*/
package jalview.gui;
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
import static jalview.util.UrlConstants.SEQUENCE_ID;
import jalview.api.AlignViewportI;
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;
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()
});
}
+ 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
+ * Do not set the default minimum size for frame
*/
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);
* Skip this step for dynamically added file formats, because
* IdentifyFile does not know how to recognise them.
*/
- boolean dynamicFormat = FileFormats.getInstance().isDynamic(format);
- if (!dynamicFormat && !FileFormat.Jalview.equals(format))
+ if (FileFormats.getInstance().isIdentifiable(format))
{
try
{
format = new IdentifyFile().identify(choice, DataSourceType.FILE);
} catch (FileFormatException e)
{
- // format is null
+ // format = null; //??
}
}
@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());
chooser.setDialogTitle(MessageManager.getString("label.save_state"));
{
if (v_client != null)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ JalviewFileChooser chooser = new JalviewFileChooser("vdj",
"Vamsas Document");
chooser.setFileView(new JalviewFileView());
{
// 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("|");
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;
{