label.sequence_id_tooltip = Sequence ID Tooltip
label.no_services = <No Services>
label.select_copy_raw_html = Select this if you want to copy raw html
-label.share_data_vamsas_applications = Share data with other vamsas applications
-label.connect_to = Connect to
-label.join_existing_vamsas_session = Join an existing vamsas session
-label.from_url = From URL
+label.from_url = from URL
label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment
label.sort_with_new_tree = Sort With New Tree
- label.from_textbox = from Textbox
+ label.from_textbox = From Textbox
label.window = Window
label.preferences = Preferences
label.tools = Tools
exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'
exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}
exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
-exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
+exception.couldnt_store_sequence_mappings = Couldn''t store sequence mappings for {0}
exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})
+ exception.invalid_matrix_identifier = Sequence identifier {0} not found in distance matrix.
exception.browser_not_found = Exception in finding browser: {0}
+exception.browser_unable_to_launch = Unable to launch browser: {0}
exception.browser_unable_to_locate = Unable to locate browser: {0}
+exception.browser_os_not_supported = Launching browser on this operating system not supported. Use URL\n{0}
exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}
exception.illegal_access_building_apple_evt= IllegalAccessException while building AppleEvent: {0}
exception.unable_to_launch_url = Unable to launch URL: {0}
if (namesleft > -1)
{
- nam = algnIds.findIdMatch(realnam);
+ nodeSequence = algnIds.findIdMatch(nodeSequenceName);
}
- if (nam != null)
+ if (nodeSequence != null)
{
- j.setElement(nam);
- if (one2many.contains(nam))
+ sn.setElement(nodeSequence);
+ if (one2many.contains(nodeSequence))
{
// countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for
+ // if (Cache.isDebugEnabled())
+ // Cache.debug("One 2 many relationship for
// "+nam.getName());
}
else
}
else
{
- j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
- j.setPlaceholder(true);
+ sn.setElement(new Sequence(nodeSequenceName, "THISISAPLACEHLDER"));
+ sn.setPlaceholder(true);
}
}
- // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
- // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+ // if (Cache.isDebugEnabled() && countOne2Many>0) {
+ // Cache.debug("There were "+countOne2Many+" alignment
// sequence ids (out of "+one2many.size()+" unique ids) linked to two or
// more leaves.");
// }
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
+import java.util.logging.ConsoleHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
import javax.swing.UIManager;
+import javax.swing.UIManager.LookAndFeelInfo;
+
+import com.threerings.getdown.util.LaunchUtil;
+
+//import edu.stanford.ejalbert.launching.IBrowserLaunching;
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.ChannelProperties;
+import jalview.util.HttpUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
+ import groovy.lang.Binding;
+ import groovy.util.GroovyScriptEngine;
+
/**
* Main class for Jalview Application <br>
* <br>
}
String ids = selectedIds.toString();
- // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
- seqFetcher.getTextArea().setText(ids);
+ seqFetcher.setQuery(ids);
- Thread worker = new Thread(seqFetcher);
+ Thread worker = new Thread(seqFetcher, "PDBFTSSeqFetcherThread");
worker.start();
delayAndEnableActionButtons();
}
{
return PDB_AUTOSEARCH;
}
-}
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.PdbFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
- }
++}
*/
package jalview.gui;
+import java.util.Locale;
+ import jalview.analysis.AlignmentSorter;
+ import jalview.analysis.AlignmentUtils;
+ import jalview.analysis.CrossRef;
+ import jalview.analysis.Dna;
+ import jalview.analysis.ParseProperties;
+ import jalview.analysis.SequenceIdMatcher;
+ import jalview.analysis.TreeModel;
+ import jalview.api.AlignExportSettingI;
+ import jalview.api.AlignViewControllerGuiI;
+ import jalview.api.AlignViewControllerI;
+ import jalview.api.AlignViewportI;
+ import jalview.api.AlignmentViewPanel;
+ import jalview.api.FeatureSettingsControllerI;
+ import jalview.api.SplitContainerI;
+ import jalview.api.ViewStyleI;
+ import jalview.bin.Cache;
+ import jalview.bin.Jalview;
+ import jalview.commands.CommandI;
+ import jalview.commands.EditCommand;
+ import jalview.commands.EditCommand.Action;
+ import jalview.commands.OrderCommand;
+ import jalview.commands.RemoveGapColCommand;
+ import jalview.commands.RemoveGapsCommand;
+ import jalview.commands.SlideSequencesCommand;
+ import jalview.commands.TrimRegionCommand;
+ import jalview.datamodel.AlignedCodonFrame;
+ import jalview.datamodel.Alignment;
+ import jalview.datamodel.AlignmentAnnotation;
+ import jalview.datamodel.AlignmentExportData;
+ import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.AlignmentOrder;
+ import jalview.datamodel.AlignmentView;
+ import jalview.datamodel.ColumnSelection;
+ import jalview.datamodel.HiddenColumns;
+ import jalview.datamodel.HiddenSequences;
+ import jalview.datamodel.PDBEntry;
+ import jalview.datamodel.SeqCigar;
+ import jalview.datamodel.Sequence;
+ import jalview.datamodel.SequenceGroup;
+ import jalview.datamodel.SequenceI;
+ import jalview.ext.archaeopteryx.AptxInit;
+ import jalview.ext.forester.io.SupportedTreeFileFilter;
+ import jalview.ext.forester.io.TreeParser;
+ import jalview.gui.ColourMenuHelper.ColourChangeListener;
+ import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+ import jalview.io.AlignmentProperties;
+ import jalview.io.AnnotationFile;
+ import jalview.io.BioJsHTMLOutput;
+ import jalview.io.DataSourceType;
+ import jalview.io.FileFormat;
+ import jalview.io.FileFormatI;
+ import jalview.io.FileFormats;
+ import jalview.io.FileLoader;
+ import jalview.io.FileParse;
+ import jalview.io.FormatAdapter;
+ import jalview.io.HtmlSvgOutput;
+ import jalview.io.IdentifyFile;
+ import jalview.io.JPredFile;
+ import jalview.io.JalviewFileChooser;
+ import jalview.io.JalviewFileView;
+ import jalview.io.JnetAnnotationMaker;
+ import jalview.io.NewickFile;
+ import jalview.io.ScoreMatrixFile;
+ import jalview.io.TCoffeeScoreFile;
+ import jalview.jbgui.GAlignFrame;
+ import jalview.schemes.ColourSchemeI;
+ import jalview.schemes.ColourSchemes;
+ import jalview.schemes.ResidueColourScheme;
+ import jalview.schemes.TCoffeeColourScheme;
+ import jalview.util.MessageManager;
+ import jalview.viewmodel.AlignmentViewport;
+ import jalview.viewmodel.ViewportRanges;
+ import jalview.ws.DBRefFetcher;
+ import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+ import jalview.ws.jws1.Discoverer;
+ import jalview.ws.jws2.Jws2Discoverer;
+ import jalview.ws.jws2.jabaws2.Jws2Instance;
+ import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Component;
+ import java.awt.Dimension;
+ import java.awt.GridLayout;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+ import java.util.StringTokenizer;
import java.util.Vector;
+import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
+ import javax.swing.JComboBox;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
+ chooseTreeFile();
+ }
+
+ @Override
+ protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
+ {
+ chooseTreeUrl();
+ }
+
+ @Override
+ protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb();
+
+ }
+
+ @Override
+ protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb();
+
+ }
+
+ @Override
+ protected void loadTreeFam_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb();
+
+ }
+
+ @Override
+ protected void loadTreePfam_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb();
+
+ }
+
+ @Override
+ protected void loadTreeBase_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb();
+
+ }
+
+
+ public void chooseTreeFile()
+ {
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
- MessageManager.getString("label.select_newick_like_tree_file"));
+ MessageManager.getString("label.select_tree_file")); // modify
chooser.setToolTipText(
- MessageManager.getString("label.load_tree_file"));
+ MessageManager.getString("label.load_tree_for_sequence_set"));
+ for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
+ .values())
+ {
+ chooser.setFileFilter(treeFormat.getTreeFilter());
+ }
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- String filePath = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", filePath);
-
-
- TreeParser treeParser = new TreeParser(filePath);
- treeParser.loadTree(viewport);
-
+ @Override
+ public void run()
+ {
+ String filePath = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
- try
- {
- fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
- DataSourceType.FILE));
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
++ TreeParser treeParser = null;
++ try {
++ treeParser = new TreeParser(filePath);
++ treeParser.loadTree(viewport);
+ } catch (Exception ex)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ MessageManager
+ .getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(),
+ MessageManager.getString(
+ "label.possible_problem_with_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ chooser.showOpenDialog(this);
+ }
+ }
+
+ /**
+ * Break up and move to TreeParser?
+ */
+ public void chooseTreeUrl()
+ {
+
+ JLabel label = new JLabel(
+ MessageManager.getString("label.tree_url_example"));
+ // add "example" button
+ final JComboBox<String> history = new JComboBox<>();
+
+ JPanel panel = new JPanel(new GridLayout(2, 1));
+ panel.add(label);
+ panel.add(history);
+ history.setPreferredSize(new Dimension(400, 20));
+ history.setEditable(true);
+ history.addItem("http://www.");
+
+ String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+ StringTokenizer st;
+
+ if (historyItems != null)
+ {
+ st = new StringTokenizer(historyItems, "\t");
+
+ while (st.hasMoreTokens())
+ {
+ history.addItem(st.nextToken());
+ }
+ }
+
+ int reply = JvOptionPane.showInternalConfirmDialog(this, panel,
+ MessageManager.getString("label.load_tree_url"),
+ JvOptionPane.OK_CANCEL_OPTION);
+
+ if (reply == JvOptionPane.OK_OPTION)
+ {
+
+ String urlString = history.getSelectedItem().toString();
+ URL treeUrl;
+
+ try
+ {
+ FileFormatI format = null;
+
+ format = new IdentifyFile().identify(urlString, DataSourceType.URL);
+ // add actual use for the format identification (jalview .jar files)
+ treeUrl = new URL(urlString);
+ AptxInit.createInstanceFromUrl(treeUrl, viewport);
+
+ } catch (IOException | RuntimeException e)
+ {
+ JvOptionPane.showMessageDialog(this, MessageManager.formatMessage(
+ "exception.failed_to_read_data_from_source", new String[]
+ { urlString }),
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.ERROR_MESSAGE);
+ e.printStackTrace();
+ }
+ }
+ else
+ {
+
+ }
+ }
+
+ public void chooseTreeDb()
+ {
-
-
-
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
- new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
- new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
++ new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this),
+ "CrossReferencesThread")
.start();
}
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
+ import jalview.ext.archaeopteryx.AptxInit;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
Object curSel = comboBox.getSelectedItem();
toolTips.clear();
DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
-
+ /*
+ * select the score models applicable to the alignment type
+ */
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+ pca.isSelected());
/*
* now we can actually add entries to the combobox,
reader2.setDaemon(true);
reader2.start();
// and a thread to append text to the textarea
- textAppender = new Thread(this);
+ textAppender = new Thread(this, "ConsoleTextAppendThread");
textAppender.setDaemon(true);
textAppender.start();
+
+ // set icons
+ frame.setIconImages(ChannelProperties.getIconList());
+ }
+
+ private void setChosenLogLevelCombo()
+ {
+ setChosenLogLevelCombo(startingLogLevel);
+ }
+
+ private void setChosenLogLevelCombo(LogLevel setLogLevel)
+ {
+ logLevelCombo.setSelectedItem(setLogLevel);
+ if (!logLevelCombo.getSelectedItem().equals(setLogLevel))
+ {
+ // setLogLevel not (yet) in list
+ if (setLogLevel != null && setLogLevel instanceof LogLevel)
+ {
+ // add new item to list (might be set via .jalview_properties)
+ boolean added = false;
+ for (int i = 0; i < logLevelCombo.getItemCount(); i++)
+ {
+ LogLevel l = (LogLevel) logLevelCombo.getItemAt(i);
+ if (l.compareTo(setLogLevel) >= 0)
+ {
+ logLevelCombo.insertItemAt(setLogLevel, i);
+ added = true;
+ break;
+ }
+ }
+ if (!added) // lower priority than others or some confusion -- add to
+ // end of list
+ {
+ logLevelCombo.addItem(setLogLevel);
+ }
+ logLevelCombo.setSelectedItem(setLogLevel);
+ }
+ else
+ {
+ logLevelCombo.setSelectedItem(LogLevel.INFO);
+ }
+ }
+ }
+
+ private void copyConsoleTextToClipboard()
+ {
+ String consoleText = textArea.getText();
+ StringSelection consoleTextSelection = new StringSelection(consoleText);
+ Clipboard cb = Toolkit.getDefaultToolkit().getSystemClipboard();
+ cb.setContents(consoleTextSelection, null);
}
PipedOutputStream pout = null, perr = null;
void showNews(boolean visible)
{
+ jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
+ showNews.setSelected(visible);
+ if (visible && !jvnews.isVisible())
{
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
- showNews.setSelected(visible);
- if (visible && !jvnews.isVisible())
+ new Thread(new Runnable()
{
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
- {
- long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"),
- now);
- jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, now);
- jvnews.showNews();
- }
+ long now = System.currentTimeMillis();
+ Desktop.instance.setProgressBar(
+ MessageManager.getString("status.refreshing_news"), now);
+ jvnews.refreshNews();
+ Desktop.instance.setProgressBar(null, now);
+ jvnews.showNews();
+ }
- }).start();
+ }, "ShowNewsWindowThread").start();
- }
}
}
@Override
public void run()
{
- new SplashScreen(true);
+ new SplashScreen(false);
}
- }).start();
+ }, "ShowAboutMenuThread").start();
}
- public StringBuffer getAboutMessage(boolean shortv)
+ /**
+ * Returns the html text for the About screen, including any available version
+ * number, build details, author details and citation reference, but without
+ * the enclosing {@code html} tags
+ *
+ * @return
+ */
+ public String getAboutMessage()
{
- StringBuffer message = new StringBuffer();
- message.append("<html>");
- if (shortv)
- {
- message.append("<h1><strong>Version: "
- + jalview.bin.Cache.getProperty("VERSION")
- + "</strong></h1>");
- message.append("<strong>Last Updated: <em>"
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "</em></strong>");
-
- }
- else
- {
+ StringBuilder message = new StringBuilder(1024);
+ message.append("<div style=\"font-family: sans-serif;\">")
+ .append("<h1><strong>Version: ")
+ .append(Cache.getProperty("VERSION")).append("</strong></h1>")
+ .append("<strong>Built: <em>")
+ .append(Cache.getDefault("BUILD_DATE", "unknown"))
+ .append("</em> from ").append(Cache.getBuildDetailsForSplash())
+ .append("</strong>");
- message.append("<strong>Version "
- + jalview.bin.Cache.getProperty("VERSION")
- + "; last updated: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
- }
-
- if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals("Checking"))
+ String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
+ if (latestVersion.equals("Checking"))
{
- message.append("<br>...Checking latest version...</br>");
+ // JBP removed this message for 2.11: May be reinstated in future version
+ // message.append("<br>...Checking latest version...</br>");
}
- else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals(jalview.bin.Cache.getProperty("VERSION")))
+ else if (!latestVersion.equals(Cache.getProperty("VERSION")))
{
boolean red = false;
- if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT)
.indexOf("automated build") == -1)
{
red = true;
MessageManager.getString("label.couldnt_save_project"),
JvOptionPane.WARNING_MESSAGE);
}
- setProgressBar(null, choice.hashCode());
+ setProgressBar(null, chosenFile.hashCode());
}
- }).start();
+ }, "SaveJalviewProjectThread").start();
}
}
if (desktop != null)
{
AlignFrame[] frames = Desktop.getAlignFrames();
-
- for (AlignFrame afr : frames)
- {
- if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
- .equals(sequenceSetId))
- {
- if (afr.alignPanels != null)
- {
- for (AlignmentPanel ap : afr.alignPanels)
- {
- if (sequenceSetId == null
- || sequenceSetId.equals(ap.av.getSequenceSetId()))
- {
- viewp.add(ap.av);
- }
- }
- }
- else
- {
- viewp.add(afr.getViewport());
- }
- }
- }
- if (viewp.size() > 0)
- {
- return viewp.toArray(new AlignmentViewport[viewp.size()]);
- }
- }
- return null;
- }
-
- /**
- * Explode the views in the given frame into separate AlignFrame
- *
- * @param af
- */
- public static void explodeViews(AlignFrame af)
- {
- int size = af.alignPanels.size();
- if (size < 2)
- {
- return;
- }
-
- for (int i = 0; i < size; i++)
- {
- AlignmentPanel ap = af.alignPanels.get(i);
- AlignFrame newaf = new AlignFrame(ap);
-
- /*
- * Restore the view's last exploded frame geometry if known. Multiple
- * views from one exploded frame share and restore the same (frame)
- * position and size.
- */
- Rectangle geometry = ap.av.getExplodedGeometry();
- if (geometry != null)
- {
- newaf.setBounds(geometry);
- }
-
- ap.av.setGatherViewsHere(false);
-
- addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- }
-
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
-
- }
-
- /**
- * Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the
- * expanded views. Note the expanded frames may themselves have multiple
- * views. We take the lot.
- *
- * @param source
- */
- public void gatherViews(AlignFrame source)
- {
- source.viewport.setGatherViewsHere(true);
- source.viewport.setExplodedGeometry(source.getBounds());
- JInternalFrame[] frames = desktop.getAllFrames();
- String viewId = source.viewport.getSequenceSetId();
-
- for (int t = 0; t < frames.length; t++)
- {
- if (frames[t] instanceof AlignFrame && frames[t] != source)
- {
- AlignFrame af = (AlignFrame) frames[t];
- boolean gatherThis = false;
- for (int a = 0; a < af.alignPanels.size(); a++)
- {
- AlignmentPanel ap = af.alignPanels.get(a);
- if (viewId.equals(ap.av.getSequenceSetId()))
- {
- gatherThis = true;
- ap.av.setGatherViewsHere(false);
- ap.av.setExplodedGeometry(af.getBounds());
- source.addAlignmentPanel(ap, false);
- }
- }
-
- if (gatherThis)
- {
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
- }
- }
- }
-
- }
-
- jalview.gui.VamsasApplication v_client = null;
-
- @Override
- public void vamsasImport_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.open_saved_vamsas_session"));
- chooser.setToolTipText(MessageManager.getString(
- "label.select_vamsas_session_opened_as_new_vamsas_session"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String fle = chooser.getSelectedFile().toString();
- if (!vamsasImport(chooser.getSelectedFile()))
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.couldnt_import_as_vamsas_session",
- new Object[]
- { fle }),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
- }
- }
- }
- else
- {
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- }
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(URL url)
- {
- // TODO: create progress bar
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- try
- {
- // copy the URL content to a temporary local file
- // TODO: be a bit cleverer here with nio (?!)
- File file = File.createTempFile("vdocfromurl", ".vdj");
- FileOutputStream fos = new FileOutputStream(file);
- BufferedInputStream bis = new BufferedInputStream(url.openStream());
- byte[] buffer = new byte[2048];
- int ln;
- while ((ln = bis.read(buffer)) > -1)
- {
- fos.write(buffer, 0, ln);
- }
- bis.close();
- fos.close();
- v_client = new jalview.gui.VamsasApplication(this, file,
- url.toExternalForm());
- } catch (Exception ex)
- {
- jalview.bin.Cache.log.error(
- "Failed to create new vamsas session from contents of URL "
- + url,
- ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- return v_client.inSession();
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(File file)
- {
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- try
- {
- v_client = new jalview.gui.VamsasApplication(this, file, null);
- } catch (Exception ex)
- {
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- jalview.bin.Cache.log.error(
- "New vamsas session from existing session file failed:", ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- return v_client.inSession();
- }
-
- public boolean joinVamsasSession(String mysesid)
- {
- if (v_client != null)
- {
- throw new Error(MessageManager
- .getString("error.try_join_vamsas_session_another"));
- }
- if (mysesid == null)
- {
- throw new Error(
- MessageManager.getString("error.invalid_vamsas_session_id"));
- }
- v_client = new VamsasApplication(this, mysesid);
- setupVamsasConnectedGui();
- v_client.initial_update();
- return (v_client.inSession());
- }
-
- @Override
- public void vamsasStart_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // Start a session.
- // we just start a default session for moment.
- /*
- * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- * getProperty("LAST_DIRECTORY"));
- *
- * chooser.setFileView(new JalviewFileView());
- * chooser.setDialogTitle("Load Vamsas file");
- * chooser.setToolTipText("Import");
- *
- * int value = chooser.showOpenDialog(this);
- *
- * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
- * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
- */
- v_client = new VamsasApplication(this);
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- }
- else
- {
- // store current data in session.
- v_client.push_update(); // TODO: thread
- }
- }
-
- protected void setupVamsasConnectedGui()
- {
- vamsasStart.setText(MessageManager.getString("label.session_update"));
- vamsasSave.setVisible(true);
- vamsasStop.setVisible(true);
- vamsasImport.setVisible(false); // Document import to existing session is
- // not possible for vamsas-client-1.0.
- }
-
- protected void setupVamsasDisconnectedGui()
- {
- vamsasSave.setVisible(false);
- vamsasStop.setVisible(false);
- vamsasImport.setVisible(true);
- vamsasStart
- .setText(MessageManager.getString("label.new_vamsas_session"));
- }
-
- @Override
- public void vamsasStop_actionPerformed(ActionEvent e)
- {
- if (v_client != null)
- {
- v_client.end_session();
- v_client = null;
- setupVamsasDisconnectedGui();
- }
- }
-
- protected void buildVamsasStMenu()
- {
- if (v_client == null)
- {
- String[] sess = null;
- try
- {
- sess = VamsasApplication.getSessionList();
- } catch (Exception e)
+
+ for (AlignFrame afr : frames)
{
- jalview.bin.Cache.log.warn("Problem getting current sessions list.",
- e);
- sess = null;
- }
- if (sess != null)
- {
- jalview.bin.Cache.log.debug(
- "Got current sessions list: " + sess.length + " entries.");
- VamsasStMenu.removeAll();
- for (int i = 0; i < sess.length; i++)
- {
- JMenuItem sessit = new JMenuItem();
- sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager
- .formatMessage("label.connect_to_session", new Object[]
- { sess[i] }));
- final Desktop dsktp = this;
- final String mysesid = sess[i];
- sessit.addActionListener(new ActionListener()
+ if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
+ {
+ if (afr.alignPanels != null)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ for (AlignmentPanel ap : afr.alignPanels)
{
- if (dsktp.v_client == null)
+ if (sequenceSetId == null
+ || sequenceSetId.equals(ap.av.getSequenceSetId()))
{
- Thread rthr = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- dsktp.v_client = new VamsasApplication(dsktp, mysesid);
- dsktp.setupVamsasConnectedGui();
- dsktp.v_client.initial_update();
- }
-
- }, "VamsasSessionThread");
- rthr.start();
+ viewp.add(ap.av);
}
- };
- });
- VamsasStMenu.add(sessit);
+ }
+ }
+ else
+ {
+ viewp.add(afr.getViewport());
+ }
}
- // don't show an empty menu.
- VamsasStMenu.setVisible(sess.length > 0);
-
}
- else
+ if (viewp.size() > 0)
{
- jalview.bin.Cache.log.debug("No current vamsas sessions.");
- VamsasStMenu.removeAll();
- VamsasStMenu.setVisible(false);
+ return viewp.toArray(new AlignmentViewport[viewp.size()]);
}
}
- else
- {
- // Not interested in the content. Just hide ourselves.
- VamsasStMenu.setVisible(false);
- }
+ return null;
}
- @Override
- public void vamsasSave_actionPerformed(ActionEvent e)
+ /**
+ * Explode the views in the given frame into separate AlignFrame
+ *
+ * @param af
+ */
+ public static void explodeViews(AlignFrame af)
{
- if (v_client != null)
+ int size = af.alignPanels.size();
+ if (size < 2)
{
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- JalviewFileChooser chooser = new JalviewFileChooser("vdj",
- "Vamsas Document");
+ return;
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_vamsas_document_archive"));
+ // FIXME: ideally should use UI interface API
+ FeatureSettings viewFeatureSettings = (af.featureSettings != null
+ && af.featureSettings.isOpen()) ? af.featureSettings : null;
+ Rectangle fsBounds = af.getFeatureSettingsGeometry();
+ for (int i = 0; i < size; i++)
+ {
+ AlignmentPanel ap = af.alignPanels.get(i);
- int value = chooser.showSaveDialog(this);
+ AlignFrame newaf = new AlignFrame(ap);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ // transfer reference for existing feature settings to new alignFrame
+ if (ap == af.alignPanel)
{
- java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel(MessageManager
- .formatMessage("label.saving_vamsas_doc", new Object[]
- { choice.getName() }));
- Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String warnmsg = null;
- String warnttl = null;
- try
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
{
- v_client.vclient.storeDocument(choice);
- } catch (Error ex)
- {
- warnttl = "Serious Problem saving Vamsas Document";
- warnmsg = ex.toString();
- jalview.bin.Cache.log
- .error("Error Whilst saving document to " + choice, ex);
+ newaf.featureSettings = viewFeatureSettings;
+ }
+ newaf.setFeatureSettingsGeometry(fsBounds);
+ }
- } catch (Exception ex)
- {
- warnttl = "Problem saving Vamsas Document.";
- warnmsg = ex.toString();
- jalview.bin.Cache.log.warn(
- "Exception Whilst saving document to " + choice, ex);
+ /*
+ * Restore the view's last exploded frame geometry if known. Multiple views from
+ * one exploded frame share and restore the same (frame) position and size.
+ */
+ Rectangle geometry = ap.av.getExplodedGeometry();
+ if (geometry != null)
+ {
+ newaf.setBounds(geometry);
+ }
- }
- removeProgressPanel(progpanel);
- if (warnmsg != null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ ap.av.setGatherViewsHere(false);
- warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
- }
+ addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ // and materialise a new feature settings dialog instance for the new
+ // alignframe
+ // (closes the old as if 'OK' was pressed)
+ if (ap == af.alignPanel && newaf.featureSettings != null
+ && newaf.featureSettings.isOpen()
+ && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+ {
+ newaf.showFeatureSettingsUI();
}
}
- }
- JPanel vamUpdate = null;
+ af.featureSettings = null;
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ }
/**
- * hide vamsas user gui bits when a vamsas document event is being handled.
+ * Gather expanded views (separate AlignFrame's) with the same sequence set
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
*
- * @param b
- * true to hide gui, false to reveal gui
+ * @param source
*/
- public void setVamsasUpdate(boolean b)
+ public void gatherViews(AlignFrame source)
{
- Cache.log.debug("Setting gui for Vamsas update "
- + (b ? "in progress" : "finished"));
-
- if (vamUpdate != null)
+ source.viewport.setGatherViewsHere(true);
+ source.viewport.setExplodedGeometry(source.getBounds());
+ JInternalFrame[] frames = desktop.getAllFrames();
+ String viewId = source.viewport.getSequenceSetId();
+ for (int t = 0; t < frames.length; t++)
{
- this.removeProgressPanel(vamUpdate);
+ if (frames[t] instanceof AlignFrame && frames[t] != source)
+ {
+ AlignFrame af = (AlignFrame) frames[t];
+ boolean gatherThis = false;
+ for (int a = 0; a < af.alignPanels.size(); a++)
+ {
+ AlignmentPanel ap = af.alignPanels.get(a);
+ if (viewId.equals(ap.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ ap.av.setGatherViewsHere(false);
+ ap.av.setExplodedGeometry(af.getBounds());
+ source.addAlignmentPanel(ap, false);
+ }
+ }
+
+ if (gatherThis)
+ {
+ if (af.featureSettings != null && af.featureSettings.isOpen())
+ {
+ if (source.featureSettings == null)
+ {
+ // preserve the feature settings geometry for this frame
+ source.featureSettings = af.featureSettings;
+ source.setFeatureSettingsGeometry(
+ af.getFeatureSettingsGeometry());
+ }
+ else
+ {
+ // close it and forget
+ af.featureSettings.close();
+ }
+ }
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+ }
+ }
}
- if (b)
+
+ // refresh the feature setting UI for the source frame if it exists
+ if (source.featureSettings != null && source.featureSettings.isOpen())
{
- vamUpdate = this.addProgressPanel(
- MessageManager.getString("label.updating_vamsas_session"));
+ source.showFeatureSettingsUI();
}
-
- vamsasStart.setVisible(!b);
- vamsasStop.setVisible(!b);
- vamsasSave.setVisible(!b);
}
public JInternalFrame[] getAllFrames()
}
// JAL-940 - disabled JWS1 service configuration - always start discoverer
// until we phase out completely
- (t0 = new Thread(discoverer)).start();
+ (t0 = new Thread(discoverer, "DiscovererThread")).start();
}
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ if (ignore_SHOW_JWS2_SERVICES_preference
+ || Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
.startDiscoverer(changeSupport);
}
}
// and call ourselves again.
- addStructure(pdbentry, seqs, chains, align, alignFrame);
+ addStructure(pdbentry, seqs, chains, alignFrame);
}
- }).start();
+ }, "Adding3DStructureQueueThread").start();
return;
}
}
{ seqs }, new String[][] { chains });
addingStructures = true;
_started = false;
- worker = new Thread(this);
- alignAddedStructures = align;
+ worker = new Thread(this, "Adding3DStructureThread");
worker.start();
return;
}
*/
package jalview.gui;
+import java.util.Locale;
+
import jalview.analysis.AlignmentSorter;
- import jalview.analysis.AverageDistanceTree;
- import jalview.analysis.NJTree;
- import jalview.analysis.TreeBuilder;
import jalview.analysis.TreeModel;
- import jalview.analysis.scoremodels.ScoreModels;
- import jalview.api.analysis.ScoreModelI;
- import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
String treeTitle; // if tree loaded
+ SimilarityParamsI similarityParams;
+
- private TreeCanvas treeCanvas;
+ TreeCanvas treeCanvas;
TreeModel tree;
public AlignmentViewport getViewPort()
{
- return treeCanvas.av;
+ // @Mungo - Why don't we return our own viewport ???
+ return getTreeCanvas().getViewport();
}
- void initTreePanel(AlignmentPanel ap, String type, String modelName,
- NewickFile newTree, AlignmentView inputData)
+ /**
+ * Initialize a tree panel based on a calculated tree
+ *
+ * @param ap
+ * @param tree
+ */
+ void initTreePanel(AlignmentPanel ap, TreeModel tree)
{
+ buildTreeCanvas(ap);
- av = ap.av;
- this.treeType = type;
- this.scoreModelName = modelName;
-
- treeCanvas = new TreeCanvas(this, ap, scrollPane);
- scrollPane.setViewportView(treeCanvas);
-
- PaintRefresher.Register(this, ap.av.getSequenceSetId());
-
- buildAssociatedViewMenu();
-
- final PropertyChangeListener listener = addAlignmentListener();
-
- /*
- * remove listener when window is closed, so that this
- * panel can be garbage collected
- */
- addInternalFrameListener(new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(InternalFrameEvent evt)
- {
- if (av != null)
- {
- av.removePropertyChangeListener(listener);
- }
- releaseReferences();
- }
- });
-
- TreeLoader tl = new TreeLoader(newTree, inputData);
+ TreeLoader tl = new TreeLoader(null, null);
tl.start();
}
{
originalSeqData.setVisible(false);
}
-
-
-
}
- else
- {
- ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
- scoreModelName, treeCanvas.getAssociatedPanel());
- TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
- ? new NJTree(av, sm, similarityParams)
- : new AverageDistanceTree(av, sm, similarityParams);
- tree = new TreeModel(njtree);
- showDistances(true);
- }
+ showTree(tree);
+ }
+
+ public void showTree(TreeModel tree)
+ {
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
treeCanvas.setTree(tree);
{
return treeTitle;
}
+ else
+ {
+ /*
+ * i18n description of Neighbour Joining or Average Distance method
+ */
+ String treecalcnm = MessageManager
+ .getString("label.tree_calc_" + treeType.toLowerCase());
- /*
- * short score model name (long description can be too long)
- */
- String smn = substitutionMatrix;
-
- /*
- * put them together as <method> Using <model>
- */
- final String ttl = MessageManager
- .formatMessage("label.treecalc_title", treecalcnm, smn);
+ /*
+ * i18n description of Neighbour Joining or Average Distance method
+ */
+ String treecalcnm = MessageManager.getString(
+ "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
+
+ /*
+ * short score model name (long description can be too long)
+ */
+ String smn = scoreModelName;
+
+ /*
+ * put them together as <method> Using <model>
+ */
+ final String ttl = MessageManager.formatMessage("label.calc_title",
+ treecalcnm, smn);
- return ttl;
+ return ttl;
+ }
}
+
+ /**
+ * Builds an EPS image and writes it to the specified file.
+ *
+ * @param outFile
+ * @param textOption
+ * true for Text character rendering, false for Lineart
+ */
+ protected void writeEpsFile(File outFile, boolean textOption)
+ {
+ try
+ {
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ FileOutputStream out = new FileOutputStream(outFile);
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
+ pg.setAccurateTextMode(!textOption);
+ treeCanvas.draw(pg, width, height);
+
+ pg.flush();
+ pg.close();
+ } catch (Exception ex)
+ {
+ System.err.println("Error writing tree as EPS");
+ ex.printStackTrace();
+ }
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public void setViewport(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ public TreeCanvas getTreeCanvas()
+ {
+ return treeCanvas;
+ }
}
@Override
public void run()
{
- Cache.log.info("Jalview updating to the Vamsas Session.");
+ Console.info("Jalview updating to the Vamsas Session.");
dealWithDocumentUpdate(true);
- Cache.log.info("Jalview finished updating to the Vamsas Session.");
+ Console.info("Jalview finished updating to the Vamsas Session.");
}
- });
+ }, "UpdateVamsasThread");
udthread.start();
}
}
AnimatedPanel ap = new AnimatedPanel();
- titlePanel.add(ap, BorderLayout.CENTER);
+ ap.setPreferredSize(new Dimension(60, 60));
+ titlePanel.add(ap, BorderLayout.WEST);
+ titlePanel.add(titleText, BorderLayout.CENTER);
+ setStatus(currentStatus);
- Thread thread = new Thread(ap);
+ Thread thread = new Thread(ap, "AnimatedPanelThread");
thread.start();
final WebserviceInfo thisinfo = this;
- frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- // System.out.println("Shutting down webservice client");
- WSClientI service = thisinfo.getthisService();
- if (service != null && service.isCancellable())
- {
- service.cancelJob();
- }
- };
- });
+ frame.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent evt)
+ {
+ // System.out.println("Shutting down webservice client");
+ WSClientI service = thisinfo.getthisService();
+ if (service != null && service.isCancellable())
+ {
+ service.cancelJob();
+ }
+ }
+ });
frame.validate();
}
*/
protected AlignFrame _LoadFileWaitTillLoaded()
{
- Thread loader = new Thread(this, "LoadFileWithWaitingThread");
- loader.start();
-
- while (loader.isAlive())
- {
- try
- {
- Thread.sleep(500);
- } catch (Exception ex)
- {
- }
- }
-
+ this.run();
-
return alignFrame;
}
{
try
{
- bootstrap = (new Integer(nbootstrap.stringMatched(1)))
+ bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
.intValue();
- HasBootstrap = true;
+ hasBootstrap = true;
} catch (Exception e)
{
Error = ErrorStringrange(Error, "Can't parse bootstrap value",
fileMenu.add(exportImageMenu);
fileMenu.add(exportFeatures);
fileMenu.add(exportAnnotations);
- fileMenu.add(loadTreeMenuItem);
+ fileMenu.add(loadTreeMenu);
fileMenu.add(associatedData);
+ if (!Platform.isJS())
+ {
+ fileMenu.add(loadVcf);
+ }
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
// JAL-574
// selectMenu.addSeparator();
// selectMenu.add(listenToViewSelections);
+
+
+ }
+
+ protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeFam_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreePfam_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeBase_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
}
+ protected void loadVcf_actionPerformed()
+ {
+ }
+
/**
* Constructs the entries on the Colour menu (but does not add them to the
* menu).
}
}
+ @Override
+ public void setD(double[] v)
+ {
+ d = v;
+ }
+
+ @Override
+ public void setE(double[] v)
+ {
+ e = v;
+ }
+
+ public double getTotal()
+ {
+ double d = 0d;
+ for (int i = 0; i < this.height(); i++)
+ {
+ for (int j = 0; j < this.width(); j++)
+ {
+ d += value[i][j];
+ }
+ }
+ return d;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean equals(MatrixI m2, double delta)
+ {
+ if (m2 == null || this.height() != m2.height()
+ || this.width() != m2.width())
+ {
+ return false;
+ }
+ for (int i = 0; i < this.height(); i++)
+ {
+ for (int j = 0; j < this.width(); j++)
+ {
+ double diff = this.getValue(i, j) - m2.getValue(i, j);
+ if (Math.abs(diff) > delta)
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+ @Override
+ public double[][] getValues()
+ {
+ return value;
+ }
}
double[] getRow(int i);
/**
+ * Answers a new matrix with a copy of the values in this one
+ *
+ * @return
+ */
+ MatrixI copy();
+
+ /**
+ * Answers all values present in the Matrix ordered by row,column
+ *
+ * @return the double array containing the values ordered in {row values} per
+ * column
+ */
+ double[][] getValues();
+
-
- MatrixI copy();
-
++ /**
+ * Returns a new matrix which is the transpose of this one
+ *
+ * @return
+ */
MatrixI transpose();
+ /**
+ * Returns a new matrix which is the result of premultiplying this matrix by
+ * the supplied argument. If this of size AxB (A rows and B columns), and the
+ * argument is CxA (C rows and A columns), the result is of size CxB.
+ *
+ * @param in
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if the number of columns in the pre-multiplier is not equal to
+ * the number of rows in the multiplicand (this)
+ */
MatrixI preMultiply(MatrixI m);
+ /**
+ * Returns a new matrix which is the result of postmultiplying this matrix by
+ * the supplied argument. If this of size AxB (A rows and B columns), and the
+ * argument is BxC (B rows and C columns), the result is of size AxC.
+ * <p>
+ * This method simply returns the result of in.preMultiply(this)
+ *
+ * @param in
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if the number of rows in the post-multiplier is not equal to the
+ * number of columns in the multiplicand (this)
+ * @see #preMultiply(Matrix)
+ */
MatrixI postMultiply(MatrixI m);
double[] getD();
}
}
+ /**
+ * Converts a list of {@code start-end} ranges to a single array of
+ * {@code start1, end1, start2, ... } ranges
+ *
+ * @param ranges
+ * @return
+ */
+ public static int[] rangeListToArray(List<int[]> ranges)
+ {
+ int rangeCount = ranges.size();
+ int[] result = new int[rangeCount * 2];
+ int j = 0;
+ for (int i = 0; i < rangeCount; i++)
+ {
+ int[] range = ranges.get(i);
+ result[j++] = range[0];
+ result[j++] = range[1];
+ }
+ return result;
+ }
+
+ /*
+ * Returns the maximal start-end positions in the given (ordered) list of
+ * ranges which is overlapped by the given begin-end range, or null if there
+ * is no overlap.
+ *
+ * <pre>
+ * Examples:
+ * if ranges is {[4, 8], [10, 12], [16, 19]}
+ * then
+ * findOverlap(ranges, 1, 20) == [4, 19]
+ * findOverlap(ranges, 6, 11) == [6, 11]
+ * findOverlap(ranges, 9, 15) == [10, 12]
+ * findOverlap(ranges, 13, 15) == null
+ * </pre>
+ *
+ * @param ranges
+ * @param begin
+ * @param end
+ * @return
+ */
+ protected static int[] findOverlap(List<int[]> ranges, final int begin,
+ final int end)
+ {
+ boolean foundStart = false;
+ int from = 0;
+ int to = 0;
+ /*
+ * traverse the ranges to find the first position (if any) >= begin,
+ * and the last position (if any) <= end
+ */
+ for (int[] range : ranges)
+ {
+ if (!foundStart)
+ {
+ if (range[0] >= begin)
+ {
+ /*
+ * first range that starts with, or follows, begin
+ */
+ foundStart = true;
+ from = Math.max(range[0], begin);
+ }
+ else if (range[1] >= begin)
+ {
+ /*
+ * first range that contains begin
+ */
+ foundStart = true;
+ from = begin;
+ }
+ }
+
+ if (range[0] <= end)
+ {
+ to = Math.min(end, range[1]);
+ }
+ }
+
+ return foundStart && to >= from ? new int[] { from, to } : null;
+ }
++
+ public static <K, V> Map<K, V> putWithDuplicationCheck(Map<K, V> map, K key,
+ V value)
+ {
+ if (!map.containsKey(key))
+ {
+ map.put(key, value);
+ }
+ else
+ {
+ jalview.bin.Cache.log.warn(
+ "Attempt to add duplicate entry detected for map with key: "
+ + key.toString() + " and value: " + value.toString());
+ }
+
+ return map;
-
+ }
}
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- Vector<SequenceI> nseq = new Vector<>();
- for (int i = 0; sequencesArray != null
- && i < sequencesArray.length; i++)
+ int n;
+ if (sequencesArray == null || (n = sequencesArray.length) == 0)
+ {
- nseq.addElement(sequencesArray[i]);
- DBRefEntry[] dbr = sequencesArray[i].getDBRefs();
+ return sequencesArray;
++ }
+ ArrayList<SequenceI> nseq = new ArrayList<>();
+ for (int i = 0; i < n; i++)
+ {
+ nseq.add(sequencesArray[i]);
+ List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
Mapping map = null;
- for (int r = 0; (dbr != null) && r < dbr.length; r++)
+ if (dbr != null)
{
- if ((map = dbr[r].getMap()) != null)
+ for (int r = 0, rn = dbr.size(); r < rn; r++)
{
- if (map.getTo() != null && !nseq.contains(map.getTo()))
+ if ((map = dbr.get(r).getMap()) != null)
{
- nseq.addElement(map.getTo());
+ if (map.getTo() != null && !nseq.contains(map.getTo()))
+ {
+ nseq.add(map.getTo());
+ }
}
}
}
sv.action, sv);
changeSupport.firePropertyChange("services",
new Vector<Jws2Instance>(), services);
- }
- }).start();
-
+ };
+ }, "LoadPreferredServiceThread").start();
-
}
});
}
--- /dev/null
+eclipse.preferences.version=1
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+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_ellipsis=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_lambda_arrow=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_try=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while=insert
+org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return=insert
+org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_throw=insert
+org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_unary_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.join_lines_in_comments=true
+org.eclipse.jdt.core.formatter.join_wrapped_lines=true
+org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
+org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=true
+org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
+org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
+org.eclipse.jdt.core.formatter.lineSplit=76
+org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
+org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
+org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
++org.eclipse.jdt.core.formatter.parentheses_positions_in_annotation=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_catch_clause=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_if_while_statement=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_lambda_declaration=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_method_delcaration=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement=common_lines
++org.eclipse.jdt.core.formatter.parentheses_positions_in_try_clause=common_lines
+org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
+org.eclipse.jdt.core.formatter.tabulation.char=space
+org.eclipse.jdt.core.formatter.tabulation.size=2
+org.eclipse.jdt.core.formatter.use_on_off_tags=true
+org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
++org.eclipse.jdt.core.formatter.wrap_before_assignment_operator=false
+org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
++org.eclipse.jdt.core.formatter.wrap_before_conditional_operator=true
+org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
+org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
+org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
-
git://source.jalview.org / jalview.git / commitdiff