getSelectionGroup();
  80     if (sg!=null)
  81     {
  82         viewport.getAlignment().addGroup(sg);
  83         return true;
  84       }
  85     return false;
  86   }
  87   @Override
  88   public boolean unGroup()
  89   {
  90     SequenceGroup sg = viewport.getSelectionGroup();
  91     if (sg!=null)
  92     {
  93         viewport.getAlignment().deleteGroup(sg);
  94         return true;
  95     }
  96     return false;
  97   }
  98   @Override
  99   public boolean deleteGroups()
 100   {
 101     if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
 102     {
 103     viewport.getAlignment().deleteAllGroups();
 104     viewport.clearSequenceColours();
 105     viewport.setSelectionGroup(null);
 106     return true;
 107     }
 108     return false;
 109   }
 110
 111   @Override
 112   public boolean markColumnsContainingFeatures(boolean invert,
 113           String featureType)
 114   {
 115     // JBPNote this routine could also mark rows, not just columns.
 116     // need a decent query structure to allow all types of feature searches
 117     BitSet bs = new BitSet();
 118     List<SequenceI> seqs = viewport.getAlignment().getSequences();
 119     int alw = viewport.getAlignment().getWidth();
 120     int nseq = 0;
 121     for (SequenceI sq : seqs)
 122     {
 123       int tfeat = 0;
 124       if (sq != null)
 125       {
 126         SequenceI dsq = sq.getDatasetSequence();
 127         while (dsq.getDatasetSequence() != null)
 128         {
 129           dsq = dsq.getDatasetSequence();
 130         }
 131         ;
 132         SequenceFeature[] sf = dsq.getSequenceFeatures();
 133         if (sf != null)
 134         {
 135           for (SequenceFeature sfpos : sf)
 136           {
 137             // future functionalty - featureType == null means mark columns
 138             // containing all displayed features
 139             if (sfpos != null && (featureType.equals(sfpos.getType())))
 140             {
 141               tfeat++;
 142               // optimisation - could consider 'spos,apos' like cursor argument
 143               // - findIndex wastes time by starting from first character and
 144               // counting
 145
 146               int i = sq.findIndex(sfpos.getBegin());
 147               int ist = sq.findIndex(sq.getStart());
 148               if (i < ist)
 149               {
 150                 i = ist;
 151               }
 152               int j = sq.findIndex(sfpos.getEnd());
 153               if (j > alw)
 154               {
 155                 j = alw;
 156               }
 157               for (; i <= j; i++)
 158               {
 159                 bs.set(i - 1);
 160               }
 161             }
 162           }
 163         }
 164
 165         if (tfeat > 0)
 166         {
 167           nseq++;
 168         }
 169       }
 170     }
 171     if (bs.cardinality() > 0 || invert)
 172     {
 173       ColumnSelection cs = viewport.getColumnSelection();
 174       if (cs == null)
 175       {
 176         cs = new ColumnSelection();
 177       }
 178       if (invert)
 179       {
 180         for (int i = bs.nextClearBit(0), ibs = bs.nextSetBit(0); i >= 0
 181                 && i < alw;)
 182         {
 183           if (ibs < 0 || i < ibs)
 184           {
 185             cs.addElement(i++);
 186           }
 187           else
 188           {
 189             i = bs.nextClearBit(ibs);
 190             ibs = bs.nextSetBit(i);
 191           }
 192         }
 193       }
 194       else
 195       {
 196         for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
 197         {
 198           cs.addElement(i);
 199         }
 200       }
 201       viewport.setColumnSelection(cs);
 202       alignPanel.paintAlignment(true);
 203       avcg.setStatus("Marked "
 204               + (invert ? alw - bs.cardinality() : bs.cardinality())
 205               + " columns containing features of type " + featureType
 206               + " across " + nseq);
 207       return true;
 208     }
 209     else
 210     {
 211       avcg.setStatus("No features of type " + featureType + " found.");
 212       return false;
 213     }
 214   }
 215 }