import jalview.structure.StructureSelectionManager;
import jalview.urls.IdOrgSettings;
import jalview.util.BrowserLauncher;
+import jalview.util.ChannelProperties;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
instance = this;
doConfigureStructurePrefs();
- setTitle("Jalview " + Cache.getProperty("VERSION"));
+ setTitle(ChannelProperties.getProperty("app_name") + " "
+ + Cache.getProperty("VERSION"));
/*
if (!Platform.isAMac())
{
}
});
- boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE",
- false);
+ boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
- boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE",
- false);
+ boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false);
desktop = new MyDesktopPane(selmemusage);
showMemusage.setSelected(selmemusage);
.getStructureSelectionManager(this);
if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
{
- ssm.setAddTempFacAnnot(Cache
- .getDefault(Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(Cache
- .getDefault(Preferences.STRUCT_FROM_PDB, true));
+ ssm.setAddTempFacAnnot(
+ Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(
+ Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
ssm.setSecStructServices(
Cache.getDefault(Preferences.USE_RNAVIEW, true));
}
}
}
}).start();
-
+
}
@Override
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
String x = Cache.getProperty(windowName + "SCREEN_X");
String y = Cache.getProperty(windowName + "SCREEN_Y");
- String width = Cache
- .getProperty(windowName + "SCREEN_WIDTH");
- String height = Cache
- .getProperty(windowName + "SCREEN_HEIGHT");
+ String width = Cache.getProperty(windowName + "SCREEN_WIDTH");
+ String height = Cache.getProperty(windowName + "SCREEN_HEIGHT");
if ((x != null) && (y != null) && (width != null) && (height != null))
{
int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
- double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
- Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
- double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
- Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
+ double sw = ((1f * screenSize.width) / (1f * Integer
+ .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer
+ .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
}
/**
- * 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");
- JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled());
+ JalviewFileChooser chooser = JalviewFileChooser.forRead(
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+ BackupFiles.getEnabled());
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
public void quit()
{
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- Cache.setProperty("SCREENGEOMETRY_WIDTH",
- screen.width + "");
- Cache.setProperty("SCREENGEOMETRY_HEIGHT",
- screen.height + "");
+ Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
getWidth(), getHeight()));
private void storeLastKnownDimensions(String string, Rectangle jc)
{
- Cache.log.debug("Storing last known dimensions for "
- + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
- + " height:" + jc.height);
+ Cache.log.debug("Storing last known dimensions for " + string + ": x:"
+ + jc.x + " y:" + jc.y + " width:" + jc.width + " height:"
+ + jc.height);
Cache.setProperty(string + "SCREEN_X", jc.x + "");
Cache.setProperty(string + "SCREEN_Y", jc.y + "");
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
{ chosenFile.getName() }), chosenFile.hashCode());
- Cache.setProperty("LAST_DIRECTORY",
- chosenFile.getParent());
+ Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile)
+ : null;
- new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
+ new Jalview2XML().saveState(
+ doBackup ? backupfiles.getTempFile() : chosenFile);
if (doBackup)
{
setProgressBar(null, chosenFile.hashCode());
}
}).start();
- }
+ }
}
@Override
"Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
- // allowBackupFiles
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two
+ // booleans:
+ // allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
chooser.setResponseHandler(0, new Runnable()
@Override
public void run()
{
- try
+ try
{
new Jalview2XML().loadJalviewAlign(selectedFile);
} catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
- }
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager
+ .getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
}, "Project Loader").start();
}
});
-
+
chooser.showOpenDialog(this);
}
// FIXME: ideally should use UI interface API
FeatureSettings viewFeatureSettings = (af.featureSettings != null
- && af.featureSettings.isOpen())
- ? af.featureSettings
- : null;
+ && af.featureSettings.isOpen()) ? af.featureSettings : null;
Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- // and materialise a new feature settings dialog instance for the new alignframe
+ // and materialise a new feature settings dialog instance for the new
+ // alignframe
// (closes the old as if 'OK' was pressed)
if (ap == af.alignPanel && newaf.featureSettings != null
&& newaf.featureSettings.isOpen()
/**
* 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
*/
}
// refresh the feature setting UI for the source frame if it exists
- if (source.featureSettings != null
- && source.featureSettings.isOpen())
+ if (source.featureSettings != null && source.featureSettings.isOpen())
{
source.showFeatureSettingsUI();
}
/**
* 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
*/
- public class MyDesktopPane extends JDesktopPane
- implements Runnable
+ public class MyDesktopPane extends JDesktopPane implements Runnable
{
private static final float ONE_MB = 1048576f;
}
/**
- * 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()
{
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
- .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ getRootPane()
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke
+ .getKeyStroke(KeyEvent.VK_Q,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx()),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
}
/**
- * 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.
*
Transferable t) throws Exception
{
- // BH 2018 changed List<String> to List<Object> to allow for File from SwingJS
+ // 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++) {
// byte[] data = getDroppedFileBytes(file);
// fileName.setText(file.getName() + " - " + data.length + " " +
// evt.getLocation());
- // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent();
+ // JTextArea target = (JTextArea) ((DropTarget)
+ // evt.getSource()).getComponent();
// target.setText(new String(data));
// }
// dtde.dropComplete(true);
}
/**
- * 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