src/jalview/ext/forester/io/ForesterTreeParser.java

   1 package jalview.ext.forester.io;
   2
   3 import jalview.ext.archaeopteryx.AptxBinding;
   4 import jalview.ext.archaeopteryx.AptxNodeAssociation;
   5 import jalview.ext.archaeopteryx.ArchaeopteryxInit;
   6 import jalview.gui.Desktop;
   7 import jalview.gui.JvOptionPane;
   8 import jalview.util.MessageManager;
   9 import jalview.viewmodel.AlignmentViewport;
  10
  11 import java.io.File;
  12 import java.io.IOException;
  13
  14 import org.forester.archaeopteryx.Archaeopteryx;
  15 import org.forester.archaeopteryx.MainFrame;
  16 import org.forester.util.ForesterUtil;
  17
  18 public class ForesterTreeParser implements ExternalTreeParserI<MainFrame>
  19 {
  20   private final String filePath;
  21
  22   private final File file;
  23
  24   public ForesterTreeParser(final String treeFilePath)
  25   {
  26     final String possibleError = ForesterUtil.isReadableFile(treeFilePath);
  27     if (possibleError != null)
  28     {
  29       JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
  30               MessageManager.getString("label.problem_reading_tree_file"),
  31               JvOptionPane.WARNING_MESSAGE);
  32
  33     }
  34     filePath = treeFilePath;
  35     file = new File(filePath);
  36
  37
  38   }
  39
  40   public ForesterTreeParser(final File treeFile) throws IOException
  41   {
  42     final String possibleError = ForesterUtil.isReadableFile(treeFile);
  43     if (possibleError != null)
  44     {
  45       JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
  46               MessageManager.getString("label.problem_reading_tree_file"),
  47               JvOptionPane.WARNING_MESSAGE);
  48
  49     }
  50     file = treeFile;
  51     filePath = file.getCanonicalPath();
  52   }
  53
  54   @Override
  55   public MainFrame loadTree(AlignmentViewport viewport)
  56   {
  57     String[] AptxArgs = new String[] { "-c",
  58         "_aptx_jalview_configuration_file", filePath };
  59     MainFrame aptx = Archaeopteryx.main(AptxArgs);
  60
  61     AptxNodeAssociation bindAptxNodes = new AptxNodeAssociation(
  62             viewport.getAlignment().getSequencesArray(),
  63             aptx.getMainPanel().getCurrentTreePanel().getPhylogeny());
  64
  65     bindAptxNodes.associateLeavesToSequences();
  66     new AptxBinding(aptx, viewport, bindAptxNodes.getAlignmentWithNodes(),
  67             bindAptxNodes.getNodesWithAlignment());
  68
  69     ArchaeopteryxInit.bindFrameToJalview(aptx);
  70
  71     return aptx;
  72
  73
  74   }
  75
  76 }
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