X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;fp=src%2Fjalview%2Fgui%2FDesktop.java;h=7d0eb7f0fe562638ebbac244c8346c1f7db35fef;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=1d76f27f39c83716cbd9a45a34d37a94697828b1;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 1d76f27..7d0eb7f 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,23 +20,32 @@ */ package jalview.gui; +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.FileFormats; import jalview.io.FileLoader; -import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; 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; @@ -71,10 +80,12 @@ import java.beans.PropertyChangeListener; 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; import java.util.List; +import java.util.ListIterator; import java.util.StringTokenizer; import java.util.Vector; import java.util.concurrent.ExecutorService; @@ -82,9 +93,12 @@ import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; import javax.swing.AbstractAction; +import javax.swing.Box; +import javax.swing.BoxLayout; import javax.swing.DefaultDesktopManager; import javax.swing.DesktopManager; import javax.swing.JButton; +import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDesktopPane; @@ -92,7 +106,6 @@ import javax.swing.JFrame; 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; @@ -382,6 +395,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements showNews.setVisible(false); + getIdentifiersOrgData(); + + checkURLLinks(); + this.addWindowListener(new WindowAdapter() { @Override @@ -443,7 +460,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); - // 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() @@ -452,11 +468,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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(); @@ -516,6 +530,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + 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) { @@ -676,10 +713,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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) @@ -882,9 +919,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); + desktop.add(frame); + windowMenu.add(menuItem); - desktop.add(frame); frame.toFront(); try { @@ -945,8 +983,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - java.util.List files = new ArrayList(); - java.util.List protocols = new ArrayList(); + List files = new ArrayList(); + List protocols = new ArrayList(); try { @@ -964,13 +1002,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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 @@ -999,11 +1037,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements @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 @@ -1015,28 +1051,35 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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")) - { - format = "Jalview"; - } - else + FileFormatI format = chooser.getSelectedFormat(); + + /* + * 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. + */ + if (FileFormats.getInstance().isIdentifiable(format)) { - format = new IdentifyFile().identify(choice, FormatAdapter.FILE); + try + { + format = new IdentifyFile().identify(choice, DataSourceType.FILE); + } catch (FileFormatException e) + { + // format = 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); } } } @@ -1077,11 +1120,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } - 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; } @@ -1092,36 +1135,46 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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); } } } @@ -1205,9 +1258,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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 @@ -1506,9 +1559,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void saveState_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] { "jvp" }, new String[] { "Jalview Project" }, + JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project"); chooser.setFileView(new JalviewFileView()); @@ -1547,11 +1598,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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()); } @@ -1579,7 +1630,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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()); @@ -1592,7 +1643,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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() { @@ -1613,12 +1664,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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()); } @@ -1903,7 +1954,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( @@ -1911,7 +1962,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } } @@ -2162,10 +2213,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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"); + // TODO: VAMSAS DOCUMENT EXTENSION is VDJ + JalviewFileChooser chooser = new JalviewFileChooser("vdj", + "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -2179,7 +2229,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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 @@ -2203,9 +2253,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements removeProgressPanel(progpanel); if (warnmsg != null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, - warnmsg, warnttl, JOptionPane.ERROR_MESSAGE); + warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); } } } @@ -2221,7 +2271,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ 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) @@ -2256,6 +2306,86 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Thread(jvq).start(); } + public void checkURLLinks() + { + // Thread off the URL link checker + addDialogThread(new Runnable() + { + @Override + public void run() + { + if (Cache.getDefault("CHECKURLLINKS", true)) + { + // check what the actual links are - if it's just the default don't + // bother with the warning + List 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 + ListIterator li = links.listIterator(); + boolean check = false; + List urls = new ArrayList(); + while (li.hasNext()) + { + String link = li.next(); + if (link.contains(SEQUENCE_ID) + && !link.equals(UrlConstants.DEFAULT_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)); + } + } + if (!check) + { + return; + } + + // 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()); + JLabel msg = new JLabel( + MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); + JLabel msg2 = new JLabel( + 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 for "don't show this again" + boolean showWarningAgain = !jcb.isSelected(); + Cache.setProperty("CHECKURLLINKS", + Boolean.valueOf(showWarningAgain).toString()); + } + }); + msgPanel.add(jcb); + + JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, + MessageManager + .getString("label.SEQUENCE_ID_no_longer_used"), + JvOptionPane.WARNING_MESSAGE); + } + } + }); + } + /** * Proxy class for JDesktopPane which optionally displays the current memory * usage and highlights the desktop area with a red bar if free memory runs @@ -2457,11 +2587,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } 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); } } @@ -2724,13 +2854,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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; { @@ -2802,7 +2927,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * jd.waitForInput(); */ - JOptionPane + JvOptionPane .showConfirmDialog( Desktop.desktop, new JLabel( @@ -2814,8 +2939,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements + "

Check the Connections and Web services tab
of the" + " Tools->Preferences dialog box to change them.

"), "Web Service Configuration Problem", - JOptionPane.DEFAULT_OPTION, - JOptionPane.ERROR_MESSAGE); + JvOptionPane.DEFAULT_OPTION, + JvOptionPane.ERROR_MESSAGE); serviceChangedDialog = null; } @@ -2872,11 +2997,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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(); } @@ -3173,7 +3298,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } public static void transferFromDropTarget(List files, - List protocols, DropTargetDropEvent evt, Transferable t) + List protocols, DropTargetDropEvent evt, + Transferable t) throws Exception { @@ -3183,12 +3309,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements { // Works on Windows and MacOSX Cache.log.debug("Drop handled as javaFileListFlavor"); - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); for (Object file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { files.add(((File) file).toString()); - protocols.add(FormatAdapter.FILE); + protocols.add(DataSourceType.FILE); } } else @@ -3200,7 +3325,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.debug("Drop handled as uriListFlavor"); // This is used by Unix drag system - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); data = (String) t.getTransferData(uriListFlavor); } if (data == null) @@ -3219,7 +3343,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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();) @@ -3234,14 +3358,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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()); } } @@ -3255,7 +3379,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.debug("Supported transfer dataflavor: " + fl.toString()); - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Object df = t.getTransferData(fl); if (df != null) {