import jalview.ext.treeviewer.ExternalTreeBuilderI;
import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Dimension;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.util.Map;
+import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.archaeopteryx.Configuration;
import org.forester.archaeopteryx.MainFrame;
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebserviceUtil;
+import org.forester.archaeopteryx.webservices.WebservicesManager;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.tol.TolParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Identifier;
+import org.forester.util.ForesterUtil;
/**
* Static class for creating Archaeopteryx tree viewer instances from calculated
*/
public final class AptxInit
{
+
+ private final static Configuration APTX_CONFIG = new Configuration(
+ "_aptx_jalview_configuration_file", false, false, false);
+
+ private final static boolean VALIDATE_PHYLOXML_XSD = APTX_CONFIG
+ .isValidatePhyloXmlAgainstSchema();
+
+ private final static boolean REPLACE_NHX_UNDERSCORES = APTX_CONFIG
+ .isReplaceUnderscoresInNhParsing();
+
+ private final static boolean INTERNAL_NUMBERS_AS_CONFIDENCE = APTX_CONFIG
+ .isInternalNumberAreConfidenceForNhParsing();
+
+ private final static boolean MIDPOINT_REROOT = APTX_CONFIG
+ .isMidpointReroot();
+
+ private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
+ .getTaxonomyExtraction();
+
+
+
+ public static MainFrame createInstanceFromCalculation(
+ final TreeBuilder calculatedTree)
+ {
+ ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
+ calculatedTree);
+
+ Phylogeny aptxTree = aptxTreeBuilder.buildTree();
+
+ MainFrame aptxApp = createAptxFrame(aptxTree,
+ calculatedTree.getAvport(), null);
+
+ return aptxApp;
+ }
+
/**
- * Test method, should generally not be used as it does not bind the tree to
- * its alignment
+ * Refactored from Archaeopteryx.main
*
- * @param aptxTrees
+ * @param filePath
+ * @param viewport
* @return
+ * @throws IOException
+ * @throws FileNotFoundException
*/
- public static MainFrame createUnboundInstance(final Phylogeny aptxTree)
+ public static MainFrame[] createInstancesFromFile(String filePath,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException
{
- Phylogeny[] aptxTrees = { aptxTree };
- return createAptxFrame(aptxTrees);
- }
+ File treeFile = new File(filePath);
+ final String err = ForesterUtil.isReadableFile(treeFile);
+ if (!ForesterUtil.isEmpty(err))
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, err,
+ MessageManager.getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(filePath);
+ }
+ boolean nhx_or_nexus = false;
+ final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType(
+ treeFile, VALIDATE_PHYLOXML_XSD);
+ if (parser instanceof NHXParser)
+ {
+ nhx_or_nexus = true;
+ final NHXParser nhx = (NHXParser) parser;
+ nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+ nhx.setIgnoreQuotes(false);
+ nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
+ }
+ else if (parser instanceof NexusPhylogeniesParser)
+ {
+ nhx_or_nexus = true;
+ final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) parser;
+ nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+ nex.setIgnoreQuotes(false);
+ }
+// else if (p instanceof PhyloXmlParser)
+// {
+// MainFrameApplication.warnIfNotPhyloXmlValidation(APTX_CONFIG);
+// }
+ Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser, treeFile);
+ MainFrame[] aptxFrames = new MainFrame[trees.length];
+ String treeTitle = treeFile.getName();
+
+ for (int i = 0; i < trees.length; i++)
+ {
+ Phylogeny tree = trees[i];
+
+ if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
+ {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, "");
+ }
+ aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
+
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+ return aptxFrames;
+ }
- // public static MainFrame createInstance(final Phylogeny[] aptxTrees,
- // AlignmentViewport jalviewAlignmentView)
- // {
- // return createAptxFrameInJalview(aptxTrees);
- //
- // }
- //
- // public static MainFrame createInstance(final Phylogeny aptxTree,
- // final AlignmentViewport jalviewAlignmentView)
- // {
- // Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
- // // several trees simultaneously
- // return createAptxFrameInJalview(aptxTrees);
- //
- // }
- public static MainFrame createInstance(
- final TreeBuilder calculatedTree) // very dense method, to be split up
+ public static MainFrame[] createInstancesFromUrl(URL treeUrl,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException, RuntimeException
{
- ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
- calculatedTree);
+
+ String treeTitle = treeUrl.getFile();
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(treeTitle);
+ }
+ Phylogeny[] trees = AptxUtil.readPhylogeniesFromUrl(treeUrl,
+ VALIDATE_PHYLOXML_XSD,
+ REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
+ TAXONOMY_EXTRACTION, MIDPOINT_REROOT);
- Phylogeny aptxTree = aptxTreeBuilder.buildTree();
- Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
- // several trees simultaneously
+ MainFrame[] aptxFrames = new MainFrame[trees.length];
+ for (int i = 0; i < trees.length; i++)
+ {
+ Phylogeny tree = trees[i];
+ aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
+ }
- MainFrame aptxApp = createAptxFrame(aptxTrees);
-
- bindNodesToJalviewSequences(aptxApp, calculatedTree.getAvport(),
- aptxTreeBuilder.getAlignmentBoundNodes(),
- aptxTreeBuilder.getNodesBoundAlignment());
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
- return bindFrameToJalview(aptxApp);
+ return aptxFrames;
}
- public static MainFrame createInstanceFromFile(String filePath,
+ /**
+ * Refactored from Forester's UrlTreeReader, this can be more efficient
+ *
+ * @param databaseIndex
+ * @param viewport
+ * @return
+ */
+ public static MainFrame[] createInstancesFromDb(int databaseIndex,
AlignmentViewport viewport)
{
- String[] AptxArgs = new String[] { "-c",
- "_aptx_jalview_configuration_file", filePath };
- MainFrame aptxApp = Archaeopteryx.main(AptxArgs);
- LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
- viewport.getAlignment().getSequencesArray(),
- aptxApp.getMainPanel().getCurrentTreePanel().getPhylogeny());
+ URL url = null;
+ Phylogeny[] trees = null;
+ final WebservicesManager webservices_manager = WebservicesManager
+ .getInstance();
+ final PhylogeniesWebserviceClient client = webservices_manager
+ .getAvailablePhylogeniesWebserviceClient(databaseIndex);
+ String identifier = JvOptionPane.showInternalInputDialog(
+ Desktop.desktop,
+ client.getInstructions() + "\n(Reference: "
+ + client.getReference() + ")",
+ client.getDescription(), JvOptionPane.QUESTION_MESSAGE);
- bindAptxNodes.associateLeavesToSequences();
+ if ((identifier != null) && (identifier.trim().length() > 0))
+ {
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(identifier);
+ }
+
+ identifier = identifier.trim();
+ if (client.isQueryInteger())
+ {
+ identifier = identifier.replaceAll("^\\D+", "");
+
+ int id;
+ try
+ {
+ id = Integer.parseInt(identifier);
+ } catch (final NumberFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Identifier is expected to be a number",
+ "Can not open URL", JvOptionPane.ERROR_MESSAGE);
+ return new MainFrame[0];
+ }
+ identifier = id + "";
+ }
+ boolean exception = false;
+ try
+ {
+ String url_str = client.getUrl();
+ url_str = url_str.replaceFirst(
+ PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier);
+ url = new URL(url_str);
+ PhylogenyParser parser = null;
+ switch (client.getReturnFormat())
+ {
+ case TOL_XML_RESPONSE:
+ parser = new TolParser();
+ break;
+ case NEXUS:
+ parser = new NexusPhylogeniesParser();
+ ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+ break;
+ case TREEBASE_TREE:
+ parser = new NexusPhylogeniesParser();
+ ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+ ((NexusPhylogeniesParser) parser)
+ .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+ break;
+ case TREEBASE_STUDY:
+ parser = new NexusPhylogeniesParser();
+ ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+ ((NexusPhylogeniesParser) parser)
+ .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+ break;
+ case NH:
+ parser = new NHXParser();
+ ((NHXParser) parser)
+ .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+ ((NHXParser) parser).setReplaceUnderscores(true);
+ ((NHXParser) parser).setGuessRootedness(true);
+ break;
+ case NH_EXTRACT_TAXONOMY:
+ parser = new NHXParser();
+ ((NHXParser) parser).setTaxonomyExtraction(
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE);
+ ((NHXParser) parser).setReplaceUnderscores(false);
+ ((NHXParser) parser).setGuessRootedness(true);
+ break;
+ case PFAM:
+ parser = new NHXParser();
+ ((NHXParser) parser).setTaxonomyExtraction(
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT);
+ ((NHXParser) parser).setReplaceUnderscores(false);
+ ((NHXParser) parser).setGuessRootedness(true);
+ break;
+ case NHX:
+ parser = new NHXParser();
+ ((NHXParser) parser)
+ .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+ ((NHXParser) parser).setReplaceUnderscores(false);
+ ((NHXParser) parser).setGuessRootedness(true);
+ break;
+ case PHYLOXML:
+ parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
+ break;
+ default:
+ throw new IllegalArgumentException(
+ "unknown format: " + client.getReturnFormat());
+ }
+ //
+ // if (_main_frame.getMainPanel().getCurrentTreePanel() != null)
+ // {
+ // _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
+ // }
+ // else
+ // {
+ // _main_frame.getMainPanel().setWaitCursor();
+ // }
+ trees = ForesterUtil.readPhylogeniesFromUrl(url, parser);
+ } catch (final MalformedURLException e)
+ {
+ exception = true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
+ "Malformed URL", JvOptionPane.ERROR_MESSAGE);
+ } catch (final IOException e)
+ {
+ exception = true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Could not read from " + url + "\n"
+ + e.getLocalizedMessage(),
+ "Failed to read tree from " + client.getName() + " for "
+ + identifier,
+ JvOptionPane.ERROR_MESSAGE);
+ } catch (final NumberFormatException e)
+ {
+ exception = true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Could not read from " + url + "\n"
+ + e.getLocalizedMessage(),
+ "Failed to read tree from " + client.getName() + " for "
+ + identifier,
+ JvOptionPane.ERROR_MESSAGE);
+ } catch (final Exception e)
+ {
+ exception = true;
+ e.printStackTrace();
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ e.getLocalizedMessage(), "Unexpected Exception",
+ JvOptionPane.ERROR_MESSAGE);
+ } finally
+ {
+ // if (_main_frame.getCurrentTreePanel() != null)
+ // {
+ // _main_frame.getCurrentTreePanel().setArrowCursor();
+ // }
+ // else
+ // {
+ // _main_frame.getMainPanel().setArrowCursor();
+ // }
+ }
+ if ((trees != null) && (trees.length > 0))
+ {
+ for (final Phylogeny phylogeny : trees)
+ {
+ if (!phylogeny.isEmpty())
+ {
+ if (client.getName().equals(WebserviceUtil.TREE_FAM_NAME))
+ {
+ phylogeny.setRerootable(false);
+ phylogeny.setRooted(true);
+ }
+ if (client.getProcessingInstructions() != null)
+ {
+ try
+ {
+ WebserviceUtil.processInstructions(client, phylogeny);
+ } catch (final PhyloXmlDataFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error:\n" + e.getLocalizedMessage(), "Error",
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ if (client.getNodeField() != null)
+ {
+ try
+ {
+ PhylogenyMethods.transferNodeNameToField(phylogeny,
+ client.getNodeField(), false);
+ } catch (final PhyloXmlDataFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error:\n" + e.getLocalizedMessage(), "Error",
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ phylogeny.setIdentifier(
+ new Identifier(identifier, client.getName()));
+ // _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
+ // _main_frame.getMenuBarOfMainFrame()
+ // .add(_main_frame.getHelpMenu());
+ // _main_frame.getMainPanel().addPhylogenyInNewTab(phylogeny,
+ // _main_frame.getConfiguration(),
+ // new File(url.getFile()).getName(), url.toString());
+
+ MainFrame aptxApp = createAptxFrame(phylogeny, viewport,
+ url.getFile());
+ String my_name_for_file = "";
+ if (!ForesterUtil.isEmpty(phylogeny.getName()))
+ {
+ my_name_for_file = new String(phylogeny.getName())
+ .replaceAll(" ", "_");
+ }
+ else if (phylogeny.getIdentifier() != null)
+ {
+ final StringBuffer sb = new StringBuffer();
+ if (!ForesterUtil
+ .isEmpty(phylogeny.getIdentifier().getProvider()))
+ {
+ sb.append(phylogeny.getIdentifier().getProvider());
+ sb.append("_");
+ }
+ sb.append(phylogeny.getIdentifier().getValue());
+ my_name_for_file = new String(
+ sb.toString().replaceAll(" ", "_"));
+ }
+ // _main_frame.getMainPanel().getCurrentTreePanel()
+ // .setTreeFile(new File(my_name_for_file));
+ AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
+ phylogeny, aptxApp.getMainPanel().getControlPanel(),
+ APTX_CONFIG);
+ // _main_frame.getMainPanel().getControlPanel().showWhole();
+
+ aptxApp.activateSaveAllIfNeeded();
+ }
+ }
+ }
+ else if (!exception)
+ {
+ JvOptionPane.showMessageDialog(null,
+ ForesterUtil.wordWrap(
+ "Failed to read in tree(s) from [" + url + "]", 80),
+ "Error", JvOptionPane.ERROR_MESSAGE);
+ }
+ if ((trees != null) && (trees.length > 0))
+ {
+ try
+ {
+ JvOptionPane.showMessageDialog(null,
+ ForesterUtil.wordWrap("Successfully read in "
+ + trees.length + " tree(s) from [" + url + "]",
+ 80),
+ "Success", JvOptionPane.INFORMATION_MESSAGE);
+ } catch (final Exception e)
+ {
+ // Not important if this fails, do nothing.
+ }
+ // _main_frame.getContentPane().repaint();
+ }
+ }
+
+ System.gc();
+
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+ return null;
- bindNodesToJalviewSequences(aptxApp, viewport,
- bindAptxNodes.getAlignmentWithNodes(),
- bindAptxNodes.getNodesWithAlignment());
- return bindFrameToJalview(aptxApp);
}
+
+
public static MainFrame createAptxFrame(
- final Phylogeny[] aptxTrees)
+ final Phylogeny aptxTree,
+ final AlignmentViewport jalviewAlignport, String treeTitle)
{
- MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
- "_aptx_jalview_configuration_file", null);
+ MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree,
+ APTX_CONFIG, treeTitle);
+
+ LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
+ bindAptxNodes.associateLeavesToSequences();
+
+ bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
+ bindAptxNodes.getAlignmentWithNodes(),
+ bindAptxNodes.getNodesWithAlignment());
+ bindTreeViewFrameToJalview(aptxApp);
+
return aptxApp;
}
+ // private static void addPartitioningSlider(MainFrame aptxFrame)
+ // {
+ // JSlider slider = new JSlider();
+ //
+ //
+ // }
public static ExternalTreeViewerBindingI<?> bindNodesToJalviewSequences(
final MainFrame aptxApp,
}
- public static MainFrame bindFrameToJalview(final MainFrame aptxApp)
+ public static MainFrame bindTreeViewFrameToJalview(
+ final MainFrame aptxApp)
{
int width = 400;
int height = 550;
}
+
}
git://source.jalview.org / jalview.git / blobdiff