package jalview.ext.archaeopteryx;
import jalview.analysis.TreeBuilder;
-import jalview.datamodel.SequenceI;
-import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
-import jalview.ext.treeviewer.ExternalTreeBuilderI;
-import jalview.ext.treeviewer.ExternalTreeFrame;
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreeNodeI;
-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.TreeBuilderI;
+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.HashMap;
-import java.util.Map;
import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.Configuration;
*/
public final class AptxInit
{
+ public final static InputStream CONFIG_LOC = AptxInit.class
+
+ .getResourceAsStream("/_aptx_jalview_configuration_file.txt");
+
public final static Configuration APTX_CONFIG = new Configuration(
- "_aptx_jalview_configuration_file",
- false, false, false);
+ CONFIG_LOC,
+ false, false);
+ // static
+ // {
+ // APTX_CONFIG.setBaseFontFamilyName(
+ // Desktop.instance.getFont().getFamily().replaceAll(" ", "_"));
+ // APTX_CONFIG.setBaseFontSize(Desktop.instance.getFont().getSize());
+ // }
private final static boolean VALIDATE_PHYLOXML_XSD = APTX_CONFIG
.isValidatePhyloXmlAgainstSchema();
private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
.getTaxonomyExtraction();
- private static Map<ExternalTreeFrame, ExternalTreeViewerBindingI> activeAptx = new HashMap<>();
-
-
-
- public static ExternalTreeFrame createInstanceFromCalculation(
+ public static TreeFrameI createInstanceFromCalculation(
final TreeBuilder calculatedTree)
{
- ExternalTreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
+ TreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
calculatedTree);
- ExternalTreeI aptxTree = aptxTreeBuilder.buildTree();
+ TreeI aptxTree = aptxTreeBuilder.buildTree();
- ExternalTreeFrame aptxApp = createAptxFrame(aptxTree,
+ TreeFrameI aptxApp = createAptxFrame(aptxTree,
calculatedTree.getAvport(), null);
return aptxApp;
}
+ public static TreeFrameI[] createInstancesFromFile(File treeFile,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException
+ {
+ TreeFrameI[] aptxFrames = null;
+ if (UtilityMethods.canForesterReadFile(treeFile))
+ {
+
+ 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;
+ }
+
/**
* Refactored from Archaeopteryx.main
*
* @throws IOException
* @throws FileNotFoundException
*/
- public static ExternalTreeFrame[] createInstancesFromFile(
+ public static TreeFrameI[] createInstancesFromFile(
String filePath,
AlignmentViewport viewport)
throws FileNotFoundException, IOException
{
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 (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);
- ExternalTreeFrame[] aptxFrames = new ExternalTreeFrame[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);
- Tree aptxTree = new Tree(aptxPhylogeny);
- aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
+ return createInstancesFromFile(treeFile, viewport);
}
- if (Desktop.instance != null)
- {
- Desktop.instance.stopLoading();
- }
- return aptxFrames;
- }
- public static ExternalTreeFrame[] createInstancesFromUrl(URL treeUrl,
+ public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
AlignmentViewport viewport)
throws FileNotFoundException, IOException, RuntimeException
{
REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
TAXONOMY_EXTRACTION, MIDPOINT_REROOT);
- ExternalTreeFrame[] aptxFrames = new ExternalTreeFrame[trees.length];
+ TreeFrameI[] aptxFrames = new TreeFrameI[trees.length];
for (int i = 0; i < trees.length; i++)
{
Phylogeny aptxTree = trees[i];
- Tree jalviewTree = new Tree(aptxTree);
- aptxFrames[i] = createAptxFrame(jalviewTree, viewport, treeTitle);
+ aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
}
if (Desktop.instance != null)
* @param viewport
* @return
*/
- public static ExternalTreeFrame[] createInstancesFromDb(
+ 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))
{
{ identifier }),
MessageManager.getString("label.invalid_url"),
JvOptionPane.ERROR_MESSAGE);
- return new ExternalTreeFrame[0];
+ return new TreeFrameI[0];
}
identifier = id + "";
}
// _main_frame.getMainPanel().setWaitCursor();
// }
trees = ForesterUtil.readPhylogeniesFromUrl(url, parser);
+ aptxFrames = new TreeFrameI[trees.length];
} catch (final MalformedURLException e)
{
exception = true;
}
if ((trees != null) && (trees.length > 0))
{
+ int i = 0;
for (final Phylogeny aptxTree : trees)
{
if (!aptxTree.isEmpty())
// _main_frame.getConfiguration(),
// new File(url.getFile()).getName(), url.toString());
- Tree jalviewTree = new Tree(aptxTree);
- ExternalTreeFrame aptxApp = createAptxFrame(jalviewTree,
+ TreeFrameI aptxApp = createAptxFrame(aptxTree,
viewport,
url.getFile());
String my_name_for_file = "";
- if (!ForesterUtil.isEmpty(jalviewTree.getTreeName()))
+ if (!ForesterUtil.isEmpty(aptxTree.getName()))
{
- my_name_for_file = new String(jalviewTree.getTreeName())
+ my_name_for_file = new String(aptxTree.getName())
.replaceAll(" ", "_");
}
else if (aptxTree.getIdentifier() != null)
aptxApp.getTreeControls().displayEntireTree();
aptxApp.checkMultipleTrees();
+ aptxFrames[i++] = aptxApp;
}
}
}
{
Desktop.instance.stopLoading();
}
- return null;
+ return aptxFrames;
}
-
-
- public static ExternalTreeFrame createAptxFrame(
- final ExternalTreeI aptxTree,
- final AlignmentViewport jalviewAlignport, String treeTitle)
+ public static TreeFrameI createAptxFrame(TreeI aptxTree,
+ 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;
- }
-
- }
- ExternalTreeFrame aptxApp = aptxTree.createInstanceFromTree(treeTitle);
-
- ExternalLoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
- jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
+ validateConfig(APTX_CONFIG);
+ TreeFrameI aptxApp = aptxTree
+ .createTreeViewerFromTree(treeTitle);
+ TreeI jalviewTree = aptxApp.getTree();
+ LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(),
+ jalviewTree);
bindAptxNodes.associateLeavesToSequences();
- bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
+ TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
bindAptxNodes.getAlignmentWithNodes(),
bindAptxNodes.getNodesWithAlignment());
- bindTreeViewFrameToJalview(aptxApp);
+ TreeViewerUtils.addTreeViewFrameToJalview(aptxApp);
// adaptAptxGui(aptxApp); //moved to AptxFrame
return aptxApp;
}
- public static ExternalTreeViewerBindingI bindNodesToJalviewSequences(
- final ExternalTreeFrame aptxApp,
- final AlignmentViewport jalviewAlignViewport,
- final Map<SequenceI, ExternalTreeNodeI> alignMappedToNodes,
- final Map<ExternalTreeNodeI, SequenceI> nodesMappedToAlign)
+ protected static TreeFrameI createAptxFrame(
+ final Phylogeny aptxTree,
+ final AlignmentViewport jalviewAlignport, String treeTitle)
{
- JalviewBinding treeBinding = new JalviewBinding(aptxApp,
- jalviewAlignViewport,
- alignMappedToNodes, nodesMappedToAlign);
- activeAptx.put(aptxApp, treeBinding);
- return treeBinding;
- }
+ validateConfig(APTX_CONFIG);
+ TreeFrameI aptxApp = new AptxFrame(aptxTree, APTX_CONFIG,
+ treeTitle);
+ TreeI jalviewTree = aptxApp.getTree();
+ LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(),
+ jalviewTree);
+ bindAptxNodes.associateLeavesToSequences();
+ TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
+ bindAptxNodes.getAlignmentWithNodes(),
+ bindAptxNodes.getNodesWithAlignment());
+ TreeViewerUtils.addTreeViewFrameToJalview(aptxApp);
- public static ExternalTreeFrame bindTreeViewFrameToJalview(
- final ExternalTreeFrame 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.getTreePanel().getTreeFile();
- if (treeFile != null)
- {
- frameTitle += MessageManager.formatMessage("label.aptx_title_append",
- new String[]
- { treeFile.getAbsolutePath() });
- }
- Desktop.addInternalFrame(aptxApp, frameTitle, true, width, height, true,
- true);
+ // adaptAptxGui(aptxApp); //moved to AptxFrame
return aptxApp;
-
}
-
- public static Map<ExternalTreeFrame, ExternalTreeViewerBindingI> getAllAptxFrames()
+ private static boolean validateConfig(Configuration aptxConfig)
{
- return activeAptx;
+ 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