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.AlignmentI;
  12 import jalview.datamodel.AnnotatedCollectionI;
  13 import jalview.datamodel.ColumnSelection;
  14 import jalview.datamodel.SequenceCollectionI;
  15 import jalview.datamodel.SequenceFeature;
  16 import jalview.datamodel.SequenceGroup;
  17 import jalview.datamodel.SequenceI;
  18
  19 public class AlignViewController implements AlignViewControllerI
  20 {
  21   AlignViewportI viewport=null;
  22   AlignmentViewPanel alignPanel=null;
  23   /**
  24    * the GUI container that is handling interactions with the user
  25    */
  26   private AlignViewControllerGuiI avcg;
  27   @Override
  28   protected void finalize() throws Throwable {
  29     viewport = null;
  30     alignPanel = null;
  31     avcg = null;
  32   };
  33
  34   public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
  35           AlignmentViewPanel alignPanel)
  36   {
  37     this.avcg = alignFrame;
  38     this.viewport=viewport;
  39     this.alignPanel = alignPanel;
  40   }
  41   @Override
  42   public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
  43   {
  44     this.alignPanel = alignPanel;
  45     this.viewport = viewport;
  46
  47   }
  48   @Override
  49   public boolean makeGroupsFromSelection()
  50   {
  51
  52     if (viewport.getSelectionGroup() != null)
  53     {
  54       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
  55               viewport.getSequenceSelection(),
  56               viewport.getAlignmentView(true).getSequenceStrings(
  57                       viewport.getGapCharacter()), viewport.getAlignment()
  58                       .getGroups());
  59       viewport.getAlignment().deleteAllGroups();
  60       viewport.clearSequenceColours();
  61       viewport.setSelectionGroup(null);
  62       // set view properties for each group
  63       for (int g = 0; g < gps.length; g++)
  64       {
  65         // gps[g].setShowunconserved(viewport.getShowUnconserved());
  66         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
  67         viewport.getAlignment().addGroup(gps[g]);
  68         Color col = new Color((int) (Math.random() * 255),
  69                 (int) (Math.random() * 255), (int) (Math.random() * 255));
  70         col = col.brighter();
  71         for (SequenceI sq : gps[g].getSequences(null))
  72           viewport.setSequenceColour(sq, col);
  73       }
  74       return true;
  75     }
  76     return false;
  77 }
  78   @Override
  79   public boolean createGroup()
  80   {
  81
  82     SequenceGroup sg = viewport.getSelectionGroup();
  83     if (sg!=null)
  84     {
  85         viewport.getAlignment().addGroup(sg);
  86         return true;
  87       }
  88     return false;
  89   }
  90   @Override
  91   public boolean unGroup()
  92   {
  93     SequenceGroup sg = viewport.getSelectionGroup();
  94     if (sg!=null)
  95     {
  96         viewport.getAlignment().deleteGroup(sg);
  97         return true;
  98     }
  99     return false;
 100   }
 101   @Override
 102   public boolean deleteGroups()
 103   {
 104     if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
 105     {
 106     viewport.getAlignment().deleteAllGroups();
 107     viewport.clearSequenceColours();
 108     viewport.setSelectionGroup(null);
 109     return true;
 110     }
 111     return false;
 112   }
 113
 114   @Override
 115   public boolean markColumnsContainingFeatures(boolean invert, boolean extendCurrent, boolean toggle, String featureType)
 116   {
 117     // JBPNote this routine could also mark rows, not just columns.
 118     // need a decent query structure to allow all types of feature searches
 119     BitSet bs = new BitSet();
 120     int alw,alStart;
 121     SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport.getAlignment() : viewport.getSelectionGroup());
 122     alStart = sqcol.getStartRes();
 123     alw = sqcol.getEndRes()+1;
 124     List<SequenceI> seqs = sqcol.getSequences();
 125     int nseq = 0;
 126     for (SequenceI sq : seqs)
 127     {
 128       int tfeat = 0;
 129       if (sq != null)
 130       {
 131         SequenceI dsq = sq.getDatasetSequence();
 132         while (dsq.getDatasetSequence() != null)
 133         {
 134           dsq = dsq.getDatasetSequence();
 135         }
 136         ;
 137         SequenceFeature[] sf = dsq.getSequenceFeatures();
 138         if (sf != null)
 139         {
 140           int ist = sq.findIndex(sq.getStart());
 141           int iend = sq.findIndex(sq.getEnd());
 142           if (iend < alStart || ist> alw)
 143           {
 144             // sequence not in region
 145             continue;
 146           }
 147           for (SequenceFeature sfpos : sf)
 148           {
 149             // future functionalty - featureType == null means mark columns
 150             // containing all displayed features
 151             if (sfpos != null && (featureType.equals(sfpos.getType())))
 152             {
 153               tfeat++;
 154               // optimisation - could consider 'spos,apos' like cursor argument
 155               // - findIndex wastes time by starting from first character and
 156               // counting
 157
 158               int i = sq.findIndex(sfpos.getBegin());
 159               int j = sq.findIndex(sfpos.getEnd());
 160               if (j<alStart || i>alw)
 161               {
 162                 // feature is outside selected region
 163                 continue;
 164               }
 165               if (i < alStart)
 166               {
 167                 i = alStart;
 168               }
 169               if (i< ist) {
 170                 i = ist;
 171               }
 172               if (j > alw)
 173               {
 174                 j = alw;
 175               }
 176               for (; i <= j; i++)
 177               {
 178                 bs.set(i - 1);
 179               }
 180             }
 181           }
 182         }
 183
 184         if (tfeat > 0)
 185         {
 186           nseq++;
 187         }
 188       }
 189     }
 190     ColumnSelection cs = viewport.getColumnSelection();
 191     if (bs.cardinality() > 0 || invert)
 192     {
 193       if (cs == null)
 194       {
 195         cs = new ColumnSelection();
 196       } else {
 197         if (!extendCurrent)
 198         {
 199           cs.clear();
 200         }
 201       }
 202       if (invert)
 203       {
 204         // invert only in the currently selected sequence region
 205         for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
 206                 && i < (alw);)
 207         {
 208           if (ibs < 0 || i < ibs)
 209           {
 210             if (toggle && cs.contains(i))
 211               {
 212                 cs.removeElement(i++);
 213               } else
 214               {
 215                 cs.addElement(i++);
 216               }
 217           }
 218           else
 219           {
 220             i = bs.nextClearBit(ibs);
 221             ibs = bs.nextSetBit(i);
 222           }
 223         }
 224       }
 225       else
 226       {
 227         for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs.nextSetBit(i + 1))
 228         {
 229           if (toggle && cs.contains(i))
 230           {
 231             cs.removeElement(i);
 232           } else
 233           {
 234             cs.addElement(i);
 235           }
 236         }
 237       }
 238       viewport.setColumnSelection(cs);
 239       alignPanel.paintAlignment(true);
 240       avcg.setStatus((toggle ? "Toggled ": "Marked ")
 241               + (invert ? (alw-alStart) - bs.cardinality() : bs.cardinality())
 242               + " columns "+(invert ? "not " : "") + "containing features of type " + featureType
 243               + " across " + nseq + " sequence(s)");
 244       return true;
 245     }
 246     else
 247     {
 248       avcg.setStatus("No features of type " + featureType + " found.");
 249       if (!extendCurrent && cs!=null)
 250       {
 251         cs.clear();
 252         alignPanel.paintAlignment(true);
 253       }
 254       return false;
 255     }
 256   }
 257 }