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.Locale;
+import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
-import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
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;
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
- "No sort");
+ String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
if (sortby.equals("Id"))
{
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (Cache.getDefault("SHOW_OVERVIEW", false))
{
this.overviewMenuItem_actionPerformed(null);
}
}
}
});
- if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("devel") > -1
- || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
- .indexOf("test") > -1)
+ || Cache.getDefault("VERSION", "DEVELOPMENT")
+ .toLowerCase(Locale.ROOT).indexOf("test") > -1)
{
formatMenu.add(vsel);
}
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, 1);
+ alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
}
break;
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, -1);
+ alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(-1, 0);
+ alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(1, 0);
+ alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
}
break;
*/
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
}
else
{
- Cache.log.error(MessageManager
+ Console.error(MessageManager
.formatMessage("label.couldnt_save_file", new Object[]
{ lastFilenameSaved }));
}
BackupFiles backupfiles = null;
if (doBackup)
{
- Cache.log.trace(
+ Console.trace(
"ALIGNFRAME making backupfiles object for " + file);
backupfiles = new BackupFiles(file);
}
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath()
: file;
- Cache.log.trace("ALIGNFRAME setting PrintWriter");
+ Console.trace("ALIGNFRAME setting PrintWriter");
PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
if (backupfiles != null)
{
- Cache.log.trace("ALIGNFRAME about to write to temp file "
+ Console.trace("ALIGNFRAME about to write to temp file "
+ backupfiles.getTempFilePath());
}
out.print(output);
- Cache.log.trace("ALIGNFRAME about to close file");
+ Console.trace("ALIGNFRAME about to close file");
out.close();
- Cache.log.trace("ALIGNFRAME closed file");
+ Console.trace("ALIGNFRAME closed file");
AlignFrame.this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
} catch (IOException e)
{
lastSaveSuccessful = false;
- Cache.log.error(
+ Console.error(
"ALIGNFRAME Something happened writing the temp file");
- Cache.log.error(e.getMessage());
- Cache.log.debug(Cache.getStackTraceString(e));
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
lastSaveSuccessful = false;
- Cache.log.error(
+ Console.error(
"ALIGNFRAME Something unexpected happened writing the temp file");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
if (doBackup)
{
backupfiles.setWriteSuccess(lastSaveSuccessful);
- Cache.log.debug("ALIGNFRAME writing temp file was "
+ Console.debug("ALIGNFRAME writing temp file was "
+ (lastSaveSuccessful ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
- Cache.log.trace(
+ Console.trace(
"ALIGNFRAME about to rollBackupsAndRenameTempFile");
lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
- Cache.log.debug(
+ Console.debug(
"ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ (lastSaveSuccessful ? "" : "un")
+ "successfully");
public void associatedData_actionPerformed(ActionEvent e)
{
final JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
String tooltip = MessageManager
.getString("label.load_jalview_annotations");
public void run()
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ Cache.setProperty("LAST_DIRECTORY", choice);
loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
}
});
{
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
if (originalSource != viewport)
{
- Cache.log.warn(
+ Console.warn(
"Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
/**
* Constructs a tree panel and adds it to the desktop
*
- * @param type
- * tree type (NJ or AV)
- * @param modelName
- * name of score model used to compute the tree
- * @param options
- * parameters for the distance or similarity calculation
+ * @param params
+ * @param treeAlgo
+ *
+ * @param tree
+ *
+ *
*/
- void newTreePanel(String type, String modelName,
- SimilarityParamsI options)
+ void newTreePanel(TreeModel tree, String treeAlgo,
+ String substitutionMatrix)
{
String frameTitle = "";
TreePanel tp;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- for (SequenceI _s : sg.getSequences())
+ for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
{
if (_s.getLength() < sg.getEndRes())
{
}
}
- tp = new TreePanel(alignPanel, type, modelName, options);
+ tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
frameTitle += " from ";
@Override
public void actionPerformed(ActionEvent e)
{
+ // adapt to Aptx
tp.sortByTree_actionPerformed();
addHistoryItem(tp.sortAlignmentIn(alignPanel));
@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());
+ }
chooser.setResponseHandler(0, new Runnable()
{
{
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(),
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);
- }
+// TODO: handle any other warnings from treeParser ?
+ // if (treeParser != null && treeParser.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)
{
return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
+ final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
+
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
+ wsmenu.add(phylogenmenu);
// No search services yet
// wsmenu.add(seqsrchmenu);
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
- boolean new_sspred = false;
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
+ // logic for 2.11.1.4 is
+ // always look to see if there is a discover. if there isn't
+ // we can't show any Jws2 services
+ // if there are services available, show them - regardless of
+ // the 'show JWS2 preference'
+ // if the discoverer is running then say so
+ // otherwise offer to trigger discovery if 'show JWS2' is not
+ // enabled
Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs != null)
{
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
- if (sv.description.toLowerCase().contains("jpred"))
+ if (sv.description.toLowerCase(Locale.ROOT)
+ .contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
}
}
}
-
}
+
if (jws2servs.isRunning())
{
JMenuItem tm = new JMenuItem(
tm.setEnabled(false);
webService.add(tm);
}
+ else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ JMenuItem enableJws2 = new JMenuItem(
+ "Discover Web Services");
+ enableJws2.setToolTipText(
+ "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
+ enableJws2.setEnabled(true);
+ enableJws2.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // start service discoverer, but ignore preference
+ Desktop.instance.startServiceDiscovery(false,
+ true);
+ }
+ });
+ webService.add(enableJws2);
+ }
}
}
build_urlServiceMenu(me.webService);
}
} catch (Exception e)
{
- Cache.log.debug(
+ Console.debug(
"Exception during web service menu building process.",
e);
}
}
buildingMenu = false;
}
- }).start();
+ }, "BuildWebServiceThread").start();
}
showProducts.setEnabled(showp);
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
- new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
+ new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this),
+ "CrossReferencesThread")
.start();
}
al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
- jalview.bin.Cache.log.error(
- "Exception during translation. Please report this !", ex);
+ Console.error("Exception during translation. Please report this !",
+ ex);
final String msg = MessageManager.getString(
"label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
ex.printStackTrace();
}
}
- }).start();
+ }, "DropFileThread").start();
}
}
}
} catch (Exception x)
{
- Cache.log.debug(
+ Console.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
});
dbRefFetcher.fetchDBRefs(false);
}
- }).start();
+ }, "BuildFetchDBMenuThread").start();
}
git://source.jalview.org / jalview.git / blobdiff