package jalview.ext.archaeopteryx;
-import jalview.analysis.TreeBuilder;
-import jalview.datamodel.SequenceI;
-import jalview.ext.treeviewer.ExternalTreeBuilderI;
-import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
+import jalview.ext.forester.io.UtilityMethods;
+import jalview.ext.treeviewer.LoadedTreeAssociationI;
+import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeViewerUtils;
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.io.InputStream;
+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.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.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyMethods;
+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
{
+ public final static InputStream CONFIG_LOC = AptxInit.class
- private final static Configuration APTX_CONFIG = new Configuration(
- "_aptx_jalview_configuration_file", false, false, false);
+ .getResourceAsStream("/_aptx_jalview_configuration_file.txt");
+
+ public final static Configuration APTX_CONFIG = new Configuration(
+ CONFIG_LOC,
+ false, false);
+ static
+ {
+ APTX_CONFIG.setBaseFontSize(Desktop.instance.getFont().getSize());
+ APTX_CONFIG
+ .setBaseFontFamilyName(Desktop.instance.getFont().getFamily());
+ }
private final static boolean VALIDATE_PHYLOXML_XSD = APTX_CONFIG
.isValidatePhyloXmlAgainstSchema();
private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
.getTaxonomyExtraction();
- /**
- * Test method, should generally not be used as it does not bind the tree to
- * its alignment
- *
- * @param aptxTrees
- * @return
- */
- public static MainFrame createUnboundInstance(final Phylogeny aptxTree)
- {
- Phylogeny[] aptxTrees = { aptxTree };
- return createAptxFrame(aptxTrees);
- }
- // 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 TreeFrameI createInstanceFromNhx(String treeTitle,
+ String nhxString, AlignmentViewport viewport)
+ throws IOException
{
- ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
- calculatedTree);
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(treeTitle);
+ }
+
+
+ Phylogeny aptxPhylogeny = Phylogeny
+ .createInstanceFromNhxString(nhxString);
+ aptxPhylogeny.setName(treeTitle);
- Phylogeny aptxTree = aptxTreeBuilder.buildTree();
- Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
- // several trees simultaneously
+ TreeFrameI aptxFrame = createAptxFrame(aptxPhylogeny, 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 aptxFrame;
}
- public static MainFrame createInstanceFromFile(String filePath,
+ /**
+ * Refactored from Archaeopteryx.main
+ *
+ * @param filePath
+ * @param viewport
+ * @return
+ * @throws IOException
+ * @throws FileNotFoundException
+ */
+ public static TreeFrameI[] createInstancesFromFile(File treeFile,
AlignmentViewport viewport)
+ throws FileNotFoundException, IOException
{
- String[] AptxArgs = new String[] { "-c",
- APTX_CONFIG.getConfigFilename(), filePath };
- MainFrame aptxApp = Archaeopteryx.main(AptxArgs);
-
- int tabCount = aptxApp.getMainPanel().getTabbedPane().getTabCount();
-
- for (int i = 0; i < tabCount; i++)
+ TreeFrameI[] aptxFrames = null;
+ if (UtilityMethods.canForesterReadFile(treeFile))
{
- // roundabout way to select each tree because getComponentAt(i) requires
- // casting to TreePanel which doesn't work
- aptxApp.getMainPanel().getTabbedPane().setSelectedIndex(i);
- Phylogeny tree = aptxApp.getMainPanel().getCurrentTreePanel()
- .getPhylogeny();
- LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
- viewport.getAlignment().getSequencesArray(),
- tree);
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(treeFile.getCanonicalPath());
+ }
+ 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 (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);
+ aptxFrames = new TreeFrameI[trees.length];
+
+ for (int i = 0; i < trees.length; i++)
+ {
+ Phylogeny aptxPhylogeny = trees[i];
+
+ if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
+ {
+ PhylogenyMethods
+ .transferInternalNodeNamesToConfidence(aptxPhylogeny, "");
+ }
+ String treeTitle = treeFile.getName() + "[" + i + "]";
+ aptxPhylogeny.setName(treeTitle);
+ aptxFrames[i] = createAptxFrame(aptxPhylogeny, viewport, treeTitle);
+
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+ }
+ return aptxFrames;
+ }
- bindAptxNodes.associateLeavesToSequences();
- bindNodesToJalviewSequences(aptxApp, viewport,
- bindAptxNodes.getAlignmentWithNodes(),
- bindAptxNodes.getNodesWithAlignment());
+ public static TreeFrameI[] createInstancesFromFile(
+ String filePath,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException
+ {
+ File treeFile = new File(filePath);
+ return createInstancesFromFile(treeFile, viewport);
+
}
- return bindFrameToJalview(aptxApp);
- }
- public static MainFrame createInstanceFromUrl(URL treeUrl,
+ public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
AlignmentViewport viewport)
throws FileNotFoundException, IOException, RuntimeException
{
+
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);
- MainFrame aptxApp = Archaeopteryx.createApplication(trees, APTX_CONFIG,
- treeTitle);
- for (Phylogeny tree : trees)
+ TreeFrameI[] aptxFrames = new TreeFrameI[trees.length];
+ for (int i = 0; i < trees.length; i++)
{
- LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
- viewport.getAlignment().getSequencesArray(), tree);
-
- bindAptxNodes.associateLeavesToSequences();
- bindNodesToJalviewSequences(aptxApp, viewport,
- bindAptxNodes.getAlignmentWithNodes(),
- bindAptxNodes.getNodesWithAlignment());
+ Phylogeny aptxTree = trees[i];
+ aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
}
- return bindFrameToJalview(aptxApp);
+ return aptxFrames;
}
+ /**
+ * Refactored from Forester's UrlTreeReader, this can be more efficient
+ *
+ * @param databaseIndex
+ * @param viewport
+ * @return
+ */
+ public static TreeFrameI[] createInstancesFromDb(
+ PhylogeniesWebserviceClient treeDbClient, String identifier,
+ AlignmentViewport viewport)
+ {
+ URL url = null;
+ Phylogeny[] trees = null;
+ TreeFrameI[] aptxFrames = 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 TreeFrameI[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);
+ aptxFrames = new TreeFrameI[trees.length];
+ } 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))
+ {
+ int i = 0;
+ for (final Phylogeny aptxTree : trees)
+ {
+ if (!aptxTree.isEmpty())
+ {
+ if (treeDbClient.getName().equals(WebserviceUtil.TREE_FAM_NAME))
+ {
+ aptxTree.setRerootable(false);
+ aptxTree.setRooted(true);
+ }
+ if (treeDbClient.getProcessingInstructions() != null)
+ {
+ try
+ {
+ WebserviceUtil.processInstructions(treeDbClient,
+ aptxTree);
+ } catch (final PhyloXmlDataFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error:\n" + e.getLocalizedMessage(), "Error",
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ if (treeDbClient.getNodeField() != null)
+ {
+ try
+ {
+ PhylogenyMethods.transferNodeNameToField(aptxTree,
+ treeDbClient.getNodeField(), false);
+ } catch (final PhyloXmlDataFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error:\n" + e.getLocalizedMessage(), "Error",
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ aptxTree.setIdentifier(
+ new Identifier(identifier, treeDbClient.getName()));
+ // _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
+ // _main_frame.getMenuBarOfExternalTreeFrameI()
+ // .add(_main_frame.getHelpMenu());
+ // _main_frame.getMainPanel().addExternalTreeIInNewTab(ExternalTreeI,
+ // _main_frame.getConfiguration(),
+ // new File(url.getFile()).getName(), url.toString());
+
+
+ TreeFrameI aptxApp = createAptxFrame(aptxTree,
+ viewport,
+ url.getFile());
+ String my_name_for_file = "";
+ if (!ForesterUtil.isEmpty(aptxTree.getName()))
+ {
+ my_name_for_file = new String(aptxTree.getName())
+ .replaceAll(" ", "_");
+ }
+ else if (aptxTree.getIdentifier() != null)
+ {
+ final StringBuffer sb = new StringBuffer();
+ if (!ForesterUtil
+ .isEmpty(aptxTree.getIdentifier().getProvider()))
+ {
+ sb.append(aptxTree.getIdentifier().getProvider());
+ sb.append("_");
+ }
+ sb.append(aptxTree.getIdentifier().getValue());
+ my_name_for_file = new String(
+ sb.toString().replaceAll(" ", "_"));
+ }
+ aptxApp.getTreePanel()
+ .setTreeFile(new File(my_name_for_file));
+ // AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
+ // aptxTree, aptxApp.getMainPanel().getControlPanel(),
+ // APTX_CONFIG);
+ aptxApp.getTreeControls().displayEntireTree();
+
+ aptxApp.enableMultipleTrees();
+ aptxFrames[i++] = aptxApp;
+ }
+ }
+ }
+ 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.
+ }
+ }
+ }
+
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+ return aptxFrames;
- public static MainFrame createAptxFrame(
- final Phylogeny[] aptxTrees)
- {
- MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
- APTX_CONFIG, null);
- return aptxApp;
}
- public static ExternalTreeViewerBindingI<?> bindNodesToJalviewSequences(
- final MainFrame aptxApp,
- final AlignmentViewport jalviewAlignViewport,
- final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
- final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
+
+ public static TreeFrameI createAptxFrame(TreeI aptxTree,
+ AlignmentViewport jalviewAlignport, String treeTitle)
{
- return new JalviewBinding(aptxApp, jalviewAlignViewport,
- alignMappedToNodes, nodesMappedToAlign);
+ validateConfig(APTX_CONFIG);
+ TreeFrameI aptxApp = aptxTree
+ .createTreeViewerFromTree(treeTitle);
+ TreeI jalviewTree = aptxApp.getTree();
+ LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(),
+ jalviewTree);
+ bindAptxNodes.associateNodesToSequences();
+
+ TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
+ bindAptxNodes.getAlignmentWithNodes(),
+ bindAptxNodes.getNodesWithAlignment());
+ TreeViewerUtils.addTreeViewFrameToJalview(aptxApp, 400, 500);
+
+ // adaptAptxGui(aptxApp); //moved to AptxFrame
+ return aptxApp;
}
- public static MainFrame bindFrameToJalview(final MainFrame aptxApp)
+ protected static TreeFrameI createAptxFrame(
+ final Phylogeny aptxTree,
+ final AlignmentViewport jalviewAlignport, String treeTitle)
{
- int width = 400;
- int height = 550;
- aptxApp.setMinimumSize(new Dimension(width, height));
- // aptxApp.setFont(Desktop.instance.getFont());
- // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());
+ validateConfig(APTX_CONFIG);
+ TreeFrameI aptxApp = new AptxFrame(aptxTree, APTX_CONFIG,
+ treeTitle);
+ TreeI jalviewTree = aptxApp.getTree();
+ LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(),
+ jalviewTree);
+ bindAptxNodes.associateNodesToSequences();
- Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true,
- width, height, true, true);
+ TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
+ bindAptxNodes.getAlignmentWithNodes(),
+ bindAptxNodes.getNodesWithAlignment());
+ TreeViewerUtils.addTreeViewFrameToJalview(aptxApp, 400, 500);
return aptxApp;
-
}
+ private static boolean validateConfig(Configuration aptxConfig)
+ {
+ if (aptxConfig == null || aptxConfig.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 false;
+ }
+
+ }
+ return true;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff