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

   1 package jalview.ext.forester.io;
   2
   3 import jalview.ext.archaeopteryx.JalviewBinding;
   4 import jalview.ext.archaeopteryx.LoadedTreeAssociation;
   5 import jalview.ext.archaeopteryx.ArchaeopteryxInit;
   6 import jalview.ext.treeviewer.ExternalTreeParserI;
   7 import jalview.gui.Desktop;
   8 import jalview.gui.JvOptionPane;
   9 import jalview.util.MessageManager;
  10 import jalview.viewmodel.AlignmentViewport;
  11
  12 import java.io.File;
  13 import java.io.IOException;
  14
  15 import org.forester.archaeopteryx.Archaeopteryx;
  16 import org.forester.archaeopteryx.MainFrame;
  17 import org.forester.util.ForesterUtil;
  18
  19 public class TreeParser implements ExternalTreeParserI<MainFrame>
  20 {
  21   private final String filePath;
  22
  23   private final File file;
  24
  25   public TreeParser(final String treeFilePath)
  26   {
  27     final String possibleError = ForesterUtil.isReadableFile(treeFilePath);
  28     if (possibleError != null)
  29     {
  30       JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
  31               MessageManager.getString("label.problem_reading_tree_file"),
  32               JvOptionPane.WARNING_MESSAGE);
  33
  34     }
  35     filePath = treeFilePath;
  36     file = new File(filePath);
  37
  38
  39   }
  40
  41   public TreeParser(final File treeFile) throws IOException
  42   {
  43     final String possibleError = ForesterUtil.isReadableFile(treeFile);
  44     if (possibleError != null)
  45     {
  46       JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
  47               MessageManager.getString("label.problem_reading_tree_file"),
  48               JvOptionPane.WARNING_MESSAGE);
  49
  50     }
  51     file = treeFile;
  52     filePath = file.getCanonicalPath();
  53   }
  54
  55   @Override
  56   public MainFrame loadTree(AlignmentViewport viewport)
  57   {
  58     String[] AptxArgs = new String[] { "-c",
  59         "_aptx_jalview_configuration_file", filePath };
  60     MainFrame aptx = Archaeopteryx.main(AptxArgs);
  61
  62     LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
  63             viewport.getAlignment().getSequencesArray(),
  64             aptx.getMainPanel().getCurrentTreePanel().getPhylogeny());
  65
  66     bindAptxNodes.associateLeavesToSequences();
  67     new JalviewBinding(aptx, viewport, bindAptxNodes.getAlignmentWithNodes(),
  68             bindAptxNodes.getNodesWithAlignment());
  69
  70     ArchaeopteryxInit.bindFrameToJalview(aptx);
  71
  72     return aptx;
  73
  74
  75   }
  76
  77 }
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