src/jalview/controller/AlignViewController.java

   1 package jalview.controller;
   2
   3 import java.awt.Color;
   4
   5 import jalview.api.AlignViewControllerI;
   6 import jalview.api.AlignViewportI;
   7 import jalview.api.AlignmentViewPanel;
   8 import jalview.datamodel.SequenceGroup;
   9 import jalview.datamodel.SequenceI;
  10
  11 public class AlignViewController implements AlignViewControllerI
  12 {
  13   AlignViewportI viewport=null;
  14   AlignmentViewPanel alignPanel=null;
  15   /**
  16    * the GUI container that is handling interactions with the user
  17    */
  18   private AlignViewControllerGuiI avcg;
  19   @Override
  20   protected void finalize() throws Throwable {
  21     viewport = null;
  22     alignPanel = null;
  23     avcg = null;
  24   };
  25
  26   public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
  27           AlignmentViewPanel alignPanel)
  28   {
  29     this.avcg = alignFrame;
  30     this.viewport=viewport;
  31     this.alignPanel = alignPanel;
  32   }
  33   @Override
  34   public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
  35   {
  36     this.alignPanel = alignPanel;
  37     this.viewport = viewport;
  38
  39   }
  40   @Override
  41   public boolean makeGroupsFromSelection()
  42   {
  43
  44     if (viewport.getSelectionGroup() != null)
  45     {
  46       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
  47               viewport.getSequenceSelection(),
  48               viewport.getAlignmentView(true).getSequenceStrings(
  49                       viewport.getGapCharacter()), viewport.getAlignment()
  50                       .getGroups());
  51       viewport.getAlignment().deleteAllGroups();
  52       viewport.clearSequenceColours();
  53       viewport.setSelectionGroup(null);
  54       // set view properties for each group
  55       for (int g = 0; g < gps.length; g++)
  56       {
  57         // gps[g].setShowunconserved(viewport.getShowUnconserved());
  58         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
  59         viewport.getAlignment().addGroup(gps[g]);
  60         Color col = new Color((int) (Math.random() * 255),
  61                 (int) (Math.random() * 255), (int) (Math.random() * 255));
  62         col = col.brighter();
  63         for (SequenceI sq : gps[g].getSequences(null))
  64           viewport.setSequenceColour(sq, col);
  65       }
  66       return true;
  67     }
  68     return false;
  69 }
  70   @Override
  71   public boolean createGroup()
  72   {
  73
  74     SequenceGroup sg = viewport.getSelectionGroup();
  75     if (sg!=null)
  76     {
  77         viewport.getAlignment().addGroup(sg);
  78         return true;
  79       }
  80     return false;
  81   }
  82   @Override
  83   public boolean unGroup()
  84   {
  85     SequenceGroup sg = viewport.getSelectionGroup();
  86     if (sg!=null)
  87     {
  88         viewport.getAlignment().deleteGroup(sg);
  89         return true;
  90     }
  91     return false;
  92   }
  93   @Override
  94   public boolean deleteGroups()
  95   {
  96     if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
  97     {
  98     viewport.getAlignment().deleteAllGroups();
  99     viewport.clearSequenceColours();
 100     viewport.setSelectionGroup(null);
 101     return true;
 102     }
 103     return false;
 104   }
 105
 106   }