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.Component;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
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 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.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);
+ public final static InputStream CONFIG_LOC = AptxInit.class
+
+ .getResourceAsStream("/_aptx_jalview_configuration_file.txt");
+
+ public final static Configuration APTX_CONFIG = new Configuration(
+ 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<MainFrame, JalviewBinding> activeAptx = new HashMap<>();
+ public static TreeFrameI createInstanceFromNhx(String treeTitle,
+ String nhxString, AlignmentViewport viewport)
+ throws IOException
+ {
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(treeTitle);
+ }
+ Phylogeny aptxPhylogeny = Phylogeny
+ .createInstanceFromNhxString(nhxString);
+ aptxPhylogeny.setName(treeTitle);
- public static MainFrame createInstanceFromCalculation(
- final TreeBuilder calculatedTree)
- {
- ExternalTreeBuilderI<Phylogeny, PhylogenyNode> aptxTreeBuilder = new AptxTreeBuilder(
- calculatedTree);
+ TreeFrameI aptxFrame = createAptxFrame(aptxPhylogeny, viewport,
+ treeTitle);
- Phylogeny aptxTree = aptxTreeBuilder.buildTree();
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
+ return aptxFrame;
- MainFrame aptxApp = createAptxFrame(aptxTree,
- calculatedTree.getAvport(), null);
-
- return aptxApp;
}
/**
* @throws IOException
* @throws FileNotFoundException
*/
- public static MainFrame[] createInstancesFromFile(String filePath,
+ public static TreeFrameI[] createInstancesFromFile(File treeFile,
AlignmentViewport viewport)
throws FileNotFoundException, IOException
{
- File treeFile = new File(filePath);
- final String err = ForesterUtil.isReadableFile(treeFile);
- if (!ForesterUtil.isEmpty(err))
+ TreeFrameI[] aptxFrames = null;
+ if (UtilityMethods.canForesterReadFile(treeFile))
{
- 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)
+ if (Desktop.instance != null)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("error.phyloxml_validation"),
- MessageManager.getString("label.file_open_error"),
- JvOptionPane.WARNING_MESSAGE );
+ Desktop.instance.startLoading(treeFile.getCanonicalPath());
}
- }
- Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser, treeFile);
- MainFrame[] aptxFrames = new MainFrame[trees.length];
-
+ 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++)
+ for (int i = 0; i < trees.length; i++)
{
- Phylogeny tree = trees[i];
+ Phylogeny aptxPhylogeny = trees[i];
- if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
+ 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)
{
- PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, "");
+ Desktop.instance.stopLoading();
}
- String treeTitle = treeFile.getName() + "[" + i + "]";
- tree.setName(treeTitle);
- aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
-
- }
- if (Desktop.instance != null)
- {
- Desktop.instance.stopLoading();
}
return aptxFrames;
- }
+ }
- public static MainFrame[] createInstancesFromUrl(URL treeUrl,
+ public static TreeFrameI[] createInstancesFromFile(
+ String filePath,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException
+ {
+ File treeFile = new File(filePath);
+ return createInstancesFromFile(treeFile, viewport);
+
+ }
+
+ public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
AlignmentViewport viewport)
throws FileNotFoundException, IOException, RuntimeException
{
REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
TAXONOMY_EXTRACTION, MIDPOINT_REROOT);
- MainFrame[] aptxFrames = new MainFrame[trees.length];
+ TreeFrameI[] aptxFrames = new TreeFrameI[trees.length];
for (int i = 0; i < trees.length; i++)
{
- Phylogeny tree = trees[i];
- aptxFrames[i] = createAptxFrame(tree, viewport, treeTitle);
+ Phylogeny aptxTree = trees[i];
+ aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
}
if (Desktop.instance != null)
* @param viewport
* @return
*/
- public static MainFrame[] 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 MainFrame[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))
{
- for (final Phylogeny phylogeny : trees)
+ int i = 0;
+ for (final Phylogeny aptxTree : trees)
{
- if (!phylogeny.isEmpty())
+ if (!aptxTree.isEmpty())
{
if (treeDbClient.getName().equals(WebserviceUtil.TREE_FAM_NAME))
{
- phylogeny.setRerootable(false);
- phylogeny.setRooted(true);
+ aptxTree.setRerootable(false);
+ aptxTree.setRooted(true);
}
if (treeDbClient.getProcessingInstructions() != null)
{
try
{
- WebserviceUtil.processInstructions(treeDbClient, phylogeny);
+ WebserviceUtil.processInstructions(treeDbClient,
+ aptxTree);
} catch (final PhyloXmlDataFormatException e)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
{
try
{
- PhylogenyMethods.transferNodeNameToField(phylogeny,
+ PhylogenyMethods.transferNodeNameToField(aptxTree,
treeDbClient.getNodeField(), false);
} catch (final PhyloXmlDataFormatException e)
{
JvOptionPane.ERROR_MESSAGE);
}
}
- phylogeny.setIdentifier(
+ aptxTree.setIdentifier(
new Identifier(identifier, treeDbClient.getName()));
// _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
- // _main_frame.getMenuBarOfMainFrame()
+ // _main_frame.getMenuBarOfExternalTreeFrameI()
// .add(_main_frame.getHelpMenu());
- // _main_frame.getMainPanel().addPhylogenyInNewTab(phylogeny,
+ // _main_frame.getMainPanel().addExternalTreeIInNewTab(ExternalTreeI,
// _main_frame.getConfiguration(),
// new File(url.getFile()).getName(), url.toString());
- MainFrame aptxApp = createAptxFrame(phylogeny, viewport,
+
+ TreeFrameI aptxApp = createAptxFrame(aptxTree,
+ viewport,
url.getFile());
String my_name_for_file = "";
- if (!ForesterUtil.isEmpty(phylogeny.getName()))
+ if (!ForesterUtil.isEmpty(aptxTree.getName()))
{
- my_name_for_file = new String(phylogeny.getName())
+ my_name_for_file = new String(aptxTree.getName())
.replaceAll(" ", "_");
}
- else if (phylogeny.getIdentifier() != null)
+ else if (aptxTree.getIdentifier() != null)
{
final StringBuffer sb = new StringBuffer();
if (!ForesterUtil
- .isEmpty(phylogeny.getIdentifier().getProvider()))
+ .isEmpty(aptxTree.getIdentifier().getProvider()))
{
- sb.append(phylogeny.getIdentifier().getProvider());
+ sb.append(aptxTree.getIdentifier().getProvider());
sb.append("_");
}
- sb.append(phylogeny.getIdentifier().getValue());
+ sb.append(aptxTree.getIdentifier().getValue());
my_name_for_file = new String(
sb.toString().replaceAll(" ", "_"));
}
- aptxApp.getMainPanel().getCurrentTreePanel()
+ aptxApp.getTreePanel()
.setTreeFile(new File(my_name_for_file));
- AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
- phylogeny, aptxApp.getMainPanel().getControlPanel(),
- APTX_CONFIG);
- // _main_frame.getMainPanel().getControlPanel().showWhole();
+ // AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
+ // aptxTree, aptxApp.getMainPanel().getControlPanel(),
+ // APTX_CONFIG);
+ aptxApp.getTreeControls().displayEntireTree();
- aptxApp.activateSaveAllIfNeeded();
+ aptxApp.checkMultipleTrees();
+ aptxFrames[i++] = aptxApp;
}
}
}
{
// Not important if this fails, do nothing.
}
- // _main_frame.getContentPane().repaint();
}
}
- System.gc();
-
if (Desktop.instance != null)
{
Desktop.instance.stopLoading();
}
- return null;
+ return aptxFrames;
}
-
-
- public static MainFrame createAptxFrame(
- final Phylogeny 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;
- }
-
- }
- MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree,
- APTX_CONFIG, treeTitle);
-
-
- LoadedTreeSequenceAssociation 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);
+ // adaptAptxGui(aptxApp); //moved to AptxFrame
return aptxApp;
}
- public static ExternalTreeViewerBindingI<?> bindNodesToJalviewSequences(
- final MainFrame aptxApp,
- final AlignmentViewport jalviewAlignViewport,
- final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
- final Map<PhylogenyNode, 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 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);
+ // adaptAptxGui(aptxApp); //moved to AptxFrame
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();
- boolean epsAdded = false;
- for (int i = 0; i < frameBar.getMenuCount();i++) {
- JMenu menu = frameBar.getMenu(i);
- int menuCount = menu.getMenuComponentCount();
-
- if (menu.getText().contains("File"))
- {
- // hide all "Read from ..." and "New" menu items and any Separators that
- // come directly after them
- Component previousComp = null;
- for (int x = 0; x < menuCount; x++)
- {
- Component menuItem = menu.getMenuComponent(x);
- if (previousComp instanceof JMenuItem)
- {
- JMenuItem previousMenuItem = (JMenuItem) previousComp;
- if (previousMenuItem.getText().startsWith("Read")
- || previousMenuItem.getText()
- .startsWith("New")
- || previousMenuItem.getText()
- .startsWith("Close Tab"))
- {
- previousComp.setVisible(false);
-
- if (menuItem instanceof JSeparator)
- {
- menuItem.setVisible(false);
- }
-
- }
-
- if ((!epsAdded) && previousMenuItem.getText()
- .startsWith("Export to"))
- {
- JMenuItem exportEps = new JMenuItem("Export to EPS file...");
- menu.add(exportEps, x);
- exportEps.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO Auto-generated method stub
- }
-
- });
- epsAdded = true;
+ 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);
- }
- }
- previousComp = menuItem;
- }
- }
- else if (menu.getText().contains("Inference"))
+ if (keepGoing == JvOptionPane.CANCEL_OPTION
+ || keepGoing == JvOptionPane.CLOSED_OPTION
+ || keepGoing == JvOptionPane.NO_OPTION)
{
- 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());
- refreshJalview.addActionListener(activeAptx.get(aptxFrame));
-
-
+ return false;
}
}
- aptxFrame.validate();
- }
-
- public static Map<MainFrame, JalviewBinding> getAllAptxFrames()
- {
- return activeAptx;
+ return true;
}
git://source.jalview.org / jalview.git / blobdiff