import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Component;
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.HashMap;
import java.util.Map;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JSeparator;
+
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.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;
/**
*/
public final class AptxInit
{
-
private final static Configuration APTX_CONFIG = new Configuration(
- "_aptx_jalview_configuration_file", false, false, false);
+ "_aptx_jalview_configuration_file",
+ false, false, false);
private final static boolean VALIDATE_PHYLOXML_XSD = APTX_CONFIG
.isValidatePhyloXmlAgainstSchema();
private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
.getTaxonomyExtraction();
+ private static Map<MainFrame, JalviewBinding> activeAptx = new HashMap<>();
+
public static MainFrame createInstanceFromCalculation(
- final TreeBuilder calculatedTree) // very dense method, to be split up
+ final TreeBuilder calculatedTree)
{
ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
calculatedTree);
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 p = ParserUtils.createParserDependingOnFileType(
+ final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType(
treeFile, VALIDATE_PHYLOXML_XSD);
- if (p instanceof NHXParser)
+ if (parser instanceof NHXParser)
{
nhx_or_nexus = true;
- final NHXParser nhx = (NHXParser) p;
+ final NHXParser nhx = (NHXParser) parser;
nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
nhx.setIgnoreQuotes(false);
nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
}
- else if (p instanceof NexusPhylogeniesParser)
+ else if (parser instanceof NexusPhylogeniesParser)
{
nhx_or_nexus = true;
- final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) p;
+ final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) parser;
nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
nex.setIgnoreQuotes(false);
}
-// else if (p instanceof PhyloXmlParser)
-// {
-// MainFrameApplication.warnIfNotPhyloXmlValidation(APTX_CONFIG);
-// }
- Phylogeny[] phylogenies = PhylogenyMethods.readPhylogenies(p, treeFile);
- MainFrame[] aptxFrames = new MainFrame[phylogenies.length];
- String treeTitle = treeFile.getName();
+ else if (parser instanceof PhyloXmlParser)
+ {
+ if (VALIDATE_PHYLOXML_XSD == false)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("error.phyloxml_validation"),
+ MessageManager.getString("label.file_open_error"),
+ JvOptionPane.WARNING_MESSAGE );
+ }
+ }
+ Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser, treeFile);
+ MainFrame[] aptxFrames = new MainFrame[trees.length];
+
- for (int i = 0; i < phylogenies.length; i++)
+ for (int i = 0; i < trees.length; i++)
{
- Phylogeny tree = phylogenies[i];
+ Phylogeny tree = trees[i];
if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
{
PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, "");
}
-
+ String treeTitle = treeFile.getName() + "[" + i + "]";
+ tree.setName(treeTitle);
aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
- }
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
return aptxFrames;
}
{
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,
aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
}
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
return aptxFrames;
}
+ /**
+ * Refactored from Forester's UrlTreeReader, this can be more efficient
+ *
+ * @param databaseIndex
+ * @param viewport
+ * @return
+ */
+ public static MainFrame[] createInstancesFromDb(
+ PhylogeniesWebserviceClient treeDbClient, String identifier,
+ AlignmentViewport viewport)
+ {
+
+ URL url = null;
+ Phylogeny[] trees = null;
+
+ if ((identifier != null) && (identifier.trim().length() > 0))
+ {
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(identifier);
+ }
+
+ identifier = identifier.trim();
+ if (treeDbClient.isQueryInteger())
+ {
+ identifier = identifier.replaceAll("^\\D+", "");
+
+ int id;
+ try
+ {
+ id = Integer.parseInt(identifier);
+ } catch (final NumberFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "error.database_id_has_letters", new String[]
+ { identifier }),
+ MessageManager.getString("label.invalid_url"),
+ JvOptionPane.ERROR_MESSAGE);
+ return new MainFrame[0];
+ }
+ identifier = id + "";
+ }
+ boolean exception = false;
+ try
+ {
+ String url_str = treeDbClient.getUrl();
+ url_str = url_str.replaceFirst(
+ PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier);
+ url = new URL(url_str);
+ PhylogenyParser parser = null;
+ switch (treeDbClient.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: " + treeDbClient.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,
+ MessageManager.formatMessage(
+ "exception.unable_to_launch_url", new String[]
+ { url.toString() }),
+ MessageManager.getString("label.invalid_url"),
+ JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
+ } catch (final IOException e)
+ {
+ exception = true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Could not read from " + url + "\n"
+ + e.getLocalizedMessage(),
+ "Failed to read tree from " + treeDbClient.getName() + " for "
+ + identifier,
+ JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
+ } catch (final NumberFormatException e)
+ {
+ exception = true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Could not read from " + url + "\n"
+ + e.getLocalizedMessage(),
+ "Failed to read tree from " + treeDbClient.getName() + " for "
+ + identifier,
+ JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
+ } catch (final Exception e)
+ {
+ exception = true;
+ e.printStackTrace();
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ e.getLocalizedMessage(), "Unexpected Exception",
+ JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
+ }
+ if ((trees != null) && (trees.length > 0))
+ {
+ for (final Phylogeny phylogeny : trees)
+ {
+ if (!phylogeny.isEmpty())
+ {
+ if (treeDbClient.getName().equals(WebserviceUtil.TREE_FAM_NAME))
+ {
+ phylogeny.setRerootable(false);
+ phylogeny.setRooted(true);
+ }
+ if (treeDbClient.getProcessingInstructions() != null)
+ {
+ try
+ {
+ WebserviceUtil.processInstructions(treeDbClient, phylogeny);
+ } catch (final PhyloXmlDataFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error:\n" + e.getLocalizedMessage(), "Error",
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ if (treeDbClient.getNodeField() != null)
+ {
+ try
+ {
+ PhylogenyMethods.transferNodeNameToField(phylogeny,
+ treeDbClient.getNodeField(), false);
+ } catch (final PhyloXmlDataFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error:\n" + e.getLocalizedMessage(), "Error",
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ phylogeny.setIdentifier(
+ new Identifier(identifier, treeDbClient.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(" ", "_"));
+ }
+ aptxApp.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) // ..what?
+ {
+ 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;
+
+
+ }
+
final Phylogeny aptxTree,
final AlignmentViewport jalviewAlignport, String treeTitle)
{
+ if (APTX_CONFIG == null || APTX_CONFIG.isCouldReadConfigFile() == false)
+ {
+ int keepGoing = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ MessageManager.getString("label.aptx_config_not_found"),
+ MessageManager.formatMessage("label.couldnt_locate",
+ new String[]
+ { "_aptx_jalview_configuration_file" }),
+ JvOptionPane.YES_NO_CANCEL_OPTION);
+
+ if (keepGoing == JvOptionPane.CANCEL_OPTION
+ || keepGoing == JvOptionPane.CLOSED_OPTION
+ || keepGoing == JvOptionPane.NO_OPTION)
+ {
+ return null;
+ }
+
+ }
MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree,
APTX_CONFIG, treeTitle);
- LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
- jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
+
+ LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
bindAptxNodes.associateLeavesToSequences();
+
bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
bindAptxNodes.getAlignmentWithNodes(),
bindAptxNodes.getNodesWithAlignment());
- bindFrameToJalview(aptxApp);
+ bindTreeViewFrameToJalview(aptxApp);
+
+ adaptAptxGui(aptxApp);
return aptxApp;
}
final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
{
- return new JalviewBinding(aptxApp, jalviewAlignViewport,
+ JalviewBinding treeBinding = new JalviewBinding(aptxApp,
+ jalviewAlignViewport,
alignMappedToNodes, nodesMappedToAlign);
+ activeAptx.put(aptxApp, treeBinding);
+ return treeBinding;
}
- public static MainFrame bindFrameToJalview(final MainFrame aptxApp)
+ public static MainFrame bindTreeViewFrameToJalview(
+ final MainFrame aptxApp)
{
int width = 400;
int height = 550;
aptxApp.setMinimumSize(new Dimension(width, height));
// aptxApp.setFont(Desktop.instance.getFont());
// aptxApp.getMainPanel().setFont(Desktop.instance.getFont());
+ String frameTitle = MessageManager.getString("label.aptx_title");
+ File treeFile = aptxApp.getMainPanel().getCurrentTreePanel()
+ .getTreeFile();
+ if (treeFile != null)
+ {
+ frameTitle += MessageManager.formatMessage("label.aptx_title_append",
+ new String[]
+ { treeFile.getAbsolutePath() });
+ }
+ Desktop.addInternalFrame(aptxApp, frameTitle, true, width, height, true,
+ true);
+ return aptxApp;
- Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true,
- width, height, true, true);
+ }
- return aptxApp;
+ /**
+ * Hides certain redundant Archaeopteryx GUI elements such as the menu items
+ * for reading in trees and adds extra items related to Jalview such as the
+ * tree sorting item.
+ *
+ *
+ * @param aptxFrame
+ */
+ private static void adaptAptxGui(MainFrame aptxFrame)
+ {
+ JMenuBar frameBar = aptxFrame.getJMenuBar();
+
+ for (int i = 0; i < frameBar.getMenuCount();i++) {
+ JMenu menu = frameBar.getMenu(i);
+
+ if (menu.getText().contains("File"))
+ {
+ // hide all "Read from ..." and "New" menu items and any Separators that
+ // come directly after them
+ Component previousMenuItem = null;
+ for (Component menuItem : menu.getMenuComponents()) {
+ if (previousMenuItem instanceof JMenuItem)
+ {
+ if (((JMenuItem) previousMenuItem).getText().startsWith("Read")
+ || ((JMenuItem) previousMenuItem).getText()
+ .startsWith("New"))
+ {
+ previousMenuItem.setVisible(false);
+
+ if (menuItem instanceof JSeparator)
+ {
+ menuItem.setVisible(false);
+ }
+ }
+ }
+ previousMenuItem = menuItem;
+ }
+ }
+ else if (menu.getText().contains("Inference"))
+ {
+ menu.setVisible(false);
+ }
+ else if (menu.getText().contains("View"))
+ {
+ menu.addSeparator();
+ JMenuItem sortByTree = new JMenuItem("Sort alignment by tree");
+ JMenuItem refreshJalview = new JMenuItem(
+ "Filter alignment to show only currently visible sequences");
+
+ refreshJalview.setFont(menu.getFont());
+
+ menu.add(sortByTree);
+ menu.add(refreshJalview);
+
+ sortByTree.setFont(menu.getFont());
+ sortByTree.setVisible(false); // don't show unless it's actually
+ // possible
+
+ refreshJalview.addActionListener(activeAptx.get(aptxFrame));
+
+ }
+
+ }
+ aptxFrame.validate();
}
+ public static Map<MainFrame, JalviewBinding> getAllAptxFrames()
+ {
+ return activeAptx;
+ }
}
git://source.jalview.org / jalview.git / blobdiff