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;
*/
String fileName = null;
+ File fileObject;
+
/**
* Creates a new AlignFrame object with specific width and height.
*
Desktop.getDesktop().propertyChange(evt);
}
+
+ /**
+ * BH 2018
+ *
+ * @return true if we have any features
+ */
+ @Override
+ 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;
+ }
+ }
+ return false;
+ }
+
/**
* initalise the alignframe from the underlying viewport data and the
* configurations
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) {
+ this.fileObject = file;
+ }
/**
* Add a KeyListener with handlers for various KeyPressed and KeyReleased
FileLoader loader = new FileLoader();
DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE;
+ ? DataSourceType.URL : DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
else
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 = (fileName.startsWith("http:")
+ ? 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())
@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)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString(
- "label.select_file_format_before_saving"),
- MessageManager.getString("label.file_format_not_specified"),
- JvOptionPane.WARNING_MESSAGE);
+ @Override
+ public void run()
+ {
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();
+ 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);
+ }
+ }).showSaveDialog(this);
}
public boolean saveAlignment(String file, FileFormatI format)
@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)
- {
- 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())
- {
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager
- .getString("label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- }
- }
+ chooser.response(
+ new jalview.util.dialogrunner.RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ {
+ @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());
+ } 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)
@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);
}
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.UrlConstants;
+ import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ParamManager;
import jalview.ws.utils.UrlDownloadClient;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDesktopPane;
- import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
public Desktop()
{
/**
- * A note to implementors. It is ESSENTIAL that any activities that might
- * block are spawned off as threads rather than waited for during this
- * constructor.
+ * A note to implementors. It is ESSENTIAL that any activities that might block
+ * are spawned off as threads rather than waited for during this constructor.
*/
instance = this;
doVamsasClientCheck();
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
- desktop.setDesktopManager(
- new MyDesktopManager(
- (Platform.isWindows() ? new DefaultDesktopManager()
- : Platform.isAMac()
- ? new AquaInternalFrameManager(
- desktop.getDesktopManager())
- : desktop.getDesktopManager())));
+ desktop.setDesktopManager(new MyDesktopManager(
+ (Platform.isWindows() ? new DefaultDesktopManager()
+ : Platform.isAMac()
+ ? new AquaInternalFrameManager(
+ desktop.getDesktopManager())
+ : desktop.getDesktopManager())));
Rectangle dims = getLastKnownDimensions("");
if (dims != null)
* @j2sNative
*/
{
- final Desktop me = this;
- // Thread off the news reader, in case there are connection problems.
- addDialogThread(new Runnable()
- {
+ final Desktop me = this;
+ // Thread off the news reader, in case there are connection problems.
+ addDialogThread(new Runnable()
+ {
@Override
public void run()
{
showNews.setVisible(true);
Cache.log.debug("Completed news thread.");
}
- });
+ });
}
}
}
/**
- * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
- * the window
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the
+ * window
*
* @param frame
*/
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- final JalviewFileChooser chooser = JalviewFileChooser
+ JalviewFileChooser chooser = JalviewFileChooser
.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- chooser.setCallback(new Runnable()
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
{
@Override
new FileLoader().LoadFile(viewport, selectedFile,
DataSourceType.FILE, format);
}
- });
-
- int value = chooser.showOpenDialog(this);
- if (value == JFileChooser.APPROVE_OPTION)
- {
- chooser.getCallback().run();
- }
-
+ }).openDialog(this);
}
/**
String dialogOption = "label.input_alignment_from_url";
desktop.dialogData = new Object[] { dialogOption, viewport, history };
- desktop.onDialogReturn(
- JvOptionPane.showInternalConfirmDialog(desktop, panel,
- MessageManager.getString(dialogOption),
+ desktop.onDialogReturn(JvOptionPane.showInternalConfirmDialog(desktop,
+ panel, MessageManager.getString(dialogOption),
JvOptionPane.OK_CANCEL_OPTION));
// no code may follow this, as SwingJS will not block
}
-
/**
* Opens the CutAndPaste window for the user to paste an alignment in to
*
/**
* 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.
+ * 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
*/
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs
- * low.
+ * usage and highlights the desktop area with a red bar if free memory runs low.
*
* @author AMW
*/
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
new Object[]
- { url }),
+ { url }),
MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
}
}
-
/**
* Accessor method to quickly get all the AlignmentFrames loaded.
*
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
- * binding when opened
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
+ * when opened
*/
protected void addQuitHandler()
{
}
/**
- * This will return the first AlignFrame holding the given viewport instance.
- * It will break if there are more than one AlignFrames viewing a particular
- * av.
+ * This will return the first AlignFrame holding the given viewport instance. It
+ * will break if there are more than one AlignFrames viewing a particular av.
*
* @param viewport
* @return alignFrame for viewport
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size
- * and location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size and
+ * location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
{
-
+
// BH 2018 changed List<String> to List<Object> to allow for File from SwingJS
- // DataFlavor[] flavors = t.getTransferDataFlavors();
- // for (int i = 0; i < flavors.length; i++) {
- // if (flavors[i].isFlavorJavaFileListType()) {
- // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- // List<File> list = (List<File>) t.getTransferData(flavors[i]);
- // for (int j = 0; j < list.size(); j++) {
- // File file = (File) list.get(j);
- // byte[] data = getDroppedFileBytes(file);
- // fileName.setText(file.getName() + " - " + data.length + " " + evt.getLocation());
- // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent();
- // target.setText(new String(data));
- // }
- // dtde.dropComplete(true);
- // return;
- // }
- //
+ // DataFlavor[] flavors = t.getTransferDataFlavors();
+ // for (int i = 0; i < flavors.length; i++) {
+ // if (flavors[i].isFlavorJavaFileListType()) {
+ // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ // List<File> list = (List<File>) t.getTransferData(flavors[i]);
+ // for (int j = 0; j < list.size(); j++) {
+ // File file = (File) list.get(j);
+ // byte[] data = getDroppedFileBytes(file);
+ // fileName.setText(file.getName() + " - " + data.length + " " +
+ // evt.getLocation());
+ // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent();
+ // target.setText(new String(data));
+ // }
+ // dtde.dropComplete(true);
+ // return;
+ // }
+ //
DataFlavor uriListFlavor = new DataFlavor(
"text/uri-list;class=java.lang.String"), urlFlavour = null;
try
{
- java.net.URL url = (URL) t.getTransferData(urlFlavour);
+ java.net.URL url = (URL) t.getTransferData(urlFlavour);
// nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
// means url may be null.
- if (url != null)
- {
- protocols.add(DataSourceType.URL);
- files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor "
- + files.get(files.size() - 1));
+ if (url != null)
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(url.toString());
+ Cache.log.debug("Drop handled as URL dataflavor "
+ + files.get(files.size() - 1));
return;
}
else
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
;
- }
+ }
} catch (Throwable ex)
{
Cache.log.debug("URL drop handler failed.", ex);
&& (source.endsWith(".lnk") || source.endsWith(".url")
|| source.endsWith(".site")))
{
- try {
+ try
+ {
Object obj = files.get(f);
- File lf = (obj instanceof File ? (File) obj : new File((String) obj));
+ File lf = (obj instanceof File ? (File) obj
+ : new File((String) obj));
// process link file to get a URL
Cache.log.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
files.set(f, fullname);
Cache.log.debug("Parsed real filename " + fullname
+ " to extract protocol: " + protocols.get(f));
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- Cache.log.error("Couldn't parse "+files.get(f)+" as a link file.",ex);
+ Cache.log.error(
+ "Couldn't parse " + files.get(f) + " as a link file.",
+ ex);
}
}
}
}
/**
- * Answers a (possibly empty) list of any structure viewer frames (currently
- * for either Jmol or Chimera) which are currently open. This may optionally
- * be restricted to viewers of a specified class, or viewers linked to a
- * specified alignment panel.
+ * Answers a (possibly empty) list of any structure viewer frames (currently for
+ * either Jmol or Chimera) which are currently open. This may optionally be
+ * restricted to viewers of a specified class, or viewers linked to a specified
+ * alignment panel.
*
* @param apanel
* if not null, only return viewers linked to this panel
git://source.jalview.org / jalview.git / commitdiff