import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
+import java.lang.reflect.Field;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.ListIterator;
+import java.util.Locale;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
implements DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
- private static final String CITATION = "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
- + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
- + "<br><br>If you use Jalview, please cite:"
- + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033";
+ private static final String CITATION;
+ static
+ {
+ URL bg_logo_url = ChannelProperties.getImageURL(
+ "bg_logo." + String.valueOf(SplashScreen.logoSize));
+ URL uod_logo_url = ChannelProperties.getImageURL(
+ "uod_banner." + String.valueOf(SplashScreen.logoSize));
+ boolean logo = (bg_logo_url != null || uod_logo_url != null);
+ StringBuilder sb = new StringBuilder();
+ sb.append(
+ "<br><br>Jalview is free software released under GPLv3.<br><br>Development is managed by The Barton Group, University of Dundee, Scotland, UK.");
+ if (logo)
+ {
+ sb.append("<br>");
+ }
+ sb.append(bg_logo_url == null ? ""
+ : "<img alt=\"Barton Group logo\" src=\""
+ + bg_logo_url.toString() + "\">");
+ sb.append(uod_logo_url == null ? ""
+ : " <img alt=\"University of Dundee shield\" src=\""
+ + uod_logo_url.toString() + "\">");
+ sb.append(
+ "<br><br>For help, see <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>");
+ sb.append("<br><br>If you use Jalview, please cite:"
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics <a href=\"https://doi.org/10.1093/bioinformatics/btp033\">doi: 10.1093/bioinformatics/btp033</a>");
+ CITATION = sb.toString();
+ }
private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)";
private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
- protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+ public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
doConfigureStructurePrefs();
setTitle(ChannelProperties.getProperty("app_name") + " "
+ Cache.getProperty("VERSION"));
- /*
- if (!Platform.isAMac())
- {
- // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
- }
- else
- {
- this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
- }
- */
- try
- {
- APQHandlers.setAPQHandlers(this);
- } catch (Throwable t)
+ /**
+ * Set taskbar "grouped windows" name for linux desktops (works in GNOME and
+ * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not
+ * officially documented or guaranteed to exist, so we access it via
+ * reflection. There appear to be unfathomable criteria about what this
+ * string can contain, and it if doesn't meet those criteria then "java"
+ * (KDE) or "jalview-bin-Jalview" (GNOME) is used. "Jalview", "Jalview
+ * Develop" and "Jalview Test" seem okay, but "Jalview non-release" does
+ * not. The reflection access may generate a warning: WARNING: An illegal
+ * reflective access operation has occurred WARNING: Illegal reflective
+ * access by jalview.gui.Desktop () to field
+ * sun.awt.X11.XToolkit.awtAppClassName which I don't think can be avoided.
+ */
+ if (Platform.isLinux())
{
- System.out.println("Error setting APQHandlers: " + t.toString());
- // t.printStackTrace();
+ try
+ {
+ Toolkit xToolkit = Toolkit.getDefaultToolkit();
+ Field[] declaredFields = xToolkit.getClass().getDeclaredFields();
+ Field awtAppClassNameField = null;
+
+ if (Arrays.stream(declaredFields)
+ .anyMatch(f -> f.getName().equals("awtAppClassName")))
+ {
+ awtAppClassNameField = xToolkit.getClass()
+ .getDeclaredField("awtAppClassName");
+ }
+
+ String title = ChannelProperties.getProperty("app_name");
+ if (awtAppClassNameField != null)
+ {
+ awtAppClassNameField.setAccessible(true);
+ awtAppClassNameField.set(xToolkit, title);
+ }
+ else
+ {
+ jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Console.debug("Error setting awtAppClassName");
+ jalview.bin.Console.trace(Cache.getStackTraceString(e));
+ }
}
+ setIconImages(ChannelProperties.getIconList());
+
addWindowListener(new WindowAdapter()
{
@Override
public void run()
{
- Cache.log.debug("Filechooser init thread started.");
+ jalview.bin.Console.debug("Filechooser init thread started.");
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
+ jalview.bin.Console.debug("Filechooser init thread finished.");
}
}).start();
// Add the service change listener
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
+ jalview.bin.Console
+ .debug("Firing service changed event for "
+ + evt.getNewValue());
JalviewServicesChanged(evt);
}
});
Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
ssm.setProcessSecondaryStructure(
Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+ // JAL-3915 - RNAView is no longer an option so this has no effect
ssm.setSecStructServices(
- Cache.getDefault(Preferences.USE_RNAVIEW, true));
+ Cache.getDefault(Preferences.USE_RNAVIEW, false));
}
else
{
@Override
public void run()
{
- Cache.log.debug("Starting news thread.");
+ jalview.bin.Console.debug("Starting news thread.");
jvnews = new BlogReader(me);
showNews.setVisible(true);
- Cache.log.debug("Completed news thread.");
+ jalview.bin.Console.debug("Completed news thread.");
}
}).start();
}
public void getIdentifiersOrgData()
{
- // Thread off the identifiers fetcher
- new Thread(new Runnable()
- {
- @Override
- public void run()
+ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+ {// Thread off the identifiers fetcher
+ new Thread(new Runnable()
{
- Cache.log.debug("Downloading data from identifiers.org");
- try
- {
- UrlDownloadClient.download(IdOrgSettings.getUrl(),
- IdOrgSettings.getDownloadLocation());
- } catch (IOException e)
+ @Override
+ public void run()
{
- Cache.log.debug("Exception downloading identifiers.org data"
- + e.getMessage());
+ jalview.bin.Console
+ .debug("Downloading data from identifiers.org");
+ try
+ {
+ UrlDownloadClient.download(IdOrgSettings.getUrl(),
+ IdOrgSettings.getDownloadLocation());
+ } catch (IOException e)
+ {
+ jalview.bin.Console
+ .debug("Exception downloading identifiers.org data"
+ + e.getMessage());
+ }
}
- }
- }).start();
-
+ }).start();
+ ;
+ }
}
@Override
void showNews(boolean visible)
{
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
if (visible && !jvnews.isVisible())
{
ih = (int) (ih * sh);
while (ix >= screenSize.width)
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height)
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Got last known dimensions for " + windowName + ": x:" + ix
+ " y:" + iy + " width:" + iw + " height:" + ih);
}
}
/*
- * add an entry for the new frame in the Window menu
- * (and remove it when the frame is closed)
+ * add an entry for the new frame in the Window menu (and remove it when the
+ * frame is closed)
*/
final JMenuItem menuItem = new JMenuItem(title);
frame.addInternalFrameListener(new InternalFrameAdapter()
PaintRefresher.RemoveComponent(frame);
/*
- * defensive check to prevent frames being
- * added half off the window
+ * defensive check to prevent frames being added half off the window
*/
if (openFrameCount > 0)
{
frame.setIcon(false);
} catch (java.beans.PropertyVetoException ex)
{
- // System.err.println(ex.toString());
+
}
}
});
{
} catch (java.lang.ClassCastException cex)
{
- Cache.log.warn(
- "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+ jalview.bin.Console.warn(
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
cex);
}
}
/*
* 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.
+ * Skip this step for dynamically added file formats, because IdentifyFile does
+ * not know how to recognise them.
*/
if (FileFormats.getInstance().isIdentifiable(format))
{
panel.add(label);
/*
- * the URL to fetch is
- * Java: an editable combobox with history
- * JS: (pending JAL-3038) a plain text field
+ * the URL to fetch is input in Java: an editable combobox with history JS:
+ * (pending JAL-3038) a plain text field
*/
JComponent history;
- String urlBase = "http://www.";
+ String urlBase = "https://www.";
if (Platform.isJS())
{
history = new JTextField(urlBase, 35);
@SuppressWarnings("unchecked")
String url = (history instanceof JTextField
? ((JTextField) history).getText()
- : ((JComboBox<String>) history).getSelectedItem()
- .toString());
+ : ((JComboBox<String>) history).getEditor().getItem()
+ .toString().trim());
- if (url.toLowerCase().endsWith(".jar"))
+ if (url.toLowerCase(Locale.ROOT).endsWith(".jar"))
{
if (viewport != null)
{
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);
+ jalview.bin.Console.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 + "");
public String getAboutMessage()
{
StringBuilder message = new StringBuilder(1024);
- message.append("<h1><strong>Version: ")
+ message.append("<div style=\"font-family: sans-serif;\">")
+ .append("<h1><strong>Version: ")
.append(Cache.getProperty("VERSION")).append("</strong></h1>")
.append("<strong>Built: <em>")
.append(Cache.getDefault("BUILD_DATE", "unknown"))
else if (!latestVersion.equals(Cache.getProperty("VERSION")))
{
boolean red = false;
- if (Cache.getProperty("VERSION").toLowerCase()
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT)
.indexOf("automated build") == -1)
{
red = true;
.append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
.append(" is available for download from ")
.append(Cache.getDefault("www.jalview.org",
- "http://www.jalview.org"))
+ "https://www.jalview.org"))
.append(" !!");
if (red)
{
message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
message.append(CITATION);
+ message.append("</div>");
+
return message.toString();
}
{
if (Platform.isJS())
{
- BrowserLauncher.openURL("http://www.jalview.org/help.html");
+ BrowserLauncher.openURL("https://www.jalview.org/help.html");
}
else
/**
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
- Cache.log.debug("Collecting garbage...");
+ jalview.bin.Console.debug("Collecting garbage...");
System.gc();
- Cache.log.debug("Finished garbage collection.");
+ jalview.bin.Console.debug("Finished garbage collection.");
}
/*
* (non-Javadoc)
*
- * @see
- * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
- * )
+ * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.
+ * ActionEvent )
*/
@Override
protected void showMemusage_actionPerformed(ActionEvent e)
+ chosenFile.getName(), oom);
} catch (Exception ex)
{
- Cache.log.error("Problems whilst trying to save to "
+ jalview.bin.Console.error("Problems whilst trying to save to "
+ chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
MessageManager.formatMessage(
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex)
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Problems whilst loading project from " + choice, ex);
JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
}
/*
- * Restore the view's last exploded frame geometry if known. Multiple
- * views from one exploded frame share and restore the same (frame)
- * position and size.
+ * Restore the view's last exploded frame geometry if known. Multiple views from
+ * one exploded frame share and restore the same (frame) position and size.
*/
Rectangle geometry = ap.av.getExplodedGeometry();
if (geometry != null)
{
source.showFeatureSettingsUI();
}
+
}
public JInternalFrame[] getAllFrames()
openGroovyConsole();
} catch (Exception ex)
{
- Cache.log.error("Groovy Shell Creation failed.", ex);
+ jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
/*
* We allow only one console at a time, so that AlignFrame menu option
- * 'Calculate | Run Groovy script' is unambiguous.
- * Disable 'Groovy Console', and enable 'Run script', when the console is
- * opened, and the reverse when it is closed
+ * 'Calculate | Run Groovy script' is unambiguous. Disable 'Groovy Console', and
+ * enable 'Run script', when the console is opened, and the reverse when it is
+ * closed
*/
Window window = (Window) groovyConsole.getFrame();
window.addWindowListener(new WindowAdapter()
((Window) groovyConsole.getFrame()).setVisible(true);
/*
- * if we got this far, enable 'Run Groovy' in AlignFrame menus
- * and disable opening a second console
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus and disable
+ * opening a second console
*/
enableExecuteGroovy(true);
}
public void enableExecuteGroovy(boolean enabled)
{
/*
- * disable opening a second Groovy console
- * (or re-enable when the console is closed)
+ * disable opening a second Groovy console (or re-enable when the console is
+ * closed)
*/
groovyShell.setEnabled(!enabled);
@Override
public void setProgressBar(String message, long id)
{
- // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
-
if (progressBars == null)
{
progressBars = new Hashtable<>();
this.inBatchMode = inBatchMode;
}
+ /**
+ * start service discovery and wait till it is done
+ */
public void startServiceDiscovery()
{
startServiceDiscovery(false);
}
+ /**
+ * start service discovery threads - blocking or non-blocking
+ *
+ * @param blocking
+ */
public void startServiceDiscovery(boolean blocking)
{
+ startServiceDiscovery(blocking, false);
+ }
+
+ /**
+ * start service discovery threads
+ *
+ * @param blocking
+ * - false means call returns immediately
+ * @param ignore_SHOW_JWS2_SERVICES_preference
+ * - when true JABA services are discovered regardless of user's JWS2
+ * discovery preference setting
+ */
+ public void startServiceDiscovery(boolean blocking,
+ boolean ignore_SHOW_JWS2_SERVICES_preference)
+ {
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
(t0 = new Thread(discoverer)).start();
}
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ if (ignore_SHOW_JWS2_SERVICES_preference
+ || Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
.startDiscoverer(changeSupport);
/*
* JalviewDialog jd =new JalviewDialog() {
*
- * @Override protected void cancelPressed() { // TODO
- * Auto-generated method stub
+ * @Override protected void cancelPressed() { // TODO Auto-generated method stub
*
- * }@Override protected void okPressed() { // TODO
- * Auto-generated method stub
+ * }@Override protected void okPressed() { // TODO Auto-generated method stub
*
- * }@Override protected void raiseClosed() { // TODO
- * Auto-generated method stub
+ * }@Override protected void raiseClosed() { // TODO Auto-generated method stub
*
- * } }; jd.initDialogFrame(new
- * JLabel("<html><table width=\"450\"><tr><td>" + ermsg +
+ * } }; jd.initDialogFrame(new JLabel("<html><table width=\"450\"><tr><td>" +
+ * ermsg +
* "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
* + " or mis-configured HTTP proxy settings.<br/>" +
- * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
- * +
- * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
- * ), true, true, "Web Service Configuration Problem", 450,
- * 400);
+ * "Check the <em>Connections</em> and <em>Web services</em> tab of the" +
+ * " Tools->Preferences dialog box to change them.</td></tr></table></html>" ),
+ * true, true, "Web Service Configuration Problem", 450, 400);
*
* jd.waitForInput();
*/
}
else
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Errors reported by JABA discovery service. Check web services preferences.\n"
+ ermsg);
}
{
if (url != null)
{
- if (Cache.log != null)
- {
- Cache.log.error("Couldn't handle string " + url + " as a URL.");
- }
- else
- {
- System.err.println(
- "Couldn't handle string " + url + " as a URL.");
- }
+ jalview.bin.Console
+ .error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
SwingUtilities.invokeAndWait(prompter);
} catch (Exception q)
{
- Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ jalview.bin.Console.warn("Unexpected Exception in dialog thread.",
+ q);
}
}
});
public void exportImage(Graphics g) throws Exception
{
paintAll(g);
- Cache.log.info("Successfully written snapshot to file "
+ jalview.bin.Console.info("Successfully written snapshot to file "
+ of.getAbsolutePath());
}
};
}
/*
- * Processing in reverse order works, forwards order leaves the first panels
- * not visible. I don't know why!
+ * Processing in reverse order works, forwards order leaves the first panels not
+ * visible. I don't know why!
*/
for (int i = viewCount - 1; i >= 0; i--)
{
/*
- * Make new top and bottom frames. These take over the respective
- * AlignmentPanel objects, including their AlignmentViewports, so the
- * cdna/protein relationships between the viewports is carried over to the
- * new split frames.
+ * Make new top and bottom frames. These take over the respective AlignmentPanel
+ * objects, including their AlignmentViewports, so the cdna/protein
+ * relationships between the viewports is carried over to the new split frames.
*
* explodedGeometry holds the (x, y) position of the previously exploded
* SplitFrame, and the (width, height) of the AlignFrame component
}
/*
- * Clear references to the panels (now relocated in the new SplitFrames)
- * before closing the old SplitFrame.
+ * Clear references to the panels (now relocated in the new SplitFrames) before
+ * closing the old SplitFrame.
*/
topPanels.clear();
bottomPanels.clear();
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 uriListFlavor = new DataFlavor(
"text/uri-list;class=java.lang.String"), urlFlavour = null;
try
"application/x-java-url; class=java.net.URL");
} catch (ClassNotFoundException cfe)
{
- Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.",
+ cfe);
}
if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
{
protocols.add(DataSourceType.URL);
files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor "
+ jalview.bin.Console.debug("Drop handled as URL dataflavor "
+ files.get(files.size() - 1));
return;
}
}
} catch (Throwable ex)
{
- Cache.log.debug("URL drop handler failed.", ex);
+ jalview.bin.Console.debug("URL drop handler failed.", ex);
}
}
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
// Works on Windows and MacOSX
- Cache.log.debug("Drop handled as javaFileListFlavor");
+ jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
for (Object file : (List) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
String data = null;
if (t.isDataFlavorSupported(uriListFlavor))
{
- Cache.log.debug("Drop handled as uriListFlavor");
+ jalview.bin.Console.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
data = (String) t.getTransferData(uriListFlavor);
}
if (data == null)
{
// fallback to text: workaround - on OSX where there's a JVM bug
- Cache.log.debug("standard URIListFlavor failed. Trying text");
+ jalview.bin.Console
+ .debug("standard URIListFlavor failed. Trying text");
// try text fallback
DataFlavor textDf = new DataFlavor(
"text/plain;class=java.lang.String");
data = (String) t.getTransferData(textDf);
}
- Cache.log.debug("Plain text drop content returned "
+ jalview.bin.Console.debug("Plain text drop content returned "
+ (data == null ? "Null - failed" : data));
}
{
while (protocols.size() < files.size())
{
- Cache.log.debug("Adding missing FILE protocol for "
+ jalview.bin.Console.debug("Adding missing FILE protocol for "
+ files.get(protocols.size()));
protocols.add(DataSourceType.FILE);
}
continue;
}
java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http"))
+ if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http"))
{
protocols.add(DataSourceType.URL);
files.add(uri.toString());
}
}
- if (Cache.log.isDebugEnabled())
+ if (jalview.bin.Console.isDebugEnabled())
{
if (data == null || !added)
{
if (t.getTransferDataFlavors() != null
&& t.getTransferDataFlavors().length > 0)
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Couldn't resolve drop data. Here are the supported flavors:");
for (DataFlavor fl : t.getTransferDataFlavors())
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
if (df != null)
{
- Cache.log.debug("Retrieves: " + df);
+ jalview.bin.Console.debug("Retrieves: " + df);
}
else
{
- Cache.log.debug("Retrieved nothing");
+ jalview.bin.Console.debug("Retrieved nothing");
}
}
}
else
{
- Cache.log.debug("Couldn't resolve dataflavor for drop: "
- + t.toString());
+ jalview.bin.Console
+ .debug("Couldn't resolve dataflavor for drop: "
+ + t.toString());
}
}
}
}
if (Platform.isWindowsAndNotJS())
{
- Cache.log.debug("Scanning dropped content for Windows Link Files");
+ jalview.bin.Console
+ .debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++)
{
- String source = files.get(f).toString().toLowerCase();
+ String source = files.get(f).toString().toLowerCase(Locale.ROOT);
if (protocols.get(f).equals(DataSourceType.FILE)
&& (source.endsWith(".lnk") || source.endsWith(".url")
|| source.endsWith(".site")))
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);
+ jalview.bin.Console.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
String fullname = wscfile.getRealFilename();
protocols.set(f, FormatAdapter.checkProtocol(fullname));
files.set(f, fullname);
- Cache.log.debug("Parsed real filename " + fullname
+ jalview.bin.Console.debug("Parsed real filename " + fullname
+ " to extract protocol: " + protocols.get(f));
} catch (Exception ex)
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Couldn't parse " + files.get(f) + " as a link file.",
ex);
}
AffineTransform t = gg.getTransform();
double scaleX = t.getScaleX();
double scaleY = t.getScaleY();
- Cache.debug(debugScaleMessage + scaleX + " (X)");
- Cache.debug(debugScaleMessage + scaleY + " (Y)");
+ jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)");
+ jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)");
debugScaleMessageDone = true;
}
else
{
- Cache.debug("Desktop graphics null");
+ jalview.bin.Console.debug("Desktop graphics null");
}
} catch (Exception e)
{
- Cache.debug(Cache.getStackTraceString(e));
+ jalview.bin.Console.debug(Cache.getStackTraceString(e));
}
}
}
git://source.jalview.org / jalview.git / blobdiff