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   @Override
  16   protected void finalize() throws Throwable {
  17     viewport = null;
  18     alignPanel = null;
  19   };
  20
  21   public AlignViewController(AlignViewportI viewport,
  22           AlignmentViewPanel alignPanel)
  23   {
  24     this.viewport=viewport;
  25     this.alignPanel = alignPanel;
  26   }
  27   @Override
  28   public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
  29   {
  30     this.alignPanel = alignPanel;
  31     this.viewport = viewport;
  32
  33   }
  34   @Override
  35   public boolean makeGroupsFromSelection()
  36   {
  37
  38     if (viewport.getSelectionGroup() != null)
  39     {
  40       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
  41               viewport.getSequenceSelection(),
  42               viewport.getAlignmentView(true).getSequenceStrings(
  43                       viewport.getGapCharacter()), viewport.getAlignment()
  44                       .getGroups());
  45       viewport.getAlignment().deleteAllGroups();
  46       viewport.clearSequenceColours();
  47       viewport.setSelectionGroup(null);
  48       // set view properties for each group
  49       for (int g = 0; g < gps.length; g++)
  50       {
  51         // gps[g].setShowunconserved(viewport.getShowUnconserved());
  52         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
  53         viewport.getAlignment().addGroup(gps[g]);
  54         Color col = new Color((int) (Math.random() * 255),
  55                 (int) (Math.random() * 255), (int) (Math.random() * 255));
  56         col = col.brighter();
  57         for (SequenceI sq : gps[g].getSequences(null))
  58           viewport.setSequenceColour(sq, col);
  59       }
  60       return true;
  61     }
  62     return false;
  63 }
  64   @Override
  65   public boolean createGroup()
  66   {
  67
  68     SequenceGroup sg = viewport.getSelectionGroup();
  69     if (sg!=null)
  70     {
  71         viewport.getAlignment().addGroup(sg);
  72         return true;
  73       }
  74     return false;
  75   }
  76   @Override
  77   public boolean unGroup()
  78   {
  79     SequenceGroup sg = viewport.getSelectionGroup();
  80     if (sg!=null)
  81     {
  82         viewport.getAlignment().deleteGroup(sg);
  83         return true;
  84     }
  85     return false;
  86   }
  87   @Override
  88   public boolean deleteGroups()
  89   {
  90     if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
  91     {
  92     viewport.getAlignment().deleteAllGroups();
  93     viewport.clearSequenceColours();
  94     viewport.setSelectionGroup(null);
  95     return true;
  96     }
  97     return false;
  98   }
  99
 100   }