import jalview.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignExportSettingBeanI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
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.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
+import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Component;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
import javax.swing.JEditorPane;
import javax.swing.JFileChooser;
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.JTextPane;
import javax.swing.SwingUtilities;
/**
Desktop.getDesktop().propertyChange(evt);
}
-
/**
- * BH 2018
- *
+ * BH 2018
+ *
* @return true if we have any features
*/
@Override
- protected boolean haveAlignmentFeatures() {
+ protected boolean haveAlignmentFeatures()
+ {
AlignmentI alignment = getViewport().getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
SequenceI seq = alignment.getSequenceAt(i);
for (String group : seq.getFeatures().getFeatureGroups(true))
{
- if (group != null)return true;
+ if (group != null)
+ return true;
}
}
- return false;
+ return false;
}
-
+
/**
* initalise the alignframe from the underlying viewport data and the
* configurations
*
*/
{
- addServiceListeners();
+ addServiceListeners();
}
setGUINucleotide();
}
setFileFormat(format);
reload.setEnabled(true);
}
-
+
/**
* 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) {
+ public void setFileObject(File file)
+ {
this.fileObject = file;
}
FileLoader loader = new FileLoader();
DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL : DataSourceType.FILE;
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
else
{
DataSourceType protocol = (fileName.startsWith("http:")
- ? DataSourceType.URL : DataSourceType.FILE);
+ ? DataSourceType.URL
+ : DataSourceType.FILE);
newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
currentFileFormat);
}
else
{
- newframe = loader.LoadFileWaitTillLoaded(fileObject, DataSourceType.FILE, currentFileFormat);
+ newframe = loader.LoadFileWaitTillLoaded(fileObject,
+ DataSourceType.FILE, currentFileFormat);
}
newframe.setBounds(bounds);
@Override
public void saveAs_actionPerformed(ActionEvent e)
{
- // TODO: JAL-3048 JalviewFileChooser - Save option
-
String format = currentFileFormat == null ? null
: currentFileFormat.getName();
- JalviewFileChooser chooser = JalviewFileChooser
+ final JalviewFileChooser chooser = JalviewFileChooser
.forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
-
+ final AlignFrame us = this;
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
- int value = chooser.showSaveDialog(this);
-
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
{
- currentFileFormat = chooser.getSelectedFormat();
- while (currentFileFormat == null)
+ @Override
+ public void run()
{
- 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)
+ while (currentFileFormat == null)
{
- return;
+ 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();
+ chooser.showSaveDialog(us);
}
+
+ fileName = chooser.getSelectedFile().getPath();
+
+ Cache.setProperty("DEFAULT_FILE_FORMAT",
+ currentFileFormat.getName());
+
+ Cache.setProperty("LAST_DIRECTORY", fileName);
+ saveAlignment(fileName, currentFileFormat);
}
+ }).showSaveDialog(this);
+ }
- fileName = chooser.getSelectedFile().getPath();
+ private boolean lastSaveSuccessful = false;
- Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ private FileFormatI lastFormatSaved;
+
+ private 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)
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { lastFilenameSaved, lastFormatSaved }));
- Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(fileName, currentFileFormat);
}
+ return lastSaveSuccessful;
}
- public boolean saveAlignment(String file, FileFormatI format)
+ public void saveAlignment(String file, FileFormatI format)
{
- boolean success = true;
-
+ lastSaveSuccessful = false;
+ lastFilenameSaved = file;
+ lastFormatSaved = format;
+ AlignFrame us = this;
if (FileFormat.Jalview.equals(format))
{
String shortName = title;
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().saveAlignment(this, file, shortName);
-
- statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format }));
-
+ lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
+ shortName);
}
else
{
- AlignmentExportData exportData = getAlignmentForExport(format,
- viewport, null);
- if (exportData.getSettings().isCancelled())
+ AlignExportSettingI settings = getAlignmentForExport(format,
+ alignPanel, null);
+ settings.addActionListener(new ActionListener()
{
- 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)
- {
- success = false;
- }
- else
- {
- try
- {
- PrintWriter out = new PrintWriter(new FileWriter(file));
-
- out.print(output);
- out.close();
- this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
- } catch (Exception ex)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- success = false;
- ex.printStackTrace();
- }
- }
- }
-
- if (!success)
- {
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { fileName }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
- }
-
- return success;
- }
- private void warningMessage(String warning, String title)
- {
- if (new jalview.util.Platform().isHeadless())
- {
- System.err.println("Warning: " + title + "\nWarning: " + warning);
+ if (settings.isCancelled())
+ {
+ lastSaveSuccessful = false;
+ return;
+ }
+ AlignmentExportData exportData = settings.getAlignExportData();
+ 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)
+ {
+ lastSaveSuccessful = false;
+ }
+ else
+ {
+ try
+ {
+ PrintWriter out = new PrintWriter(new FileWriter(file));
+
+ out.print(output);
+ out.close();
+ us.setTitle(file);
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format.getName() }));
+ } catch (Exception ex)
+ {
+ lastSaveSuccessful = false;
+ ex.printStackTrace();
+ }
+ }
+ }
+ });
+ settings.doShowSettings();
}
- else
- {
- JvOptionPane.showInternalMessageDialog(this, warning, title,
- JvOptionPane.WARNING_MESSAGE);
- }
- return;
}
/**
{
FileFormatI fileFormat = FileFormats.getInstance()
.forName(e.getActionCommand());
- AlignmentExportData exportData = getAlignmentForExport(fileFormat,
- viewport, null);
- if (exportData.getSettings().isCancelled())
- {
- 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)
+ AlignExportSettingI settings = getAlignmentForExport(fileFormat,
+ alignPanel, null);
+ settings.addActionListener(new ActionListener()
{
- new OOMWarning("Outputting alignment as " + e.getActionCommand(),
- oom);
- cap.dispose();
- }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (settings.isCancelled())
+ {
+ return;
+ }
+ AlignmentExportData exportData = settings.getAlignExportData();
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ try
+ {
+ FileFormatI format = fileFormat;
+ cap.setText(new FormatAdapter(alignPanel, settings)
+ .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();
+ }
+ // TODO Auto-generated method stub
+ }
+ });
+ settings.doShowSettings();
}
- public static AlignmentExportData getAlignmentForExport(
- FileFormatI format, AlignViewportI viewport,
- AlignExportSettingI exportSettings)
+ public static AlignExportSettingI getAlignmentForExport(
+ FileFormatI format, AlignmentPanel alignPanel,
+ AlignExportSettingBeanI 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());
- }
- int[] alignmentStartEnd = new int[2];
- if (hasHiddenSeqs && settings.isExportHiddenSequences())
- {
- alignmentToExport = hiddenSeqs.getFullAlignment();
- }
- else
- {
- alignmentToExport = viewport.getAlignment();
- }
- alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
- .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
- AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
- omitHidden, alignmentStartEnd, settings);
- return ed;
+ return new AlignExportSettings(alignPanel, format, exportSettings);
}
/**
@Override
public void associatedData_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
+ final JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_jalview_annotations"));
chooser.setToolTipText(
MessageManager.getString("label.load_jalview_annotations"));
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ {
- Desktop.getDesktop().dialogData = new Object[] { "SelectedFile",
- new Runnable()
- {
-
- @Override
- public void run()
- {
- Object[] data = Desktop.getDesktop().dialogData;
- int value = ((Integer) data[0]).intValue();
-
- if (value == JFileChooser.APPROVE_OPTION)
- {
- JalviewFileChooser chooser = (JalviewFileChooser) data[2];
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice, null, null, null);
- }
- }
-
- }, chooser };
-
- chooser.showOpenDialog(null);
-
+ @Override
+ public void run()
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
+ }
+ });
+ chooser.openDialog(this);
}
/**
@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 (/** @j2sNative true || */
+ false)
+ {
+ JLabel textLabel = new JLabel();
+ textLabel.setText(content);
+ textLabel.setBackground(Color.WHITE);
+
+ pane = new JPanel(new BorderLayout());
+ ((JPanel) pane).setOpaque(true);
+ ((JPanel) pane).add(textLabel, BorderLayout.CENTER);
+ }
+ else
+ {
+ 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[]
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
- // TODO: JAL-3048 JalviewFileChooser
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.response(new jalview.util.dialogrunner.RunResponse(
+ JalviewFileChooser.APPROVE_OPTION)
{
- String filePath = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
- try
- {
- fin = new NewickFile(filePath, DataSourceType.FILE);
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
- } 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())
+ @Override
+ public void run()
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager
- .getString("label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
+ 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());
+ } 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);
+ }
}
- }
+ }).openDialog(this);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
*/
public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
{
- // BH 2018
+ // 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<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
ArrayList<Object> filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
- // BH 2018
+ // BH 2018
Object file = files.get(i);
String fileName = file.toString();
String pdbfn = "";
- DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
+ DataSourceType protocol = (file instanceof File
+ ? DataSourceType.FILE
+ : FormatAdapter.checkProtocol(fileName));
if (protocol == DataSourceType.FILE)
{
- File fl = (file instanceof File ? (File) file : new File(fileName));
+ File fl = (file instanceof File ? (File) file
+ : new File(fileName));
pdbfn = fl.getName();
}
else if (protocol == DataSourceType.URL)
int assocfiles = 0;
if (filesmatched.size() > 0)
{
- boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+ boolean autoAssociate = Cache
+ .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
if (!autoAssociate)
{
String msg = MessageManager.formatMessage(
@Override
protected void loadVcf_actionPerformed()
{
- // TODO: JAL-3048 - No VCF support in JsJalview
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+ final AlignFrame us = this;
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ {
+ @Override
+ public void run()
+ {
- int value = chooser.showOpenDialog(null);
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, this);
- }
+ };
+ }).openDialog(null);
}
git://source.jalview.org / jalview.git / blobdiff