X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=63d88a0834dd058489505395d987313ceee224b7;hb=954039bbfbde3648ac4c795277e788e49be5181b;hp=ac957d8baa69886c6f3a29914d38d8c509fad81a;hpb=2da3a29ae39b692964b85456353985d388aa3858;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index ac957d8..63d88a0 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; @@ -125,6 +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(); @@ -323,19 +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); @@ -390,6 +386,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements showConsole(showjconsole); showNews.setVisible(false); + + experimentalFeatures.setSelected(showExperimental()); + + getIdentifiersOrgData(); checkURLLinks(); @@ -484,6 +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 @@ -524,6 +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) { @@ -713,7 +749,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements public static synchronized void addInternalFrame( final JInternalFrame frame, String title, int w, int h) { - addInternalFrame(frame, title, true, w, h, true); + addInternalFrame(frame, title, true, w, h, true, false); } /** @@ -735,7 +771,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements final JInternalFrame frame, String title, boolean makeVisible, int w, int h) { - addInternalFrame(frame, title, makeVisible, w, h, true); + addInternalFrame(frame, title, makeVisible, w, h, true, false); } /** @@ -756,7 +792,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements final JInternalFrame frame, String title, int w, int h, boolean resizable) { - addInternalFrame(frame, title, true, w, h, resizable); + addInternalFrame(frame, title, true, w, h, resizable, false); } /** @@ -775,10 +811,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements * height * @param resizable * Allow resize + * @param ignoreMinSize + * Do not set the default minimum size for frame */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, boolean makeVisible, - int w, int h, boolean resizable) + int w, int h, boolean resizable, boolean ignoreMinSize) { // TODO: allow callers to determine X and Y position of frame (eg. via @@ -804,6 +842,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements openFrameCount++; + if (!ignoreMinSize) + { + frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH, + DEFAULT_MIN_HEIGHT)); + } frame.setVisible(makeVisible); frame.setClosable(true); frame.setResizable(resizable); @@ -1025,20 +1068,21 @@ 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; //?? } } @@ -1529,8 +1573,8 @@ 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()); chooser.setDialogTitle(MessageManager.getString("label.save_state")); @@ -2183,8 +2227,8 @@ 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 + // TODO: VAMSAS DOCUMENT EXTENSION is VDJ + JalviewFileChooser chooser = new JalviewFileChooser("vdj", "Vamsas Document"); chooser.setFileView(new JalviewFileView()); @@ -2288,7 +2332,8 @@ 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 @@ -2298,7 +2343,8 @@ 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("|"); @@ -2460,8 +2506,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements } - protected JMenuItem groovyShell; - /** * Accessor method to quickly get all the AlignmentFrames loaded. * @@ -2547,6 +2591,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Add Groovy Support to Jalview */ + @Override public void groovyShell_actionPerformed() { try @@ -2822,13 +2867,8 @@ 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; { @@ -3366,4 +3406,14 @@ 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)); + } }