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.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.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+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.util.ForesterUtil;
/**
* Static class for creating Archaeopteryx tree viewer instances from calculated
*/
public final class AptxInit
{
- /**
- * 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(
+ 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) // very dense method, to be split up
{
ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
calculatedTree);
Phylogeny aptxTree = aptxTreeBuilder.buildTree();
- Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
- // several trees simultaneously
- MainFrame aptxApp = createAptxFrame(aptxTrees);
+ MainFrame aptxApp = createAptxFrame(aptxTree,
+ calculatedTree.getAvport(), null);
- bindNodesToJalviewSequences(aptxApp, calculatedTree.getAvport(),
- aptxTreeBuilder.getAlignmentBoundNodes(),
- aptxTreeBuilder.getNodesBoundAlignment());
-
- return bindFrameToJalview(aptxApp);
-
+ return aptxApp;
}
- public static MainFrame createInstanceFromFile(String filePath,
+ /**
+ * Refactored from Archaeopteryx.main
+ *
+ * @param filePath
+ * @param viewport
+ * @return
+ * @throws IOException
+ * @throws FileNotFoundException
+ */
+ public static MainFrame[] createInstancesFromFile(String filePath,
AlignmentViewport viewport)
+ throws FileNotFoundException, IOException
{
- 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());
-
- bindAptxNodes.associateLeavesToSequences();
-
- bindNodesToJalviewSequences(aptxApp, viewport,
- bindAptxNodes.getAlignmentWithNodes(),
- bindAptxNodes.getNodesWithAlignment());
+ 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);
+ }
+ boolean nhx_or_nexus = false;
+ final PhylogenyParser p = ParserUtils.createParserDependingOnFileType(
+ treeFile, VALIDATE_PHYLOXML_XSD);
+ if (p instanceof NHXParser)
+ {
+ nhx_or_nexus = true;
+ final NHXParser nhx = (NHXParser) p;
+ nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+ nhx.setIgnoreQuotes(false);
+ nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
+ }
+ else if (p instanceof NexusPhylogeniesParser)
+ {
+ nhx_or_nexus = true;
+ final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) p;
+ 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();
+
+ for (int i = 0; i < phylogenies.length; i++)
+ {
+ Phylogeny tree = phylogenies[i];
+
+ if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
+ {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, "");
+ }
+
+ aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
+ }
+
+ return aptxFrames;
+ }
+
+
+ public static MainFrame[] createInstancesFromUrl(URL treeUrl,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException, RuntimeException
+ {
+
+ String treeTitle = treeUrl.getFile();
+ Phylogeny[] trees = AptxUtil.readPhylogeniesFromUrl(treeUrl,
+ VALIDATE_PHYLOXML_XSD,
+ REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
+ TAXONOMY_EXTRACTION, MIDPOINT_REROOT);
+
+ MainFrame[] aptxFrames = new MainFrame[trees.length];
+ for (int i = 0; i < trees.length; i++)
+ {
+ Phylogeny tree = trees[i];
+ aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
+ }
+
+ return aptxFrames;
- return bindFrameToJalview(aptxApp);
}
- public static MainFrame createInstanceFromUrl(URL url)
- {
-
- return null;
- // void readPhylogeniesFromURL() {
- // URL url = null;
- // Phylogeny[] phys = null;
- // final String message = "Please enter a complete URL, for example
- // \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
- // final String url_string = JOptionPane
- // .showInputDialog( this,
- // message,
- // "Use URL/webservice to obtain a phylogeny",
- // JOptionPane.QUESTION_MESSAGE );
- // boolean nhx_or_nexus = false;
- // if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
- // try {
- // url = new URL( url_string );
- // PhylogenyParser parser = null;
- // if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
- // parser = new TolParser();
- // }
- // else {
- // parser = ParserUtils
- // .createParserDependingOnUrlContents( url,
- // getConfiguration().isValidatePhyloXmlAgainstSchema() );
- // }
- // if ( parser instanceof NexusPhylogeniesParser ) {
- // nhx_or_nexus = true;
- // }
- // else if ( parser instanceof NHXParser ) {
- // nhx_or_nexus = true;
- // }
- // if ( _mainpanel.getCurrentTreePanel() != null ) {
- // _mainpanel.getCurrentTreePanel().setWaitCursor();
- // }
- // else {
- // _mainpanel.setWaitCursor();
- // }
- // final PhylogenyFactory factory =
- // ParserBasedPhylogenyFactory.getInstance();
- // phys = factory.create( url.openStream(), parser );
- // }
- // catch ( final MalformedURLException e ) {
- // JOptionPane.showMessageDialog( this,
- // "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
- // "Malformed URL",
- // JOptionPane.ERROR_MESSAGE );
- // }
- // catch ( final IOException e ) {
- // JOptionPane.showMessageDialog( this,
- // "Could not read from " + url + "\n"
- // + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- // "Failed to read URL",
- // JOptionPane.ERROR_MESSAGE );
- // }
- // catch ( final Exception e ) {
- // JOptionPane.showMessageDialog( this,
- // ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- // "Unexpected Exception",
- // JOptionPane.ERROR_MESSAGE );
- // }
- // finally {
- // if ( _mainpanel.getCurrentTreePanel() != null ) {
- // _mainpanel.getCurrentTreePanel().setArrowCursor();
- // }
- // else {
- // _mainpanel.setArrowCursor();
- // }
- // }
- // if ( ( phys != null ) && ( phys.length > 0 ) ) {
- // if ( nhx_or_nexus &&
- // getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
- // for( final Phylogeny phy : phys ) {
- // PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
- // }
- // }
- // AptxUtil.addPhylogeniesToTabs( phys,
- // new File( url.getFile() ).getName(),
- // new File( url.getFile() ).toString(),
- // getConfiguration(),
- // getMainPanel() );
- // _mainpanel.getControlPanel().showWhole();
- // }
- // }
- // activateSaveAllIfNeeded();
- // System.gc();
- // }
- }
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);
+ LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
+
+ bindAptxNodes.associateLeavesToSequences();
+ bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
+ bindAptxNodes.getAlignmentWithNodes(),
+ bindAptxNodes.getNodesWithAlignment());
+ bindFrameToJalview(aptxApp);
return aptxApp;
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff