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Viewing changes to src/figtree/flutree/FluTreeApplet.java

  • Committer: Bazaar Package Importer
  • Author(s): Andreas Tille
  • Date: 2011-02-21 08:17:38 UTC
  • Revision ID: james.westby@ubuntu.com-20110221081738-80pe2ulo8rg7up10
Tags: upstream-1.3.1
Import upstream version 1.3.1

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src/figtree/flutree/FluTreeApplet.java
 
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package figtree.flutree;
 
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import jebl.evolution.trees.Tree;
 
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import jebl.evolution.io.NewickImporter;
 
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import jebl.evolution.io.ImportException;
 
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import jam.controlpalettes.ControlPalette;
 
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import jam.panels.SearchPanel;
 
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import jam.panels.SearchPanelListener;
 
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import jam.panels.StatusBar;
 
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import figtree.application.FigTreeNexusImporter;
 
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import figtree.treeviewer.*;
 
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import figtree.panel.SimpleTreeViewer;
 
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import figtree.panel.FigTreePanel;
 
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import figtree.panel.SimpleControlPalette;
 
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import javax.swing.*;
 
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import java.awt.*;
 
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import java.io.*;
 
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import java.util.*;
 
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import java.net.URL;
 
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import java.net.MalformedURLException;
 
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/**
 
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 * @author Andrew Rambaut
 
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 * @author Alexei Drummond
 
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 * @version $Id: FigTreeApplet.java,v 1.1 2007/08/14 15:50:41 rambaut Exp $
 
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 */
 
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public class FluTreeApplet extends JApplet {
 
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    private ControlPalette controlPalette1;
 
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    private ControlPalette controlPalette2;
 
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    private FigTreePanel figTreePanel;
 
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    private StatusBar statusBar;
 
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    private SearchPanel filterPanel;
 
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    private JPopupMenu filterPopup;
 
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    private TreeViewer treeViewer;
 
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    public void init() {
 
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        FigTreePanel.Style style = FigTreePanel.Style.DEFAULT;
 
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        String styleParam = getParameter("style");
 
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        if (styleParam != null) {
 
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            style = FigTreePanel.Style.valueOf(styleParam.trim().toUpperCase());
 
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        }
 
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        treeViewer = new MultiPaneTreeViewer();
 
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        controlPalette1 = new SimpleControlPalette();
 
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        controlPalette2 = new SimpleControlPalette();
 
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        figTreePanel = new FigTreePanel(treeViewer, controlPalette1, controlPalette2, style);
 
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        filterPopup = new JPopupMenu();
 
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        for (TreeViewer.TextSearchType searchType : TreeViewer.TextSearchType.values()) {
 
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            filterPopup.add(searchType.toString());
 
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        }
 
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        filterPanel = new SearchPanel("Filter", filterPopup, true);
 
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        filterPanel.setOpaque(false);
 
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        filterPanel.addSearchPanelListener(new SearchPanelListener() {
 
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            /**
 
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             * Called when the user requests a search by pressing return having
 
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             * typed a search string into the text field. If the continuousUpdate
 
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             * flag is true then this method is called when the user types into
 
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             * the text field.
 
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             *
 
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             * @param searchString the user's search string
 
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             */
 
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            public void searchStarted(String searchString) {
 
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                int index = filterPopup.getSelectionModel().getSelectedIndex();
 
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                if (index == -1) index = 0;
 
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                TreeViewer.TextSearchType searchType = TreeViewer.TextSearchType.values()[index];
 
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                treeViewer.selectTaxa("!name", searchType, searchString, false);
 
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            }
 
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            /**
 
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             * Called when the user presses the cancel search button or presses
 
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             * escape while the search is in focus.
 
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             */
 
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            public void searchStopped() {
 
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                treeViewer.clearSelectedTaxa();
 
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            }
 
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        });
 
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//              statusBar = new StatusBar("");
 
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//              statusBar.setStatusProvider(treeViewer);
 
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//              statusBar.add(filterPanel, BorderLayout.EAST);
 
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//              if (style != FigTreePanel.Style.ICARUS_SMALL) {
 
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//                      getContentPane().add(statusBar, BorderLayout.NORTH);
 
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//              }
 
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        getContentPane().add(figTreePanel, BorderLayout.CENTER);
 
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    }
 
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    public void start() {
 
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        String tree = getParameter("tree");
 
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        String treefile = getParameter("treefile");
 
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        if (tree != null && tree.length() > 0) {
 
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            URL fileURL = null;
 
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            try {
 
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                fileURL = new URL(tree);
 
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                BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(fileURL.openStream()));
 
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                readData(bufferedReader, true);
 
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            } catch (MalformedURLException e) {
 
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//                              treeViewer.setStatusText(e.getMessage());
 
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            } catch (IOException e) {
 
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//                              treeViewer.setStatusText(e.getMessage());
 
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            }
 
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        } else if (treefile != null && treefile.length() > 0) {
 
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            try {
 
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                BufferedReader bufferedReader = new BufferedReader(new StringReader(treefile));
 
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                readData(bufferedReader, true);
 
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            } catch (IOException e) {
 
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//                              treeViewer.setStatusText(e.getMessage());
 
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            }
 
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        } else {
 
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//                      treeViewer.setStatusText("Tree not specified");
 
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        }
 
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    }
 
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    public void stop() {
 
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    }
 
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    protected boolean readData(Reader reader, boolean isNexus) throws IOException {
 
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        java.util.List<Tree> trees = new ArrayList<Tree>();
 
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        try {
 
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            Map<String, Object> settings = new HashMap<String, Object>();
 
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            // First of all, fully populate the settings map so that
 
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            // all the settings have defaults
 
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            controlPalette1.getSettings(settings);
 
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            controlPalette2.getSettings(settings);
 
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            if (isNexus) {
 
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                FigTreeNexusImporter importer = new FigTreeNexusImporter(reader);
 
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                while (importer.hasTree()) {
 
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                    Tree tree = importer.importNextTree();
 
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                    trees.add(tree);
 
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                }
 
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                // Try to find a figtree block and if found, parse the settings
 
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                while (true) {
 
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                    try {
 
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                        importer.findNextBlock();
 
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                        if (importer.getNextBlockName().equalsIgnoreCase("FIGTREE")) {
 
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                            importer.parseFigTreeBlock(settings);
 
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                        }
 
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                    } catch (EOFException ex) {
 
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                        break;
 
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                    }
 
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                }
 
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            } else {
 
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                NewickImporter importer = new NewickImporter(reader, true);
 
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                while (importer.hasTree()) {
 
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                    Tree tree = importer.importNextTree();
 
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                    trees.add(tree);
 
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                }
 
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            }
 
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            if (trees.size() == 0) {
 
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                throw new ImportException("This file contained no trees.");
 
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            }
 
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            treeViewer.setTrees(trees);
 
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            controlPalette1.setSettings(settings);
 
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            controlPalette2.setSettings(settings);
 
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        } catch (ImportException ie) {
 
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            JOptionPane.showMessageDialog(this, "Error reading tree file: " + ie,
 
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                    "Import Error",
 
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                    JOptionPane.ERROR_MESSAGE);
 
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            return false;
 
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        }
 
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        return true;
 
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    }
 
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}
 
 
b'\\ No newline at end of file'