X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=4877d7f7f56f908b30eb4b70a1e11bdf57aa2488;hb=c3b3dc0d34e9da7507211ba332c35d3791a481c5;hp=77bc7d4fddf614d71e537ac95a77b69790d2c04a;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 77bc7d4..4877d7f 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,7 +20,6 @@ */ package jalview.gui; -import static jalview.util.UrlConstants.EMBLEBI_STRING; import static jalview.util.UrlConstants.SEQUENCE_ID; import jalview.api.AlignViewportI; @@ -31,6 +30,7 @@ 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.IdentifyFile; import jalview.io.JalviewFileChooser; @@ -38,11 +38,14 @@ 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; @@ -77,6 +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; @@ -102,7 +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; @@ -126,6 +129,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider { + private static int DEFAULT_MIN_WIDTH = 300; + + private static int DEFAULT_MIN_HEIGHT = 250; + + private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); @@ -324,19 +332,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements instance = this; doVamsasClientCheck(); - groovyShell = new JMenuItem(); - groovyShell.setText(MessageManager.getString("label.groovy_console")); - groovyShell.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - groovyShell_actionPerformed(); - } - }); - toolsMenu.add(groovyShell); - groovyShell.setVisible(true); - doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); @@ -391,6 +386,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements showConsole(showjconsole); showNews.setVisible(false); + + experimentalFeatures.setSelected(showExperimental()); + + getIdentifiersOrgData(); checkURLLinks(); @@ -455,7 +454,6 @@ 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() @@ -466,9 +464,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.log.debug("Filechooser init thread started."); String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), - // jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, - // jalview.io.AppletFormatAdapter.READABLE_FNAMES, - fileFormat, true); + fileFormat); Cache.log.debug("Filechooser init thread finished."); } }).start(); @@ -488,6 +484,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + /** + * Answers true if user preferences to enable experimental features is True + * (on), else false + * + * @return + */ + public boolean showExperimental() + { + String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, + Boolean.FALSE.toString()); + return Boolean.valueOf(experimental).booleanValue(); + } + public void doConfigureStructurePrefs() { // configure services @@ -528,6 +537,29 @@ 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) { @@ -808,6 +840,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements openFrameCount++; + frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH, + DEFAULT_MIN_HEIGHT)); frame.setVisible(makeVisible); frame.setClosable(true); frame.setResizable(resizable); @@ -894,9 +928,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements } }); + desktop.add(frame); + windowMenu.add(menuItem); - desktop.add(frame); frame.toFront(); try { @@ -1013,10 +1048,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser chooser = JalviewFileChooser.forRead( - Cache.getProperty("LAST_DIRECTORY"), - // AppletFormatAdapter.READABLE_EXTENSIONS, - // AppletFormatAdapter.READABLE_FNAMES, - fileFormat, true); + Cache.getProperty("LAST_DIRECTORY"), fileFormat); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1031,20 +1063,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); - FileFormatI format = null; - FileFormatI selectedFormat = chooser.getSelectedFormat(); - if (FileFormat.Jalview.equals(selectedFormat)) - { - format = FileFormat.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)) { try { format = new IdentifyFile().identify(choice, DataSourceType.FILE); } catch (FileFormatException e) { - // format is null + // format = null; //?? } } @@ -1535,8 +1568,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void saveState_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project", + JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project"); chooser.setFileView(new JalviewFileView()); @@ -2190,9 +2222,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (v_client != null) { - JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ - "Vamsas Document", "Vamsas Document"); + // TODO: VAMSAS DOCUMENT EXTENSION is VDJ + JalviewFileChooser chooser = new JalviewFileChooser("vdj", + "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -2295,7 +2327,8 @@ 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 @@ -2305,7 +2338,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements while (li.hasNext()) { String link = li.next(); - if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING)) + if (link.contains(SEQUENCE_ID) + && !link.equals(UrlConstants.DEFAULT_STRING)) { check = true; int barPos = link.indexOf("|"); @@ -2467,8 +2501,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements } - protected JMenuItem groovyShell; - /** * Accessor method to quickly get all the AlignmentFrames loaded. * @@ -2554,6 +2586,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Add Groovy Support to Jalview */ + @Override public void groovyShell_actionPerformed() { try @@ -2829,13 +2862,8 @@ 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; { @@ -3373,4 +3401,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } } + + /** + * Sets the Preferences property for experimental features to True or False + * depending on the state of the controlling menu item + */ + @Override + protected void showExperimental_actionPerformed(boolean selected) + { + Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected)); + } }