package jalview.gui;
import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.ListIterator;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
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;
}
});
- // 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()
public void run()
{
Cache.log.debug("Filechooser init thread started.");
- new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
- jalview.io.AppletFormatAdapter.READABLE_FNAMES,
- jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+ fileFormat);
Cache.log.debug("Filechooser init thread finished.");
}
}).start();
String file = (String) contents
.getTransferData(DataFlavor.stringFlavor);
- String format = new IdentifyFile().identify(file,
- FormatAdapter.PASTE);
+ FileFormatI format = new IdentifyFile().identify(file,
+ DataSourceType.PASTE);
- new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
+ new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
}
} catch (Exception ex)
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- java.util.List<String> files = new ArrayList<String>();
- java.util.List<String> protocols = new ArrayList<String>();
+ List<String> files = new ArrayList<String>();
+ List<DataSourceType> protocols = new ArrayList<DataSourceType>();
try
{
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
- String protocol = (protocols == null) ? FormatAdapter.FILE
- : (String) protocols.get(i);
- String format = null;
+ DataSourceType protocol = (protocols == null) ? DataSourceType.FILE
+ : protocols.get(i);
+ FileFormatI format = null;
if (file.endsWith(".jar"))
{
- format = "Jalview";
+ format = FileFormat.Jalview;
}
else
@Override
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
- jalview.io.AppletFormatAdapter.READABLE_FNAMES,
- jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser chooser = JalviewFileChooser.forRead(
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
- String format = null;
- if (chooser.getSelectedFormat() != null
- && chooser.getSelectedFormat().equals("Jalview"))
+ FileFormatI format = null;
+ FileFormatI selectedFormat = chooser.getSelectedFormat();
+ if (FileFormat.Jalview.equals(selectedFormat))
{
- format = "Jalview";
+ format = FileFormat.Jalview;
}
else
{
- format = new IdentifyFile().identify(choice, FormatAdapter.FILE);
+ try
+ {
+ format = new IdentifyFile().identify(choice, DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
+ // format is null
+ }
}
if (viewport != null)
{
- new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
+ new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
format);
}
else
{
- new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
+ new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
}
}
}
}
}
- 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 (viewport != null)
{
- new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
- "Jalview");
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ FileFormat.Jalview);
}
else
{
- new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+ new FileLoader().LoadFile(url, DataSourceType.URL,
+ FileFormat.Jalview);
}
}
else
{
- String format = new IdentifyFile().identify(url, FormatAdapter.URL);
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileFormatException e)
+ {
+ // TODO revise error handling, distinguish between
+ // URL not found and response not valid
+ }
- if (format.equals("URL NOT FOUND"))
+ 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;
}
if (viewport != null)
{
- new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+ new FileLoader()
+ .LoadFile(viewport, url, DataSourceType.URL, format);
}
else
{
- new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+ new FileLoader().LoadFile(url, DataSourceType.URL, format);
}
}
}
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
public void saveState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- new String[] { "jvp" }, new String[] { "Jalview Project" },
- "Jalview Project");
+ Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_state"));
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());
}
public void loadState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
+ Cache.getProperty("LAST_DIRECTORY"), new String[] {
"jvp", "jar" }, new String[] { "Jalview Project",
"Jalview Project (old)" }, "Jalview Project");
chooser.setFileView(new JalviewFileView());
final File selectedFile = chooser.getSelectedFile();
setProjectFile(selectedFile);
final String choice = selectedFile.getAbsolutePath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ Cache.setProperty("LAST_DIRECTORY",
selectedFile.getParent());
new Thread(new Runnable()
{
{
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(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- new String[] { "Vamsas Document" }, "Vamsas Document");
+ Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ "Vamsas Document");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
"label.saving_vamsas_doc",
new Object[] { choice.getName() }));
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
try
removeProgressPanel(progpanel);
if (warnmsg != null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+ warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
}
}
}
*/
public void setVamsasUpdate(boolean b)
{
- jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+ Cache.log.debug("Setting gui for Vamsas update "
+ (b ? "in progress" : "finished"));
if (vamUpdate != null)
// check what the actual links are - if it's just the default don't
// bother with the warning
Vector<String> links = Preferences.sequenceURLLinks;
- if (links == null || links.size() < 1)
+
+ // only need to check links if there is one with a
+ // SEQUENCE_ID which is not the default EMBL_EBI link
+ ListIterator<String> li = links.listIterator();
+ boolean check = false;
+ List<JLabel> urls = new ArrayList<JLabel>();
+ while (li.hasNext())
{
- // there are no links
- return;
+ String link = li.next();
+ if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING))
+ {
+ check = true;
+ int barPos = link.indexOf("|");
+ String urlMsg = barPos == -1 ? link : link.substring(0,
+ barPos) + ": " + link.substring(barPos + 1);
+ urls.add(new JLabel(urlMsg));
+ }
}
- else if ((links.size() == 1)
- && links.get(0).equals(EMBLEBI_STRING))
+ if (!check)
{
- // the only link is the default EMBL-EBI link
return;
}
- // check in case URL links use old style tokens ($SEQUENCE_ID$ for
- // sequence id _or_ accession id)
+ // ask user to check in case URL links use old style tokens
+ // ($SEQUENCE_ID$ for sequence id _or_ accession id)
JPanel msgPanel = new JPanel();
msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
msgPanel.add(Box.createVerticalGlue());
MessageManager
.getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
msgPanel.add(msg);
+ for (JLabel url : urls)
+ {
+ msgPanel.add(url);
+ }
msgPanel.add(msg2);
final JCheckBox jcb = new JCheckBox(
MessageManager.getString("label.do_not_display_again"));
jcb.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- // update Cache settings if checkbox is selected
- if (jcb.isSelected())
- {
- Cache.setProperty("CHECKURLLINKS", "false");
- }
- else
- {
- Cache.setProperty("CHECKURLLINKS", "true");
- }
+ // update Cache settings for "don't show this again"
+ boolean showWarningAgain = !jcb.isSelected();
+ Cache.setProperty("CHECKURLLINKS",
+ Boolean.valueOf(showWarningAgain).toString());
}
});
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);
}
}
*
* 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();
}
}
public static void transferFromDropTarget(List<String> files,
- List<String> protocols, DropTargetDropEvent evt, Transferable t)
+ List<DataSourceType> protocols, DropTargetDropEvent evt,
+ Transferable t)
throws Exception
{
.getTransferData(DataFlavor.javaFileListFlavor))
{
files.add(((File) file).toString());
- protocols.add(FormatAdapter.FILE);
+ protocols.add(DataSourceType.FILE);
}
}
else
{
Cache.log.debug("Adding missing FILE protocol for "
+ files.get(protocols.size()));
- protocols.add(FormatAdapter.FILE);
+ protocols.add(DataSourceType.FILE);
}
for (java.util.StringTokenizer st = new java.util.StringTokenizer(
data, "\r\n"); st.hasMoreTokens();)
java.net.URI uri = new java.net.URI(s);
if (uri.getScheme().toLowerCase().startsWith("http"))
{
- protocols.add(FormatAdapter.URL);
+ protocols.add(DataSourceType.URL);
files.add(uri.toString());
}
else
{
// otherwise preserve old behaviour: catch all for file objects
java.io.File file = new java.io.File(uri);
- protocols.add(FormatAdapter.FILE);
+ protocols.add(DataSourceType.FILE);
files.add(file.toString());
}
}
git://source.jalview.org / jalview.git / blobdiff