X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=dc16a5798bad154f8465b0535b811edd4ad73569;hb=b0f76adef2787dd14566525e66a4073278e75d67;hp=d06dd2656febb412e50d884989f50d02d7821758;hpb=a3b90af5d2d63a54e94e827022325c3c0313384c;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index d06dd26..dc16a57 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,26 +20,32 @@ */ package jalview.gui; -import static jalview.util.UrlConstants.EMBLEBI_STRING; 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; @@ -74,6 +80,7 @@ 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; @@ -99,7 +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; @@ -389,6 +395,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements showNews.setVisible(false); + getIdentifiersOrgData(); + checkURLLinks(); this.addWindowListener(new WindowAdapter() @@ -452,7 +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() @@ -461,11 +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(); @@ -525,6 +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) { @@ -685,10 +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) @@ -891,9 +919,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); + desktop.add(frame); + windowMenu.add(menuItem); - desktop.add(frame); frame.toFront(); try { @@ -954,8 +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 { @@ -973,13 +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 @@ -1008,11 +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 @@ -1024,28 +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); } } } @@ -1086,11 +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; } @@ -1101,36 +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); } } } @@ -1214,9 +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 @@ -1515,9 +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()); @@ -1556,11 +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()); } @@ -1588,7 +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()); @@ -1601,7 +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() { @@ -1622,12 +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()); } @@ -1912,7 +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( @@ -1920,7 +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); } } } @@ -2171,10 +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 @@ -2188,7 +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 @@ -2212,9 +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); } } } @@ -2230,7 +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) @@ -2277,17 +2318,26 @@ public class Desktop extends jalview.jbgui.GDesktop implements { // check what the actual links are - if it's just the default don't // bother with the warning - Vector links = Preferences.sequenceURLLinks; + 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; - while (li.hasNext() && !check) + boolean check = false; + List urls = new ArrayList(); + while (li.hasNext()) { String link = li.next(); - check = (link.contains(SEQUENCE_ID) && !link - .equals(EMBLEBI_STRING)); + 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) { @@ -2306,6 +2356,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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( @@ -2315,23 +2369,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void actionPerformed(ActionEvent e) { - // update Cache settings if checkbox is selected - if (jcb.isSelected()) - { - Cache.setProperty("CHECKURLLINKS", "false"); - } - else - { - Cache.setProperty("CHECKURLLINKS", "true"); - } + // update Cache settings for "don't show this again" + boolean showWarningAgain = !jcb.isSelected(); + Cache.setProperty("CHECKURLLINKS", + Boolean.valueOf(showWarningAgain).toString()); } }); msgPanel.add(jcb); - JOptionPane.showMessageDialog(Desktop.desktop, msgPanel, + JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, MessageManager .getString("label.SEQUENCE_ID_no_longer_used"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } }); @@ -2538,11 +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); } } @@ -2883,7 +2932,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * jd.waitForInput(); */ - JOptionPane + JvOptionPane .showConfirmDialog( Desktop.desktop, new JLabel( @@ -2895,8 +2944,8 @@ 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; } @@ -2953,11 +3002,11 @@ 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(); } @@ -3254,7 +3303,8 @@ 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 { @@ -3268,7 +3318,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements .getTransferData(DataFlavor.javaFileListFlavor)) { files.add(((File) file).toString()); - protocols.add(FormatAdapter.FILE); + protocols.add(DataSourceType.FILE); } } else @@ -3298,7 +3348,7 @@ 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();) @@ -3313,14 +3363,14 @@ 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()); } }