X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=429a2c149356527c8f081d6eb1b7add66b44518b;hb=7d92d3994908aae709e7c85cc5e1a1c4775907ed;hp=666fb4e0188e813792dbf2583bbfd84cc85619dc;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 666fb4e..429a2c1 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -140,24 +140,32 @@ import jalview.ws.utils.UrlDownloadClient;
public class Desktop extends jalview.jbgui.GDesktop
implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider {
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));
+ 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("
Development managed by The Barton Group, University of Dundee, Scotland, UK.");
- if (logo) {
+ sb.append(
+ "
Jalview is free software released under GPLv3.
Development is managed by The Barton Group, University of Dundee, Scotland, UK.");
+ if (logo)
+ {
sb.append("
");
}
- sb.append(bg_logo_url == null ? "" : "");
+ sb.append(bg_logo_url == null ? ""
+ : "");
sb.append(uod_logo_url == null ? ""
- : " ");
+ : " ");
sb.append(
- "
For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list");
+ "
For help, see www.jalview.org/faq and join discourse.jalview.org");
sb.append("
If you use Jalview, please cite:"
- + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "
Bioinformatics doi: 10.1093/bioinformatics/btp033");
+ + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "
Bioinformatics doi: 10.1093/bioinformatics/btp033");
CITATION = sb.toString();
}
@@ -382,11 +390,11 @@ public class Desktop extends jalview.jbgui.GDesktop
awtAppClassNameField.setAccessible(true);
awtAppClassNameField.set(xToolkit, title);
} else {
- Cache.log.debug("XToolkit: awtAppClassName not found");
+ jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
}
} catch (Exception e) {
- Cache.debug("Error setting awtAppClassName");
- Cache.trace(Cache.getStackTraceString(e));
+ jalview.bin.Console.debug("Error setting awtAppClassName");
+ jalview.bin.Console.trace(Cache.getStackTraceString(e));
}
}
@@ -401,8 +409,8 @@ public class Desktop extends jalview.jbgui.GDesktop
System.out.println("Cannot set APQHandlers");
// e.printStackTrace();
} catch (Throwable t) {
- Cache.warn("Error setting APQHandlers: " + t.toString());
- Cache.trace(Cache.getStackTraceString(t));
+ jalview.bin.Console.warn("Error setting APQHandlers: " + t.toString());
+ jalview.bin.Console.trace(Cache.getStackTraceString(t));
}
setIconImages(ChannelProperties.getIconList());
@@ -487,10 +495,10 @@ public class Desktop extends jalview.jbgui.GDesktop
new Thread(new Runnable() {
@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
@@ -498,7 +506,7 @@ public class Desktop extends jalview.jbgui.GDesktop
@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);
}
});
@@ -551,7 +559,8 @@ public class Desktop extends jalview.jbgui.GDesktop
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.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, true));
+ // JAL-3915 - RNAView is no longer an option so this has no effect
+ ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, false));
} else {
ssm.setAddTempFacAnnot(false);
ssm.setProcessSecondaryStructure(false);
@@ -565,28 +574,36 @@ public class Desktop extends jalview.jbgui.GDesktop
new Thread(new Runnable() {
@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() {
- if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) {
- // Thread off the identifiers fetcher
- new Thread(new Runnable() {
+ public void getIdentifiersOrgData()
+ {
+ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+ {// Thread off the identifiers fetcher
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
- Cache.log.debug("Downloading data from identifiers.org");
- try {
- UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation());
- } catch (IOException e) {
- Cache.log.debug("Exception downloading identifiers.org data" + e.getMessage());
+ public void run()
+ {
+ 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();
+ ;
}
}
@@ -596,7 +613,7 @@ public class Desktop extends jalview.jbgui.GDesktop
}
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()) {
new Thread(new Runnable() {
@@ -642,14 +659,14 @@ public class Desktop extends jalview.jbgui.GDesktop
iy = (int) (iy * sh);
ih = (int) (ih * sh);
while (ix >= screenSize.width) {
- Cache.log.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+ jalview.bin.Console.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height) {
- Cache.log.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+ jalview.bin.Console.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- Cache.log.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ jalview.bin.Console.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ " height:" + ih);
}
// return dimensions for new instance
@@ -851,7 +868,7 @@ public class Desktop extends jalview.jbgui.GDesktop
frame.requestFocus();
} catch (java.beans.PropertyVetoException ve) {
} catch (java.lang.ClassCastException cex) {
- Cache.log.warn(
+ 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);
}
@@ -1139,7 +1156,7 @@ public class Desktop extends jalview.jbgui.GDesktop
}
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
+ 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 + "");
@@ -1274,9 +1291,9 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
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.");
}
/*
@@ -1440,7 +1457,7 @@ public class Desktop extends jalview.jbgui.GDesktop
} catch (OutOfMemoryError oom) {
new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom);
} catch (Exception ex) {
- Cache.log.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
+ jalview.bin.Console.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
MessageManager.formatMessage("label.error_whilst_saving_current_state_to",
new Object[] { chosenFile.getName() }),
@@ -1495,7 +1512,7 @@ public class Desktop extends jalview.jbgui.GDesktop
} catch (OutOfMemoryError oom) {
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex) {
- Cache.log.error("Problems whilst loading project from " + choice, ex);
+ jalview.bin.Console.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);
@@ -1982,7 +1999,7 @@ public class Desktop extends jalview.jbgui.GDesktop
try {
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"),
@@ -2293,7 +2310,7 @@ public class Desktop extends jalview.jbgui.GDesktop
});
}
} else {
- Cache.log.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
+ jalview.bin.Console.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
}
}
}
@@ -2364,11 +2381,7 @@ public class Desktop extends jalview.jbgui.GDesktop
Desktop.showUrl(url);
} catch (Exception x) {
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.
}
@@ -2414,7 +2427,7 @@ public class Desktop extends jalview.jbgui.GDesktop
try {
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);
}
}
});
@@ -2448,7 +2461,7 @@ public class Desktop extends jalview.jbgui.GDesktop
@Override
public void exportImage(Graphics g) throws Exception {
paintAll(g);
- Cache.log.info("Successfully written snapshot to file " + of.getAbsolutePath());
+ jalview.bin.Console.info("Successfully written snapshot to file " + of.getAbsolutePath());
}
};
String title = "View of desktop";
@@ -2607,7 +2620,7 @@ public class Desktop extends jalview.jbgui.GDesktop
try {
urlFlavour = new DataFlavor("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)) {
@@ -2619,7 +2632,7 @@ public class Desktop extends jalview.jbgui.GDesktop
if (url != null) {
protocols.add(DataSourceType.URL);
files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
+ jalview.bin.Console.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
return;
} else {
if (Platform.isAMacAndNotJS()) {
@@ -2627,12 +2640,12 @@ public class Desktop extends jalview.jbgui.GDesktop
}
}
} 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)) {
files.add(file);
protocols.add(DataSourceType.FILE);
@@ -2642,25 +2655,25 @@ public class Desktop extends jalview.jbgui.GDesktop
boolean added = false;
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");
if (t.isDataFlavorSupported(textDf)) {
data = (String) t.getTransferData(textDf);
}
- Cache.log.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
+ jalview.bin.Console.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
}
if (data != null) {
while (protocols.size() < files.size()) {
- Cache.log.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
+ jalview.bin.Console.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
protocols.add(DataSourceType.FILE);
}
for (java.util.StringTokenizer st = new java.util.StringTokenizer(data, "\r\n"); st.hasMoreTokens();) {
@@ -2683,28 +2696,28 @@ public class Desktop extends jalview.jbgui.GDesktop
}
}
- if (Cache.log.isDebugEnabled()) {
+ if (jalview.bin.Console.isDebugEnabled()) {
if (data == null || !added) {
if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) {
- Cache.log.debug("Couldn't resolve drop data. Here are the supported flavors:");
+ jalview.bin.Console.debug("Couldn't resolve drop data. Here are the supported flavors:");
for (DataFlavor fl : t.getTransferDataFlavors()) {
- Cache.log.debug("Supported transfer dataflavor: " + fl.toString());
+ 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++) {
@@ -2715,14 +2728,14 @@ public class Desktop extends jalview.jbgui.GDesktop
Object obj = files.get(f);
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 + " to extract protocol: " + protocols.get(f));
+ jalview.bin.Console.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f));
} catch (Exception ex) {
- Cache.log.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
+ jalview.bin.Console.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
}
}
}
@@ -2781,14 +2794,14 @@ public class Desktop extends jalview.jbgui.GDesktop
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));
}
}
}