*/
package jalview.gui;
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
import static jalview.util.UrlConstants.SEQUENCE_ID;
import jalview.api.AlignViewportI;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.UrlConstants;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
import java.awt.BorderLayout;
import java.awt.Color;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileOutputStream;
+import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Hashtable;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
+ private static int DEFAULT_MIN_WIDTH = 300;
+
+ private static int DEFAULT_MIN_HEIGHT = 250;
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
showNews.setVisible(false);
+ getIdentifiersOrgData();
+
checkURLLinks();
this.addWindowListener(new WindowAdapter()
}
});
- // displayed.
// Thread off a new instance of the file chooser - this reduces the time it
// takes to open it later on.
new Thread(new Runnable()
Cache.log.debug("Filechooser init thread started.");
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
- // jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
- // jalview.io.AppletFormatAdapter.READABLE_FNAMES,
- fileFormat, true);
+ fileFormat);
Cache.log.debug("Filechooser init thread finished.");
}
}).start();
});
}
+ public void getIdentifiersOrgData()
+ {
+ // Thread off the identifiers fetcher
+ addDialogThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Downloading data from identifiers.org");
+ UrlDownloadClient client = new UrlDownloadClient();
+ try
+ {
+ client.download(IdOrgSettings.getUrl(),
+ IdOrgSettings.getDownloadLocation());
+ } catch (IOException e)
+ {
+ Cache.log.debug("Exception downloading identifiers.org data"
+ + e.getMessage());
+ }
+ }
+ });
+ }
+
@Override
protected void showNews_actionPerformed(ActionEvent e)
{
public static synchronized void addInternalFrame(
final JInternalFrame frame, String title, int w, int h)
{
- addInternalFrame(frame, title, true, w, h, true);
+ addInternalFrame(frame, title, true, w, h, true, false);
}
/**
final JInternalFrame frame, String title, boolean makeVisible,
int w, int h)
{
- addInternalFrame(frame, title, makeVisible, w, h, true);
+ addInternalFrame(frame, title, makeVisible, w, h, true, false);
}
/**
final JInternalFrame frame, String title, int w, int h,
boolean resizable)
{
- addInternalFrame(frame, title, true, w, h, resizable);
+ addInternalFrame(frame, title, true, w, h, resizable, false);
}
/**
* height
* @param resizable
* Allow resize
+ * @param ignoreMinSize
+ * No minimum size is set for the dialog
*/
public static synchronized void addInternalFrame(
final JInternalFrame frame, String title, boolean makeVisible,
- int w, int h, boolean resizable)
+ int w, int h, boolean resizable, boolean ignoreMinSize)
{
// TODO: allow callers to determine X and Y position of frame (eg. via
openFrameCount++;
+ if (!ignoreMinSize)
+ {
+ frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH,
+ DEFAULT_MIN_HEIGHT));
+ }
frame.setVisible(makeVisible);
frame.setClosable(true);
frame.setResizable(resizable);
}
});
+ desktop.add(frame);
+
windowMenu.add(menuItem);
- desktop.add(frame);
frame.toFront();
try
{
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser.forRead(
- Cache.getProperty("LAST_DIRECTORY"),
- // AppletFormatAdapter.READABLE_EXTENSIONS,
- // AppletFormatAdapter.READABLE_FNAMES,
- fileFormat, true);
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
- FileFormatI format = null;
- FileFormatI selectedFormat = chooser.getSelectedFormat();
- if (FileFormat.Jalview.equals(selectedFormat))
- {
- format = FileFormat.Jalview;
- }
- else
+ FileFormatI format = chooser.getSelectedFormat();
+
+ /*
+ * Call IdentifyFile to verify the file contains what its extension implies.
+ * Skip this step for dynamically added file formats, because
+ * IdentifyFile does not know how to recognise them.
+ */
+ if (FileFormats.getInstance().isIdentifiable(format))
{
try
{
format = new IdentifyFile().identify(choice, DataSourceType.FILE);
} catch (FileFormatException e)
{
- // format is null
+ // format = null; //??
}
}
}
}
- int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+ int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
MessageManager.getString("label.input_alignment_from_url"),
- JOptionPane.OK_CANCEL_OPTION);
+ JvOptionPane.OK_CANCEL_OPTION);
- if (reply != JOptionPane.OK_OPTION)
+ if (reply != JvOptionPane.OK_OPTION)
{
return;
}
if (format == null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
new Object[] { url }), MessageManager
.getString("label.url_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
// StringBuffer message = getAboutMessage(false);
- // JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
//
- // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
@Override
@Override
public void saveState_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project",
+ JalviewFileChooser chooser = new JalviewFileChooser("jvp",
"Jalview Project");
chooser.setFileView(new JalviewFileView());
Cache.log.error(
"Problems whilst trying to save to " + choice.getName(),
ex);
- JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
+ JvOptionPane.showMessageDialog(me, MessageManager.formatMessage(
"label.error_whilst_saving_current_state_to",
new Object[] { choice.getName() }), MessageManager
.getString("label.couldnt_save_project"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
{
Cache.log.error("Problems whilst loading project from "
+ choice, ex);
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage(
"label.error_whilst_loading_project_from",
new Object[] { choice }), MessageManager
.getString("label.couldnt_load_project"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager.formatMessage(
new Object[] { fle }),
MessageManager
.getString("label.vamsas_document_import_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
{
if (v_client != null)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- "Vamsas Document", "Vamsas Document");
+ // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ JalviewFileChooser chooser = new JalviewFileChooser("vdj",
+ "Vamsas Document");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
removeProgressPanel(progpanel);
if (warnmsg != null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+ warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
}
}
}
{
// check what the actual links are - if it's just the default don't
// bother with the warning
- Vector<String> links = Preferences.sequenceURLLinks;
+ List<String> links = Preferences.sequenceUrlLinks
+ .getLinksForMenu();
// only need to check links if there is one with a
// SEQUENCE_ID which is not the default EMBL_EBI link
while (li.hasNext())
{
String link = li.next();
- if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING))
+ if (link.contains(SEQUENCE_ID)
+ && !link.equals(UrlConstants.DEFAULT_STRING))
{
check = true;
int barPos = link.indexOf("|");
});
msgPanel.add(jcb);
- JOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
MessageManager
.getString("label.SEQUENCE_ID_no_longer_used"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
});
} catch (Exception ex)
{
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
- {
- jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
- }
t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
changeSupport);
-
}
Thread t3 = null;
{
*
* jd.waitForInput();
*/
- JOptionPane
+ JvOptionPane
.showConfirmDialog(
Desktop.desktop,
new JLabel(
+ "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ " Tools->Preferences dialog box to change them.</p></html>"),
"Web Service Configuration Problem",
- JOptionPane.DEFAULT_OPTION,
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.ERROR_MESSAGE);
serviceChangedDialog = null;
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager
.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
git://source.jalview.org / jalview.git / blobdiff