package jalview.gui;
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.Map;
+import java.util.Map.Entry;
+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 javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebservicesManager;
+
+import ext.vamsas.ServiceHandle;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
-import jalview.api.AlignExportSettingI;
+import jalview.analysis.TreeModel;
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
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.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignExportSettingsAdapter;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
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.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
+import jalview.ext.treeviewer.TreeViewerUtils;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.TCoffeeScoreFile;
import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
+import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.DBRefUtils;
+import jalview.util.HttpUtils;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
*/
String fileName = null;
+ File fileObject;
+
/**
* Creates a new AlignFrame object with specific width and height.
*
*/
void init()
{
+ // setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
// 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"))
{
if (Desktop.desktop != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
+ if (!Platform.isJS())
+ {
+ addServiceListeners();
+ }
setGUINucleotide();
}
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (Cache.getDefault("SHOW_OVERVIEW", false))
{
this.overviewMenuItem_actionPerformed(null);
}
addKeyListener();
- final List<AlignmentPanel> selviews = new ArrayList<>();
+ final List<AlignmentViewPanel> selviews = new ArrayList<>();
final List<AlignmentPanel> origview = new ArrayList<>();
final String menuLabel = MessageManager
.getString("label.copy_format_from");
}
}
});
- 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);
}
}
/**
+ * JavaScript will have this, maybe others. More dependable than a file name
+ * and maintains a reference to the actual bytes loaded.
+ *
+ * @param file
+ */
+ public void setFileObject(File file)
+ {
+ this.fileObject = file;
+ }
+
+ /**
* Add a KeyListener with handlers for various KeyPressed and KeyReleased
* events
*/
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, 1,
- evt.isShiftDown() && !evt.isAltDown());
+ alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
}
break;
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, -1,
- evt.isShiftDown() && !evt.isAltDown());
+ alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
}
+
break;
case KeyEvent.VK_LEFT:
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
{
- cut_actionPerformed(null);
+ cut_actionPerformed();
}
else
{
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.keyboard_editing_mode", new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
- };
+ }
});
// Finally, build the menu once to get current service state
new Thread(new Runnable()
*/
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
}
@Override
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
- new jalview.gui.SequenceFetcher(this);
+ new SequenceFetcher(this);
}
@Override
Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
: DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
Rectangle bounds = this.getBounds();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE;
- AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
- protocol, currentFileFormat);
+
+ AlignFrame newframe = null;
+
+ if (fileObject == null)
+ {
+
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
+ fileName) ? DataSourceType.URL : DataSourceType.FILE;
+ newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
+ currentFileFormat);
+ }
+ else
+ {
+ newframe = loader.LoadFileWaitTillLoaded(fileObject,
+ DataSourceType.FILE, currentFileFormat);
+ }
newframe.setBounds(bounds);
if (featureSettings != null && featureSettings.isShowing())
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
- || fileName.startsWith("http"))
+ || HttpUtils.startsWithHttpOrHttps(fileName))
{
- saveAs_actionPerformed(null);
+ saveAs_actionPerformed();
}
else
{
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Saves the alignment to a file with a name chosen by the user, if necessary
+ * warning if a file would be overwritten
*/
@Override
- public void saveAs_actionPerformed(ActionEvent e)
+ public void saveAs_actionPerformed()
{
String format = currentFileFormat == null ? null
: currentFileFormat.getName();
int value = chooser.showSaveDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
+ return;
+ }
+ currentFileFormat = chooser.getSelectedFormat();
+ // todo is this (2005) test now obsolete - value is never null?
+ while (currentFileFormat == null)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.select_file_format_before_saving"),
+ MessageManager.getString("label.file_format_not_specified"),
+ JvOptionPane.WARNING_MESSAGE);
currentFileFormat = chooser.getSelectedFormat();
- while (currentFileFormat == null)
+ value = chooser.showSaveDialog(this);
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString(
- "label.select_file_format_before_saving"),
- MessageManager.getString("label.file_format_not_specified"),
- JvOptionPane.WARNING_MESSAGE);
- currentFileFormat = chooser.getSelectedFormat();
- value = chooser.showSaveDialog(this);
- if (value != JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
+ return;
}
+ }
- fileName = chooser.getSelectedFile().getPath();
+ fileName = chooser.getSelectedFile().getPath();
- Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ Cache.setProperty("LAST_DIRECTORY", fileName);
+ saveAlignment(fileName, currentFileFormat);
+ }
- Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(fileName, currentFileFormat);
+ boolean lastSaveSuccessful = false;
+
+ FileFormatI lastFormatSaved;
+
+ String lastFilenameSaved;
+
+ /**
+ * Raise a dialog or status message for the last call to saveAlignment.
+ *
+ * @return true if last call to saveAlignment(file, format) was successful.
+ */
+ public boolean isSaveAlignmentSuccessful()
+ {
+
+ if (!lastSaveSuccessful)
+ {
+ if (!Platform.isHeadless())
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ Console.error(MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }));
+ }
}
+ else
+ {
+
+ setStatus(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { lastFilenameSaved, lastFormatSaved }));
+
+ }
+ return lastSaveSuccessful;
}
- public boolean saveAlignment(String file, FileFormatI format)
+ /**
+ * Saves the alignment to the specified file path, in the specified format,
+ * which may be an alignment format, or Jalview project format. If the
+ * alignment has hidden regions, or the format is one capable of including
+ * non-sequence data (features, annotations, groups), then the user may be
+ * prompted to specify what to include in the output.
+ *
+ * @param file
+ * @param format
+ */
+ public void saveAlignment(String file, FileFormatI format)
{
- boolean success = true;
+ lastSaveSuccessful = true;
+ lastFilenameSaved = file;
+ lastFormatSaved = format;
if (FileFormat.Jalview.equals(format))
{
String shortName = title;
-
- if (shortName.indexOf(java.io.File.separatorChar) > -1)
+ if (shortName.indexOf(File.separatorChar) > -1)
{
- shortName = shortName.substring(
- shortName.lastIndexOf(java.io.File.separatorChar) + 1);
+ shortName = shortName
+ .substring(shortName.lastIndexOf(File.separatorChar) + 1);
}
-
- success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+ lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ file, format }));
+ return;
}
- else
+
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable cancelAction = new Runnable()
{
- AlignmentExportData exportData = getAlignmentForExport(format,
- viewport, null);
- if (exportData.getSettings().isCancelled())
- {
- return false;
- }
- FormatAdapter f = new FormatAdapter(alignPanel,
- exportData.getSettings());
- String output = f.formatSequences(format, exportData.getAlignment(), // class
- // cast
- // exceptions
- // will
- // occur in the distant future
- exportData.getOmitHidden(), exportData.getStartEndPostions(),
- f.getCacheSuffixDefault(format),
- viewport.getAlignment().getHiddenColumns());
-
- if (output == null)
+ @Override
+ public void run()
{
- success = false;
+ lastSaveSuccessful = false;
}
- else
+ };
+ Runnable outputAction = new Runnable()
+ {
+ @Override
+ public void run()
{
- // create backupfiles object and get new temp filename destination
- Cache.log.trace("ALIGNFRAME making backupfiles object for " + file);
- BackupFiles backupfiles = new BackupFiles(file);
-
- try
- {
- String tempFilePath = backupfiles.getTempFilePath();
- Cache.log.trace(
- "ALIGNFRAME setting PrintWriter to " + tempFilePath);
- PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
-
- Cache.log.trace(
- "ALIGNFRAME about to write to temp file " + tempFilePath);
-
- out.print(output);
- Cache.log.trace("ALIGNFRAME about to close file");
- out.close();
- Cache.log.trace("ALIGNFRAME closed file");
- this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { file, format.getName() }));
- } catch (IOException e)
- {
- success = false;
- Cache.log.error(
- "ALIGNFRAME Something happened writing the temp file");
- Cache.log.error(e.getMessage());
- Cache.log.debug(Cache.getStackTraceString(e));
-
- } catch (Exception ex)
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport
+ .getAlignExportData(options);
+ String output = new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns());
+ if (output == null)
{
- success = false;
- Cache.log.error(
- "ALIGNFRAME Something unexpected happened writing the temp file");
- Cache.log.error(ex.getMessage());
- Cache.log.debug(Cache.getStackTraceString(ex));
+ lastSaveSuccessful = false;
}
+ else
+ {
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = null;
+ if (doBackup)
+ {
+ Console.trace(
+ "ALIGNFRAME making backupfiles object for " + file);
+ backupfiles = new BackupFiles(file);
+ }
+ try
+ {
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+ : file;
+ Console.trace("ALIGNFRAME setting PrintWriter");
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
- backupfiles.setWriteSuccess(success);
- Cache.log.debug("ALIGNFRAME writing temp file was "
- + (success ? "" : "NOT ") + "successful");
- // do the backup file roll and rename the temp file to actual file
- Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
- success = backupfiles.rollBackupsAndRenameTempFile();
- Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
- + (success ? "" : "un") + "successfully");
+ if (backupfiles != null)
+ {
+ Console.trace("ALIGNFRAME about to write to temp file "
+ + backupfiles.getTempFilePath());
+ }
- }
- }
+ out.print(output);
+ Console.trace("ALIGNFRAME about to close file");
+ out.close();
+ Console.trace("ALIGNFRAME closed file");
+ AlignFrame.this.setTitle(file);
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format.getName() }));
+ lastSaveSuccessful = true;
+ } catch (IOException e)
+ {
+ lastSaveSuccessful = false;
+ Console.error(
+ "ALIGNFRAME Something happened writing the temp file");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
+ } catch (Exception ex)
+ {
+ lastSaveSuccessful = false;
+ Console.error(
+ "ALIGNFRAME Something unexpected happened writing the temp file");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
+ }
- if (!success)
- {
- if (!Platform.isHeadless())
- {
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { file }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ Console.debug("ALIGNFRAME writing temp file was "
+ + (lastSaveSuccessful ? "" : "NOT ") + "successful");
+ // do the backup file roll and rename the temp file to actual file
+ Console.trace(
+ "ALIGNFRAME about to rollBackupsAndRenameTempFile");
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ Console.debug(
+ "ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ + (lastSaveSuccessful ? "" : "un")
+ + "successfully");
+ }
+ }
}
- }
-
- return success;
- }
+ };
- private void warningMessage(String warning, String title)
- {
- if (new jalview.util.Platform().isHeadless())
+ /*
+ * show dialog with export options if applicable; else just do it
+ */
+ if (AlignExportOptions.isNeeded(viewport, format))
{
- System.err.println("Warning: " + title + "\nWarning: " + warning);
-
+ AlignExportOptions choices = new AlignExportOptions(
+ alignPanel.getAlignViewport(), format, options);
+ choices.setResponseAction(0, outputAction);
+ choices.setResponseAction(1, cancelAction);
+ choices.showDialog();
}
else
{
- JvOptionPane.showInternalMessageDialog(this, warning, title,
- JvOptionPane.WARNING_MESSAGE);
+ outputAction.run();
}
- return;
}
/**
- * DOCUMENT ME!
+ * Outputs the alignment to textbox in the requested format, if necessary
+ * first prompting the user for whether to include hidden regions or
+ * non-sequence data
*
- * @param e
- * DOCUMENT ME!
+ * @param fileFormatName
*/
@Override
- protected void outputText_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String fileFormatName)
{
FileFormatI fileFormat = FileFormats.getInstance()
- .forName(e.getActionCommand());
- AlignmentExportData exportData = getAlignmentForExport(fileFormat,
- viewport, null);
- if (exportData.getSettings().isCancelled())
+ .forName(fileFormatName);
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable outputAction = new Runnable()
{
- return;
- }
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(null);
- try
- {
- FileFormatI format = fileFormat;
- cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(format, exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getAlignment().getHiddenColumns()));
- Desktop.addInternalFrame(cap, MessageManager
- .formatMessage("label.alignment_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Outputting alignment as " + e.getActionCommand(),
- oom);
- cap.dispose();
- }
-
- }
-
- public static AlignmentExportData getAlignmentForExport(
- FileFormatI format, AlignViewportI viewport,
- AlignExportSettingI exportSettings)
- {
- AlignmentI alignmentToExport = null;
- AlignExportSettingI settings = exportSettings;
- String[] omitHidden = null;
-
- HiddenSequences hiddenSeqs = viewport.getAlignment()
- .getHiddenSequences();
-
- alignmentToExport = viewport.getAlignment();
-
- boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
- if (settings == null)
- {
- settings = new AlignExportSettings(hasHiddenSeqs,
- viewport.hasHiddenColumns(), format);
- }
- // settings.isExportAnnotations();
-
- if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
- {
- omitHidden = viewport.getViewAsString(false,
- settings.isExportHiddenSequences());
- }
+ @Override
+ public void run()
+ {
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport
+ .getAlignExportData(options);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ try
+ {
+ FileFormatI format = fileFormat;
+ cap.setText(new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { fileFormat.getName() }), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + fileFormat.getName(),
+ oom);
+ cap.dispose();
+ }
+ }
+ };
- int[] alignmentStartEnd = new int[2];
- if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ /*
+ * show dialog with export options if applicable; else just do it
+ */
+ if (AlignExportOptions.isNeeded(viewport, fileFormat))
{
- alignmentToExport = hiddenSeqs.getFullAlignment();
+ AlignExportOptions choices = new AlignExportOptions(
+ alignPanel.getAlignViewport(), fileFormat, options);
+ choices.setResponseAction(0, outputAction);
+ choices.showDialog();
}
else
{
- alignmentToExport = viewport.getAlignment();
+ outputAction.run();
}
- alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
- .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
- AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
- omitHidden, alignmentStartEnd, settings);
- return ed;
}
/**
}
/**
- * DOCUMENT ME!
+ * Creates a PNG image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
*
- * @param e
- * DOCUMENT ME!
+ * @param f
*/
@Override
public void createPNG(File f)
{
- alignPanel.makePNG(f);
+ alignPanel.makeAlignmentImage(TYPE.PNG, f);
}
/**
- * DOCUMENT ME!
+ * Creates an EPS image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
*
- * @param e
- * DOCUMENT ME!
+ * @param f
*/
@Override
public void createEPS(File f)
{
- alignPanel.makeEPS(f);
+ alignPanel.makeAlignmentImage(TYPE.EPS, f);
}
+ /**
+ * Creates an SVG image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
+ *
+ * @param f
+ */
@Override
public void createSVG(File f)
{
- alignPanel.makeSVG(f);
+ alignPanel.makeAlignmentImage(TYPE.SVG, f);
}
@Override
@Override
public void associatedData_actionPerformed(ActionEvent e)
{
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ final JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.load_jalview_annotations"));
- chooser.setToolTipText(
- MessageManager.getString("label.load_jalview_annotations"));
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ String tooltip = MessageManager
+ .getString("label.load_jalview_annotations");
+ chooser.setDialogTitle(tooltip);
+ chooser.setToolTipText(tooltip);
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice, null, null, null);
- }
+ @Override
+ public void run()
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
+ }
+ });
+ chooser.showOpenDialog(this);
}
/**
/**
* DOCUMENT ME!
*/
- void updateEditMenuBar()
+ public void updateEditMenuBar()
{
if (viewport.getHistoryList().size() > 0)
{
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();
}
/**
- * DOCUMENT ME!
+ * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
+ * or the sequence under cursor in keyboard mode
*
* @param up
- * DOCUMENT ME!
+ * or down (if !up)
*/
public void moveSelectedSequences(boolean up)
{
if (sg == null)
{
+ if (viewport.cursorMode)
+ {
+ sg = new SequenceGroup();
+ sg.addSequence(viewport.getAlignment().getSequenceAt(
+ alignPanel.getSeqPanel().seqCanvas.cursorY), false);
+ }
+ else
+ {
+ return;
+ }
+ }
+
+ if (sg.getSize() < 1)
+ {
return;
}
+
+ // TODO: JAL-3733 - add an event to the undo buffer for this !
+
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true, false);
synchronized void slideSequences(boolean right, int size)
{
List<SequenceI> sg = new ArrayList<>();
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
- .getSize() != viewport.getAlignment().getHeight())
- {
- sg = viewport.getSelectionGroup()
- .getSequences(viewport.getHiddenRepSequences());
- }
-
- if (sg.size() == 0 && viewport.cursorMode)
+ if (viewport.cursorMode)
{
sg.add(viewport.getAlignment()
.getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
}
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
+ {
+ sg = viewport.getSelectionGroup()
+ .getSequences(viewport.getHiddenRepSequences());
+ }
if (sg.size() < 1)
{
* DOCUMENT ME!
*/
@Override
- protected void copy_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
{
Desktop.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
{ Integer.valueOf(seqs.length).toString() }));
}
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
- Vector newDs = (importDs) ? new Vector() : null; // used to create
+ Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+ // create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
{
// propagate alignment changed.
- viewport.getRanges().setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action Cut (delete and copy) the selected region
*/
@Override
- protected void cut_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
{
- copy_actionPerformed(null);
- delete_actionPerformed(null);
+ copy_actionPerformed();
+ delete_actionPerformed();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Performs menu option to Delete the currently selected region
*/
@Override
- protected void delete_actionPerformed(ActionEvent evt)
+ protected void delete_actionPerformed()
{
SequenceGroup sg = viewport.getSelectionGroup();
return;
}
- /*
- * If the cut affects all sequences, warn, remove highlighted columns
- */
- if (sg.getSize() == viewport.getAlignment().getHeight())
+ Runnable okAction = new Runnable()
{
- boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
- + 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (isEntireAlignWidth)
+ @Override
+ public void run()
{
- int confirm = JvOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JvOptionPane.OK_CANCEL_OPTION);
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
+
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(),
+ sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
- if (confirm == JvOptionPane.CANCEL_OPTION
- || confirm == JvOptionPane.CLOSED_OPTION)
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
{
- return;
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
}
}
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
-
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
+ };
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
+ /*
+ * If the cut affects all sequences, prompt for confirmation
+ */
+ boolean wholeHeight = sg.getSize() == viewport.getAlignment()
+ .getHeight();
+ boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ + 1) == viewport.getAlignment().getWidth()) ? true : false;
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] {
+ MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ }
+ else
{
- try
- {
- this.setClosed(true);
- } catch (Exception ex)
- {
- }
+ okAction.run();
}
}
column, viewport.getAlignment());
}
- statusBar.setText(MessageManager
- .formatMessage("label.removed_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_columns",
+ new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
- .formatMessage("label.removed_empty_columns", new Object[]
+ setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+ new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
- new Finder(alignPanel);
+ new Finder(alignPanel, false, null);
}
/**
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
@Override
public void alignmentProperties()
{
- JEditorPane editPane = new JEditorPane("text/html", "");
- editPane.setEditable(false);
+ JComponent pane;
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
+
.formatAsHtml();
- editPane.setText(
- MessageManager.formatMessage("label.html_content", new Object[]
- { contents.toString() }));
+ String content = MessageManager.formatMessage("label.html_content",
+ new Object[]
+ { contents.toString() });
+ contents = null;
+
+ if (Platform.isJS())
+ {
+ JLabel textLabel = new JLabel();
+ textLabel.setText(content);
+ textLabel.setBackground(Color.WHITE);
+
+ pane = new JPanel(new BorderLayout());
+ ((JPanel) pane).setOpaque(true);
+ pane.setBackground(Color.WHITE);
+ ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ JEditorPane editPane = new JEditorPane("text/html", "");
+ editPane.setEditable(false);
+ editPane.setText(content);
+ pane = editPane;
+ }
+
JInternalFrame frame = new JInternalFrame();
- frame.getContentPane().add(new JScrollPane(editPane));
+
+ frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.alignment_properties", new Object[]
{
overview.dispose();
alignPanel.setOverviewPanel(null);
- };
+ }
});
if (getKeyListeners().length > 0)
{
/**
* 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 ";
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
+ Hashtable<String, String> scoreSorts = new Hashtable<>();
AlignmentAnnotation aann[];
for (SequenceI sqa : viewport.getAlignment().getSequences())
{
}
}
}
- Enumeration labels = scoreSorts.keys();
+ Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
- addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
}
}
+
/**
* Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
* TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
List<Component> comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
List<TreePanel> treePanels = new ArrayList<>();
+
+ Map<TreeFrameI, TreeViewerBindingI> aptxFrames = TreeViewerUtils
+ .getActiveTreeViews();
+
for (Component comp : comps)
{
+ // old treepanels
if (comp instanceof TreePanel)
{
treePanels.add((TreePanel) comp);
}
+
}
- if (treePanels.size() < 1)
+ if (treePanels.isEmpty() && aptxFrames.isEmpty())
{
sortByTreeMenu.setVisible(false);
return;
sortByTreeMenu.setVisible(true);
+ for (Entry<TreeFrameI, TreeViewerBindingI> aptxFrameWithBinding : aptxFrames
+ .entrySet())
+ {
+ TreeFrameI aptxFrame = aptxFrameWithBinding.getKey();
+ TreeViewerBindingI binding = aptxFrameWithBinding.getValue();
+
+ // future support for multiple tabs
+ // for (org.forester.archaeopteryx.TreePanel aptxTree : aptxFrame
+ // .getMainPanel().getTreePanels())
+ {
+ final JMenuItem item = new JMenuItem(
+ aptxFrame.getTree().getTreeName());
+
+ item.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ binding.sortByTree_actionPerformed(); // redundant here??
+ addHistoryItem(binding.sortAlignmentIn(alignPanel));
+ }
+
+ });
+ sortByTreeMenu.add(item);
+ }
+
+
+
+ }
+
+
+
+
+
+ // old treepanels
for (final TreePanel tp : treePanels)
{
final JMenuItem item = new JMenuItem(tp.getTitle());
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
+ chooseTreeFile();
+ }
+
+ @Override
+ protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
+ {
+ chooseTreeUrl();
+ }
+
+ @Override
+ protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb(0, null);
+
+ }
+
+ @Override
+ protected void loadTreeBase_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb(1, null);
+
+ }
+ @Override
+ protected void loadTreePfam_actionPerformed(ActionEvent e)
+ {
+
+ // only DBRefs of first sequence are checked for matching DB for now,
+ // iterating through them all seems excessive
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+ String dbId = null;
+ for (DBRefEntry pfamRef : DBRefUtils
+ .searchRefsForSource(seq.getDBRefs(), "pfam"))
+ {
+ if (pfamRef.getAccessionId().startsWith("PF"))
+ {
+ dbId = pfamRef.getAccessionId().replaceAll("[A-Za-z]", "");
+ }
+
+ }
+ chooseTreeDb(2, dbId);
+
+ }
+ @Override
+ protected void loadTreeFam_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb(3, null);
+
+ }
+
+ @Override
+ protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb(4, null);
+
+ }
+
+
+
+
+
+ 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"));
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ MessageManager.getString("label.load_tree_for_sequence_set"));
+ for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
+ .values())
+ {
+ chooser.setFileFilter(treeFormat.getTreeFilter());
+ }
+ final AlignFrame us=this;
+ chooser.setResponseHandler(0, new Runnable()
{
+ @Override
+ public void run()
+ {
String filePath = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
+
+
+ NewickFile fin = null; // old tree
try
{
- fin = new NewickFile(filePath, DataSourceType.FILE);
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
+ AptxInit.createInstancesFromFile(filePath, viewport);
+
+ // fin = new NewickFile(filePath, DataSourceType.FILE);
+ // viewport.setCurrentTree(viewport.getAlignPanel().alignFrame
+ // .showNewickTree(fin, filePath).getTree());
+
} catch (Exception ex)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ JvOptionPane.showMessageDialog(us, ex.getMessage(),
MessageManager.getString("label.problem_reading_tree_file"),
JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
- if (fin != null && fin.hasWarningMessage())
+ }
+ });
+ 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)
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager
- .getString("label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
+ 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.createInstancesFromUrl(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
+ {
+
+ }
+ }
+
+ /**
+ * Disgustingly hardcoded atm.
+ *
+ * @param databaseIndex
+ */
+ public void chooseTreeDb(int databaseIndex, String defaultIdentifier)
+ {
+ 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();
+
+ AptxInit.createInstancesFromDb(client, identifier, viewport);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
private boolean buildingMenu = false;
+ public void BuildTreeDbMenu()
+ {
+
+ }
/**
* Generates menu items and listener event actions for web service clients
*
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)
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
+ Vector<ServiceHandle> secstrpr = Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
+ final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
int p = secstrmenu.getItemCount();
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();
+ }, "BuildWebService").start();
}
*
* @param webService
*/
- private void build_urlServiceMenu(JMenu webService)
+ protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
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),
+ "CrossReferences")
.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
* Try to load a features file onto the alignment.
*
* @param file
- * contents or path to retrieve file
+ * contents or path to retrieve file or a File object
* @param sourceType
* access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed correctly.
*/
- public boolean parseFeaturesFile(String file, DataSourceType sourceType)
+ public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
{
+ // BH 2018
return avc.parseFeaturesFile(file, sourceType,
Cache.getDefault("RELAXEDSEQIDMATCHING", false));
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
+
final AlignFrame thisaf = this;
- final List<String> files = new ArrayList<>();
+ final List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
* Object[] { String,SequenceI}
*/
ArrayList<Object[]> filesmatched = new ArrayList<>();
- ArrayList<String> filesnotmatched = new ArrayList<>();
+ ArrayList<Object> filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
- String file = files.get(i).toString();
+ // BH 2018
+ Object file = files.get(i);
+ String fileName = file.toString();
String pdbfn = "";
- DataSourceType protocol = FormatAdapter.checkProtocol(file);
+ DataSourceType protocol = (file instanceof File
+ ? DataSourceType.FILE
+ : FormatAdapter.checkProtocol(fileName));
if (protocol == DataSourceType.FILE)
{
- File fl = new File(file);
+ File fl;
+ if (file instanceof File)
+ {
+ fl = (File) file;
+ Platform.cacheFileData(fl);
+ }
+ else
+ {
+ fl = new File(fileName);
+ }
pdbfn = fl.getName();
}
else if (protocol == DataSourceType.URL)
{
- URL url = new URL(file);
+ URL url = new URL(fileName);
pdbfn = url.getFile();
}
if (pdbfn.length() > 0)
}
if (mtch != null)
{
- FileFormatI type = null;
+ FileFormatI type;
try
{
type = new IdentifyFile().identify(file, protocol);
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
+ .associatePdbWithSeq(fm[0].toString(),
(DataSourceType) fm[1], toassoc, false,
Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
- + ((String) fm[0]) + " with "
+ + (fm[0].toString()) + " with "
+ toassoc.getDisplayId(true));
assocfiles++;
}
*/
for (Object[] o : filesmatched)
{
- filesnotmatched.add((String) o[0]);
+ filesnotmatched.add(o[0]);
}
}
}
{
return;
}
- for (String fn : filesnotmatched)
+ for (Object fn : filesnotmatched)
{
loadJalviewDataFile(fn, null, null, null);
}
ex.printStackTrace();
}
}
- }).start();
+ }, "DropFile").start();
}
}
* @param file
* either a filename or a URL string.
*/
- public void loadJalviewDataFile(String file, DataSourceType sourceType,
+ public void loadJalviewDataFile(Object file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
{
+ // BH 2018 was String file
try
{
if (sourceType == null)
changeColour(
new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar.setText(MessageManager.getString(
+ setStatus(MessageManager.getString(
"label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
}
} catch (Exception x)
{
- Cache.log.debug(
+ Console.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
new FileParse(file, sourceType));
sm.parse();
// todo: i18n this message
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.successfully_loaded_matrix",
sm.getMatrixName()));
}
if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
- String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
- JvOptionPane.QUESTION_MESSAGE);
+ String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
+ String reply = JvOptionPane.showInputDialog(msg, ttl);
if (reply != null)
{
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ }
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
});
dbRefFetcher.fetchDBRefs(false);
}
- }).start();
+ }, "BuildFetchDBMenu").start();
}
});
rfetch.add(fetchr);
- final AlignFrame me = this;
new Thread(new Runnable()
{
@Override
public void run()
{
final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton(me);
+ .getSequenceFetcherSingleton();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- String[] dbclasses = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
+ String[] dbclasses = sf.getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
{
continue;
}
- // List<DbSourceProxy> dbs=otherdb;
- // otherdb=new ArrayList<DbSourceProxy>();
- // for (DbSourceProxy db:dbs)
- // {
- // if (!db.isA(DBRefSource.ALIGNMENTDB)
- // }
if (mname == null)
{
mname = "From " + dbclass;
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ final AlignFrame us = this;
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, this);
- }
+ @Override
+ public void run()
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
+ }
+ });
+ chooser.showOpenDialog(null);
}
git://source.jalview.org / jalview.git / blobdiff