package jalview.ext.archaeopteryx;
import jalview.analysis.TreeBuilder;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.ext.treeviewer.ExternalTreeBuilderI;
import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
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.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.archaeopteryx.webservices.WebservicesManager;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
public final class AptxInit
{
- 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();
-
private static Map<MainFrame, JalviewBinding> activeAptx = new HashMap<>();
AlignmentViewport viewport)
throws FileNotFoundException, IOException
{
+ Configuration APTX_CONFIG = new Configuration(Cache.getDefault(
+ "APTXCONFIG",
+ Desktop.instance.getClass()
+ .getResource("/_aptx_jalview_configuration_file.txt")
+ .toString()),
+ false, false, false);
File treeFile = new File(filePath);
final String err = ForesterUtil.isReadableFile(treeFile);
if (!ForesterUtil.isEmpty(err))
}
boolean nhx_or_nexus = false;
final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType(
- treeFile, VALIDATE_PHYLOXML_XSD);
+ treeFile,
+ APTX_CONFIG.isValidatePhyloXmlAgainstSchema());
if (parser instanceof NHXParser)
{
nhx_or_nexus = true;
final NHXParser nhx = (NHXParser) parser;
- nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+ nhx.setReplaceUnderscores(
+ APTX_CONFIG.isReplaceUnderscoresInNhParsing());
nhx.setIgnoreQuotes(false);
- nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
+ nhx.setTaxonomyExtraction(APTX_CONFIG.getTaxonomyExtraction());
}
else if (parser instanceof NexusPhylogeniesParser)
{
nhx_or_nexus = true;
final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) parser;
- nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+ nex.setReplaceUnderscores(
+ APTX_CONFIG.isReplaceUnderscoresInNhParsing());
nex.setIgnoreQuotes(false);
}
else if (parser instanceof PhyloXmlParser)
{
- if ( VALIDATE_PHYLOXML_XSD ) {
- JvOptionPane.showInternalMessageDialog( null,
- ForesterUtil.wordWrap(
- "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
- 80 ),
- "Warning",
+ if (APTX_CONFIG.isValidatePhyloXmlAgainstSchema() == false)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("error.phyloxml_validation"),
+ MessageManager.getString("label.file_open_error"),
JvOptionPane.WARNING_MESSAGE );
}
}
{
Phylogeny tree = trees[i];
- if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
+ if (nhx_or_nexus
+ && APTX_CONFIG.isInternalNumberAreConfidenceForNhParsing())
{
PhylogenyMethods.transferInternalNodeNamesToConfidence(tree, "");
}
AlignmentViewport viewport)
throws FileNotFoundException, IOException, RuntimeException
{
-
+ Configuration APTX_CONFIG = new Configuration(Cache.getDefault(
+ "APTXCONFIG",
+ Desktop.instance.getClass()
+ .getResource("/_aptx_jalview_configuration_file.txt")
+ .toString()),
+ false, false, false);
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);
+ APTX_CONFIG.isValidatePhyloXmlAgainstSchema(),
+ APTX_CONFIG.isReplaceUnderscoresInNhParsing(),
+ APTX_CONFIG.isInternalNumberAreConfidenceForNhParsing(),
+ APTX_CONFIG.getTaxonomyExtraction(),
+ APTX_CONFIG.isMidpointReroot());
MainFrame[] aptxFrames = new MainFrame[trees.length];
for (int i = 0; i < trees.length; i++)
* @param viewport
* @return
*/
- public static MainFrame[] createInstancesFromDb(int databaseIndex,
- AlignmentViewport viewport, String defaultIdentifier)
+ public static MainFrame[] createInstancesFromDb(
+ PhylogeniesWebserviceClient treeDbClient, String identifier,
+ AlignmentViewport viewport)
{
-
+ Configuration APTX_CONFIG = new Configuration(Cache.getDefault(
+ "APTXCONFIG",
+ Desktop.instance.getClass()
+ .getResource("/_aptx_jalview_configuration_file.txt")
+ .toString()),
+ false, false, false);
URL url = null;
Phylogeny[] trees = null;
- final WebservicesManager webservices_manager = WebservicesManager
- .getInstance();
- final PhylogeniesWebserviceClient client = webservices_manager
- .getAvailablePhylogeniesWebserviceClient(databaseIndex);
- String identifier = JvOptionPane.showInternalInputDialog(
- Desktop.desktop,
- client.getInstructions() + "\n(Reference: "
- + client.getReference() + ")",
- client.getDescription(), JvOptionPane.QUESTION_MESSAGE, null,
- null, defaultIdentifier).toString();
if ((identifier != null) && (identifier.trim().length() > 0))
{
}
identifier = identifier.trim();
- if (client.isQueryInteger())
+ if (treeDbClient.isQueryInteger())
{
identifier = identifier.replaceAll("^\\D+", "");
} catch (final NumberFormatException e)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Identifier is expected to be a number",
- "Can not open URL", JvOptionPane.ERROR_MESSAGE);
+ 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 = client.getUrl();
+ String url_str = treeDbClient.getUrl();
url_str = url_str.replaceFirst(
PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier);
url = new URL(url_str);
PhylogenyParser parser = null;
- switch (client.getReturnFormat())
+ switch (treeDbClient.getReturnFormat())
{
case TOL_XML_RESPONSE:
parser = new TolParser();
break;
default:
throw new IllegalArgumentException(
- "unknown format: " + client.getReturnFormat());
+ "unknown format: " + treeDbClient.getReturnFormat());
}
//
// if (_main_frame.getMainPanel().getCurrentTreePanel() != null)
{
exception = true;
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
- "Malformed URL", JvOptionPane.ERROR_MESSAGE);
+ 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 " + client.getName() + " for "
+ "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 " + client.getName() + " for "
+ "Failed to read tree from " + treeDbClient.getName() + " for "
+ identifier,
JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
} catch (final Exception e)
{
exception = true;
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
e.getLocalizedMessage(), "Unexpected Exception",
JvOptionPane.ERROR_MESSAGE);
- } finally
- {
- // if (_main_frame.getCurrentTreePanel() != null)
- // {
- // _main_frame.getCurrentTreePanel().setArrowCursor();
- // }
- // else
- // {
- // _main_frame.getMainPanel().setArrowCursor();
- // }
+ System.err.println(e.getLocalizedMessage());
}
if ((trees != null) && (trees.length > 0))
{
{
if (!phylogeny.isEmpty())
{
- if (client.getName().equals(WebserviceUtil.TREE_FAM_NAME))
+ if (treeDbClient.getName().equals(WebserviceUtil.TREE_FAM_NAME))
{
phylogeny.setRerootable(false);
phylogeny.setRooted(true);
}
- if (client.getProcessingInstructions() != null)
+ if (treeDbClient.getProcessingInstructions() != null)
{
try
{
- WebserviceUtil.processInstructions(client, phylogeny);
+ WebserviceUtil.processInstructions(treeDbClient, phylogeny);
} catch (final PhyloXmlDataFormatException e)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
JvOptionPane.ERROR_MESSAGE);
}
}
- if (client.getNodeField() != null)
+ if (treeDbClient.getNodeField() != null)
{
try
{
PhylogenyMethods.transferNodeNameToField(phylogeny,
- client.getNodeField(), false);
+ treeDbClient.getNodeField(), false);
} catch (final PhyloXmlDataFormatException e)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
}
}
phylogeny.setIdentifier(
- new Identifier(identifier, client.getName()));
+ new Identifier(identifier, treeDbClient.getName()));
// _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
// _main_frame.getMenuBarOfMainFrame()
// .add(_main_frame.getHelpMenu());
my_name_for_file = new String(
sb.toString().replaceAll(" ", "_"));
}
- // _main_frame.getMainPanel().getCurrentTreePanel()
- // .setTreeFile(new File(my_name_for_file));
+ aptxApp.getMainPanel().getCurrentTreePanel()
+ .setTreeFile(new File(my_name_for_file));
AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
phylogeny, aptxApp.getMainPanel().getControlPanel(),
APTX_CONFIG);
}
}
}
- else if (!exception)
+ else if (!exception) // ..what?
{
JvOptionPane.showMessageDialog(null,
ForesterUtil.wordWrap(
final Phylogeny aptxTree,
final AlignmentViewport jalviewAlignport, String treeTitle)
{
+ Configuration APTX_CONFIG = new Configuration(Cache.getDefault(
+ "APTXCONFIG",
+ Desktop.instance.getClass()
+ .getResource("/_aptx_jalview_configuration_file.txt")
+ .toString()),
+ false, false, false);
+ 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);
bindAptxNodes.associateLeavesToSequences();
bindAptxNodes.getNodesWithAlignment());
bindTreeViewFrameToJalview(aptxApp);
+ adaptAptxGui(aptxApp);
return aptxApp;
}
- // private static void addPartitioningSlider(MainFrame aptxFrame)
- // {
- // JSlider slider = new JSlider();
- //
- //
- // }
public static ExternalTreeViewerBindingI<?> bindNodesToJalviewSequences(
final MainFrame 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