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 ? "" : "\"Barton"); + sb.append(bg_logo_url == null ? "" + : "\"Barton"); sb.append(uod_logo_url == null ? "" - : " \"University"); + : " \"University"); 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)); } } }