[file name or url to open #1] ..."); System.exit(1); } // Get the main class of the target program - Class mainClass = null; - try{ - mainClass = Class.forName(args[0]); - } catch(Exception e){ - System.err.println("Could not find main class "+args[0]); - System.exit(2); - } + Class mainClass = findMainClass(args.length == 0); + if(mainClass == null && args.length == 0){ + System.err.println("Usage: java "+SingletonApplication.class.getName()+ + "

[file name or url to open #1] ..."); + System.exit(15); + } + if(mainClass == null){ + try{ + mainClass = Class.forName(args[0]); + } catch(Exception e){ + System.err.println("Could not find main class "+args[0]); + System.exit(2); + } + // Pass along all args except the first, the main class name + String programArgs[] = new String[args.length-1]; + System.arraycopy(args, 1, programArgs, 0, programArgs.length); + args = programArgs; + } Class mainArgs[] = {String[].class}; Method main = null; try{ @@ -65,19 +87,6 @@ System.exit(10); } - // Pass along all args except the first, the main class name - String programArgs[] = new String[args.length-1]; - System.arraycopy(args, 1, programArgs, 0, programArgs.length); - -// FileOutputStream fos = null; -// try{ -// fos = new FileOutputStream(lockFile); -// } catch(Exception e){ -// System.err.println("Failed to get output stream for file " + lockFile.getAbsolutePath()+": "+e.getMessage()); -// e.printStackTrace(); -// System.exit(12); -// } - FileLock lock = null; try{ lock = lockFile.getChannel().tryLock(); @@ -106,7 +115,7 @@ System.exit(4); } try{ - callOpen(port, programArgs); + callOpen(port, args); } catch(Exception e){ System.err.println("While calling open on existing "+main.getName()+" process: " + e.getMessage()); e.printStackTrace(); @@ -127,7 +136,7 @@ // first instance, or the app doesn't implement the right interface (why are you using this, then?) (new File(lockFileAbsolutePath)).deleteOnExit(); try{ - callMain(main, programArgs, lock); + callMain(main, args, lock); } catch(Exception e){ System.err.println("While calling main method of "+main.getName()+": " + e.getMessage()); e.printStackTrace(); @@ -135,6 +144,49 @@ } } + private static Class findMainClass(boolean require){ + String className = null; + ClassLoader classLoader = Thread.currentThread().getContextClassLoader(); + String resourceName = "META-INF/services/"+SingletonApplication.class.getName(); + URL resURL = classLoader.getResource(resourceName); + if(resURL == null){ + if(require){ + System.err.println("NNo command line arg for the main class was provided, and the "+ + "resource " + resourceName + " could not be found"); + System.exit(16); + } + else{ + return null; + } + } + try{ + LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream())); + for(String line = reader.readLine(); line != null; line = reader.readLine()){ + if(!line.trim().startsWith("#")){ + className = line.trim(); + break; + } + } + } catch(Exception e){ + System.err.println("Error reading " + resURL+": "+e.getMessage()); + e.printStackTrace(); + System.exit(14); + } + if(className == null){ + System.err.println("Could not find main class name in " + resURL); + System.exit(15); + } + + try{ + return Class.forName(className); + } catch(Exception e){ + System.err.println("Could not load class " + className + ": " + e.getMessage()); + e.printStackTrace(); + System.exit(15); + } + return null; //should never get here + } + // Start the target program, passing the command-line arguments private static void callMain(Method main, String[] programArgs, FileLock lock) throws Exception{ // Write to the lock file the port on which we'll listen for "file open" requests From gordonp at dev.open-bio.org Thu Feb 3 17:05:37 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 17:05:37 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032205.p13M5bPb021662@dev.open-bio.org> gordonp Thu Feb 3 17:05:37 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv21626/src/main/org/biomoby/shared/data Modified Files: MobyDataFloat.java Log Message: Unparseable floats are not set to zero instead of causing exception moby-live/Java/src/main/org/biomoby/shared/data MobyDataFloat.java,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataFloat.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataFloat.java 2008/01/07 22:11:36 1.11 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataFloat.java 2011/02/03 22:05:37 1.12 @@ -2,6 +2,7 @@ package org.biomoby.shared.data; import java.math.BigDecimal; import java.math.BigInteger; +import java.util.logging.*; import org.biomoby.registry.meta.Registry; import org.biomoby.shared.MobyDataType; @@ -21,6 +22,7 @@ public class MobyDataFloat extends MobyDataObject{ private BigDecimal value; + private static Logger logger = Logger.getLogger(MobyDataFloat.class.getName()); /** * Construct the object using a DOM fragment. @@ -102,7 +104,12 @@ public MobyDataFloat(String articleName, String stringNumber, Registry registry) throws NumberFormatException{ super(articleName, registry); setDataType(MobyDataType.getDataType(MobyTags.MOBYFLOAT, registry)); - value = new BigDecimal(stringNumber.trim()); + try{ + value = new BigDecimal(stringNumber.trim()); + } catch(Exception e){ + logger.log(Level.WARNING, "Could not parse '"+stringNumber+"' as a decimal number, using zero instead"); + value = BigDecimal.ZERO; + } } public MobyDataFloat(String stringNumber){ From gordonp at dev.open-bio.org Fri Feb 4 13:36:35 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 4 Feb 2011 13:36:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102041836.p14IaZ1S011991@dev.open-bio.org> gordonp Fri Feb 4 13:36:35 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv11955/src/main/ca/ucalgary/seahawk/util Modified Files: CloseTabIcon.java Added Files: CloseTabListener.java Log Message: Implemented 'Undo close tab' for Seahawk moby-live/Java/src/main/ca/ucalgary/seahawk/util CloseTabListener.java,NONE,1.1 CloseTabIcon.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/CloseTabIcon.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/CloseTabIcon.java 2007/06/16 00:27:44 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/CloseTabIcon.java 2011/02/04 18:36:35 1.3 @@ -9,6 +9,7 @@ import java.awt.Graphics; import java.awt.Component; import java.net.URL; +import java.util.Vector; public class CloseTabIcon extends CombinedIcon{ public static final String CLOSE_TAB_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/tabclose.gif"; @@ -17,6 +18,7 @@ private JTabbedPane tabbedPane = null; private Rectangle closeIconArea; + private Vector listeners; public CloseTabIcon() throws Exception{ this(new NullIcon()); @@ -34,6 +36,14 @@ super(getIcon(), otherIcon, spacerWidth, orient); } + public CloseTabIcon addCloseTabListener(CloseTabListener listener){ + if(listeners == null){ + listeners = new Vector(); + } + listeners.add(listener); + return this; + } + public Rectangle getCloseIconArea(){ return closeIconArea; } @@ -102,9 +112,18 @@ // Don't respond unless the close tab icon is actually showing return; } + Component tab = tabbedPane.getComponentAt(tabIndex); + if(listeners != null){ + for(CloseTabListener listener: listeners){ + listener.tabClosing(tab); + } + } + tabbedPane.remove(tabIndex); e.consume(); // so other tabs aren't closed by mistake tabbedPane.removeMouseListener(this); + tabbedPane = null; // so if the tab is added back at some point, the listen is readded in paintIcon() + } } } From gordonp at dev.open-bio.org Fri Feb 4 13:36:35 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 4 Feb 2011 13:36:35 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102041836.p14IaZIT012013@dev.open-bio.org> gordonp Fri Feb 4 13:36:35 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv11955/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyContentPane.java MobyContentGUI.java Log Message: Implemented 'Undo close tab' for Seahawk moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.34,1.35 MobyContentGUI.java,1.24,1.25 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v retrieving revision 1.34 retrieving revision 1.35 diff -u -r1.34 -r1.35 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java 2011/02/03 21:50:50 1.34 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java 2011/02/04 18:36:35 1.35 @@ -243,12 +243,12 @@ tabbedPane.getTabCount() > 1){ try{ if(currentIcon == null){ - tabbedPane.setIconAt(tabIndex, new CloseTabIcon()); + tabbedPane.setIconAt(tabIndex, (new CloseTabIcon()).addCloseTabListener(getContentGUI())); return; } // If there's a real (non-close-tab) single icon, add the close tab icon if(!(currentIcon instanceof CloseTabIcon)){ - try{tabbedPane.setIconAt(tabIndex, new CloseTabIcon(currentIcon, TAB_ICON_SPACER));} + try{tabbedPane.setIconAt(tabIndex, (new CloseTabIcon(currentIcon, TAB_ICON_SPACER)).addCloseTabListener(getContentGUI()));} catch(Exception e){e.printStackTrace();} tabbedPane.setDisabledIconAt(tabIndex, currentIcon); } @@ -257,7 +257,7 @@ e.printStackTrace(); } - } else{ + } else{ //Don't display X widget (closer) unless it's the active tab if(currentIcon != null && currentIcon instanceof CloseTabIcon){ tabbedPane.setIconAt(tabIndex, ((CloseTabIcon) currentIcon).getSecondIcon()); tabbedPane.setDisabledIconAt(tabIndex, ((CloseTabIcon) currentIcon).getSecondIcon()); @@ -982,7 +982,7 @@ int tabIndex = tabbedPane.indexOfComponent(this); if(tabIndex > -1){ try{tabbedPane.setIconAt(tabIndex, - new CloseTabIcon(failedIcon, TAB_ICON_SPACER));} + (new CloseTabIcon(failedIcon, TAB_ICON_SPACER)).addCloseTabListener(getContentGUI()));} catch(Exception e){e.printStackTrace(); tabbedPane.setIconAt(tabIndex, failedIcon);} } @@ -1005,7 +1005,7 @@ int tabIndex = tabbedPane.indexOfComponent(this); if(tabIndex > -1 && tabbedPane.getTabCount() > 1){ try{tabbedPane.setIconAt(tabIndex, - new CloseTabIcon(loadedIcon, TAB_ICON_SPACER));} + (new CloseTabIcon(loadedIcon, TAB_ICON_SPACER)).addCloseTabListener(getContentGUI()));} catch(Exception e){e.printStackTrace(); tabbedPane.setIconAt(tabIndex, loadedIcon);} } @@ -1476,7 +1476,7 @@ int tabIndex = tabbedPane.indexOfComponent(this); if(tabIndex > -1){ try{tabbedPane.setIconAt(tabIndex, - new CloseTabIcon(hourglassIcon, TAB_ICON_SPACER));} + (new CloseTabIcon(hourglassIcon, TAB_ICON_SPACER)).addCloseTabListener(getContentGUI()));} catch(Exception e){e.printStackTrace(); tabbedPane.setIconAt(tabIndex, hourglassIcon);} } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java 2011/02/03 21:47:57 1.24 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java 2011/02/04 18:36:35 1.25 @@ -37,7 +37,7 @@ * @author Paul Gordon (gordonp at ucalgary.ca) */ -public class MobyContentGUI extends JFrame implements ActionListener, ComponentListener, KeyListener, MobyRequestEventHandler, MouseListener, FontSizeChangeListener, ArgumentListener{ +public class MobyContentGUI extends JFrame implements ActionListener, ComponentListener, KeyListener, MobyRequestEventHandler, MouseListener, FontSizeChangeListener, ArgumentListener, CloseTabListener{ // Variables used to coordinate component finding with the unit test cases public final static String BACK_BUTTON_NAME = "MCGbackButton"; @@ -63,9 +63,11 @@ public final static String DEFAULT_XSLT_CONVERTER_URL = "ca/ucalgary/seahawk/resources/moby2HTML.xsl"; public final static int MAX_TAB_NAME_LENGTH = 25; public final static String CLIPBOARD_TAB_TOOLTIP = "Right-click for clipboard options"; - public final static String TAB_TOOLTIP = "Right-click for tab options, or Ctrl-T for new tab"; + public final static String TAB_TOOLTIP = "Right-click tabs for options, or Ctrl-T for new tab"; public final static String CLOSE_TAB_OPTION = "Close This Tab"; public final static String CLOSE_OTHERS_OPTION = "Close Other Tabs"; + public final static String UNDO_CLOSE_TAB_OPTION = "Undo Close Tab"; + public final static String UNDO_CLOSE_TABS_OPTION = "Undo Close Tabs"; public final static String FILE_OPEN_OPTION = "Open File"; public final static String WEB_OPEN_OPTION = "Open Web Page"; @@ -96,6 +98,9 @@ private MobyContentHelpPane helpPane; private DataFlowRecorder dataRecorder; // used for workflow export, etc. private SeahawkOptionsGUI settingsGUI; + private java.util.List closedTabs; + private java.util.List closedTabTitles; + private java.util.List closedTabIcons; private boolean setup; private Map request2tab; @@ -231,7 +236,7 @@ // See OptionsTabbedPaneUI class definiton at the end of this file (overrides right-click behaviour) tabbedPane.setUI(new OptionsTabbedPaneUI(this)); tabbedPane.setSize(getContentSize()); - tabbedPane.setToolTipText("Hit to display a new tab"); + tabbedPane.setToolTipText(TAB_TOOLTIP); tabbedPane.addKeyListener(this); try{ @@ -249,6 +254,10 @@ tabbedPane.add(clipboard); clipboard.init(); + closedTabs = new ArrayList(); + closedTabTitles = new ArrayList(); + closedTabIcons = new ArrayList(); + settingsGUI = new SeahawkOptionsGUI(this, this); // params are frame owner, font change listener } @@ -1015,9 +1024,33 @@ // Don't close clipboard, if somehow we were asked... } else{ + closedTabs.add(tabbedPane.getComponentAt(activeTabIndex)); + closedTabTitles.add(tabbedPane.getTitleAt(activeTabIndex)); + closedTabIcons.add(tabbedPane.getIconAt(activeTabIndex)); tabbedPane.remove(activeTabIndex); } } + else if(UNDO_CLOSE_TAB_OPTION.equals(cmd)){ + Object lastClose = closedTabs.get(closedTabs.size()-1); + if(lastClose instanceof java.util.List){ // Closed more than one tab last time + java.util.List tabsList = (java.util.List) lastClose; + java.util.List tabTitlesList = (java.util.List) closedTabTitles.get(closedTabTitles.size()-1); + java.util.List tabIconsList = (java.util.List) closedTabIcons.get(closedTabIcons.size()-1); + for(int i = 0; i < tabsList.size(); i++){ + tabbedPane.addTab((String) tabTitlesList.get(i), + (Icon) tabIconsList.get(i), + (Component) tabsList.get(i)); + } + } + else{ // Single tab being unclosed + tabbedPane.addTab((String) closedTabTitles.get(closedTabTitles.size()-1), + (Icon) closedTabIcons.get(closedTabIcons.size()-1), + (Component) lastClose); + } + closedTabs.remove(closedTabs.size()-1); // no longer in close history + closedTabTitles.remove(closedTabTitles.size()-1); // no longer in close history + closedTabIcons.remove(closedTabIcons.size()-1); // no longer in close history + } else if(MobyContentClipboard.CLEAR_CLIPBOARD_OPTION.equals(cmd)){ clipboard.clearData(); } @@ -1027,13 +1060,32 @@ return; } Component keeper = tabbedPane.getComponentAt(activeTabIndex); + ArrayList otherTabs = new ArrayList(); + ArrayList otherTabTitles = new ArrayList(); + ArrayList otherTabIcons = new ArrayList(); for(int i = 0; i < tabbedPane.getTabCount(); i++){ Component comp = tabbedPane.getComponentAt(i); - if(comp != keeper && comp != clipboard){ + if(comp != keeper && comp != clipboard){ + // This is slightly lazy, we could actually destroy the component + // and save the tab's history rather than put the component in the history. + // If memory becomes an issue, this would be a place to start saving... + otherTabs.add(comp); + otherTabTitles.add(tabbedPane.getTitleAt(i)); + otherTabIcons.add(tabbedPane.getIconAt(i)); tabbedPane.remove(comp); i--; } } + if(otherTabs.size() == 1){ // Was it just one tab? + closedTabs.add(otherTabs.get(0)); + closedTabTitles.add(otherTabTitles.get(0)); + closedTabIcons.add(otherTabIcons.get(0)); + } + else{ + closedTabs.add(otherTabs); + closedTabTitles.add(otherTabTitles); + closedTabIcons.add(otherTabIcons); + } } else{ logger.warn(getClass().getName() + " ignoring unrecognized action command: " + cmd); @@ -1139,8 +1191,8 @@ tabOptions.add(item); } else if(tabbedPane.getTabCount() > 1){ - item = new JMenuItem(MobyContentGUI.CLOSE_TAB_OPTION); - item.setActionCommand(MobyContentGUI.CLOSE_TAB_OPTION); + item = new JMenuItem(CLOSE_TAB_OPTION); + item.setActionCommand(CLOSE_TAB_OPTION); item.addActionListener(gui); tabOptions.add(item); } @@ -1148,13 +1200,29 @@ if(tabbedPane.getComponentAt(index) == clipboard && tabbedPane.getTabCount() > 1 || tabbedPane.getTabCount() > 2 || tabbedPane.indexOfComponent(clipboard) == -1 && tabbedPane.getTabCount() >= 2){ - item = new JMenuItem(MobyContentGUI.CLOSE_OTHERS_OPTION); - item.setActionCommand(MobyContentGUI.CLOSE_OTHERS_OPTION); + item = new JMenuItem(CLOSE_OTHERS_OPTION); + item.setActionCommand(CLOSE_OTHERS_OPTION); item.addActionListener(gui); tabOptions.add(item); } - - tabOptions.show(gui, e.getX(), e.getY()); + item = new JMenuItem(UNDO_CLOSE_TAB_OPTION); + item.setActionCommand(UNDO_CLOSE_TAB_OPTION); + if(closedTabs.isEmpty()){ + item.setEnabled(false); // show just so they know this is an option later... + } + else{ + item.addActionListener(gui); + // more than one tab closed last time + if(closedTabs.get(closedTabs.size()-1) instanceof java.util.List){ + System.err.println("Set unclose tabS"); + item.setText(UNDO_CLOSE_TABS_OPTION); + } + // else nothing more needs to be done, the default menu + // label for the task to reopen just one tab + } + tabOptions.add(item); + + tabOptions.show(gui, e.getX()+7, e.getY()+12); } else{ // Otherwise do whatever this handler normally does @@ -1342,4 +1410,11 @@ ((MobyContentPane) tabbedPane.getComponentAt(i)).setFontSize(fontSize); } } + + public void tabClosing(Component closingTab){ + closedTabs.add(closingTab); + int closingTabIndex = tabbedPane.indexOfComponent(closingTab); + closedTabTitles.add(tabbedPane.getTitleAt(closingTabIndex)); + closedTabIcons.add(tabbedPane.getIconAt(closingTabIndex)); + } } From drepchevski at dev.open-bio.org Thu Feb 24 08:35:40 2011 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Thu, 24 Feb 2011 08:35:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102241335.p1ODZe05000346@dev.open-bio.org> drepchevski Thu Feb 24 08:35:40 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/cache In directory dev.open-bio.org:/tmp/cvs-serv310 Modified Files: CacheConfig.java Log Message: Added a posibility to save a cache without XML Document event generation. moby-live/Java/src/main/org/inb/biomoby/central/cache CacheConfig.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/cache/CacheConfig.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/cache/CacheConfig.java 2009/12/16 15:24:36 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/cache/CacheConfig.java 2011/02/24 13:35:39 1.2 @@ -151,15 +151,21 @@ } } + public void save(List entities, Writer writer) throws Exception + { + save(entities, writer, true); + } + /** * Generic method to save BioMoby entities to the provided writer * * @param - the entity type to save * @param entities - the list of entities to be saved * @param writer - the writer where entities are saved + * @param isFragment - whether or not document level events will be generated * @throws Exception */ - public void save(List entities, Writer writer) throws Exception + public void save(List entities, Writer writer, boolean isFragment) throws Exception { CacheListWrapper wrapper = new CacheListWrapper(entities); @@ -171,6 +177,7 @@ Marshaller m = jc.createMarshaller(); m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE); + m.setProperty(Marshaller.JAXB_FRAGMENT, Boolean.valueOf(isFragment)); BufferedWriter out = new BufferedWriter(writer); From drepchevski at dev.open-bio.org Wed Feb 2 13:23:41 2011 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Feb 2011 08:23:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102021323.p12DNfTJ016946@dev.open-bio.org> drepchevski Wed Feb 2 08:23:41 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv16893/registry Modified Files: RegisterServiceOperation.java Log Message: registerService() was broken in MobyCentral library moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry RegisterServiceOperation.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RegisterServiceOperation.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RegisterServiceOperation.java 2009/09/09 19:47:48 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RegisterServiceOperation.java 2011/02/02 13:23:41 1.2 @@ -194,27 +194,27 @@ @XmlTransient protected static class Data { - private List collection; - private List simple; + private List collections; + private List simples; @XmlElement(name = "Collection") - public List getCollection() + public List getCollections() { - if (collection == null) + if (collections == null) { - collection = new ArrayList(); + collections = new ArrayList(); } - return this.collection; + return this.collections; } @XmlElement(name = "Simple") - public List getSimple() + public List getSimples() { - if (simple == null) + if (simples == null) { - simple = new ArrayList(); + simples = new ArrayList(); } - return this.simple; + return this.simples; } } @@ -269,7 +269,7 @@ public static class Simple { private String objectType; - private List namespace; + private List namespaces; private String articleName; @XmlElement(required = true) @@ -284,14 +284,14 @@ } @XmlElement(name = "Namespace") - public List getNamespace() + public List getNamespaces() { - if (namespace == null) + if (namespaces == null) { - namespace = new ArrayList(); + namespaces = new ArrayList(); } - return this.namespace; + return namespaces; } @XmlAttribute(required = true) From drepchevski at dev.open-bio.org Wed Feb 2 13:23:41 2011 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Feb 2011 08:23:41 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102021323.p12DNfP2016928@dev.open-bio.org> drepchevski Wed Feb 2 08:23:41 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv16893 Modified Files: JAXBMobyCentralImpl.java Log Message: registerService() was broken in MobyCentral library moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb JAXBMobyCentralImpl.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java 2009/09/09 19:47:48 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java 2011/02/02 13:23:40 1.2 @@ -71,7 +71,168 @@ request.setAuthURI(service.getAuthURI()); request.setContactEmail(service.getContactEmail()); request.setDescription(service.getDescription()); - + + request.setURL(service.getUrl()); + request.setCategory(service.getCategory().name()); + + request.setAuthoritativeService(service.isAuthoritative() ? 1 : 0); + + ServiceType serviceType = service.getServiceType(); + request.setServiceType(serviceType == null ? "" : serviceType.getName()); + + Input input = service.getInput(); + + if (input != null) + { + RegisterServiceOperation.Input in = new RegisterServiceOperation.Input(); + + for (Simple simple : input.getSimples()) + { + RegisterServiceOperation.Simple sm = new RegisterServiceOperation.Simple(); + sm.setArticleName(simple.getArticleName()); + + ObjectType objectType = simple.getObjectType(); + + if (objectType != null) + { + sm.setObjectType(objectType.getName()); + } + + for (Namespace namespace : simple.getNamespaces()) + { + sm.getNamespaces().add(namespace.getName()); + } + + in.getSimples().add(sm); + } + + for (Collection collection : input.getCollections()) + { + RegisterServiceOperation.Collection cl = new RegisterServiceOperation.Collection(); + + cl.setArticleName(collection.getArticleName()); + + Simple simple = collection.getSimple(); + + if (simple != null) + { + RegisterServiceOperation.Simple sm = new RegisterServiceOperation.Simple(); + sm.setArticleName(simple.getArticleName()); + + ObjectType objectType = simple.getObjectType(); + + if (objectType != null) + { + sm.setObjectType(objectType.getName()); + } + + for (Namespace namespace : simple.getNamespaces()) + { + sm.getNamespaces().add(namespace.getName()); + } + + cl.setSimple(sm); + } + + in.getCollections().add(cl); + } + + request.setInput(in); + } + + Output output = service.getOutput(); + + if (output != null) + { + RegisterServiceOperation.Output out = new RegisterServiceOperation.Output(); + + for (Simple simple : output.getSimples()) + { + RegisterServiceOperation.Simple sm = new RegisterServiceOperation.Simple(); + sm.setArticleName(simple.getArticleName()); + + ObjectType objectType = simple.getObjectType(); + + if (objectType != null) + { + sm.setObjectType(objectType.getName()); + } + + for (Namespace namespace : simple.getNamespaces()) + { + sm.getNamespaces().add(namespace.getName()); + } + + out.getSimples().add(sm); + } + + for (Collection collection : output.getCollections()) + { + RegisterServiceOperation.Collection cl = new RegisterServiceOperation.Collection(); + + cl.setArticleName(collection.getArticleName()); + + Simple simple = collection.getSimple(); + + if (simple != null) + { + RegisterServiceOperation.Simple sm = new RegisterServiceOperation.Simple(); + sm.setArticleName(simple.getArticleName()); + + ObjectType objectType = simple.getObjectType(); + + if (objectType != null) + { + sm.setObjectType(objectType.getName()); + } + + for (Namespace namespace : simple.getNamespaces()) + { + sm.getNamespaces().add(namespace.getName()); + } + + cl.setSimple(sm); + } + + out.getCollections().add(cl); + } + + request.setOutput(out); + } + + List parameters = service.getSecondaryArticles(); + + if (!parameters.isEmpty()) + { + RegisterServiceOperation.SecondaryArticles sa = new RegisterServiceOperation.SecondaryArticles(); + + for (Parameter parameter :service.getSecondaryArticles()) + { + RegisterServiceOperation.Parameter p = new RegisterServiceOperation.Parameter(); + + p.setDatatype(parameter.getDatatype().name()); + p.setArticleName(parameter.getArticleName()); + p.setDefault(parameter.getDefault()); + p.setDescription(parameter.getDescription()); + p.setMin(parameter.getMin()); + p.setMax(parameter.getMax()); + + List enums = parameter.getEnum(); + + if (!enums.isEmpty()) + { + for (String _enum : enums) + { + p.getEnum().add(_enum); + } + } + + sa.getParameter().add(p); + } + + request.setSecondaryArticles(sa); + } + MobyRegistration response = endpoint.call(request); Registration registration = new Registration(); From drepchevski at dev.open-bio.org Thu Feb 3 17:34:01 2011 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Thu, 3 Feb 2011 12:34:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102031734.p13HY153015378@dev.open-bio.org> drepchevski Thu Feb 3 12:34:00 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv15343 Modified Files: MobyDispatch.java Log Message: fixed argument parsing when it is specified as soap type instead of schema (string/base64Binary) moby-live/Java/src/main/org/inb/biomoby/client MobyDispatch.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java 2010/08/31 16:15:44 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java 2011/02/03 17:34:00 1.3 @@ -15,6 +15,7 @@ import java.util.ArrayList; import java.util.List; import java.util.logging.Logger; +import javax.xml.XMLConstants; import org.inb.biomoby.MobyMessageContext; import javax.xml.bind.JAXBContext; import javax.xml.bind.JAXBElement; @@ -61,6 +62,7 @@ import org.inb.wsrf.rp2.QueryResourceProperties; import org.inb.wsrf.rp2.QueryResourcePropertiesResponse; import org.w3c.dom.Element; +import org.w3c.dom.NamedNodeMap; import org.w3c.dom.Node; /** @@ -287,6 +289,37 @@ Node method = body.getFirstChild(); // check mobyService.getName() + "Response"? Node argument = method.getFirstChild(); + // fixing method argument type {http://schemas.xmlsoap.org/soap/encoding/}string => {http://www.w3.org/2001/XMLSchema}string + // Actually JAXB shouldn't support soap types in a first place... + + NamedNodeMap attributes = argument.getAttributes(); + if (attributes != null) + { + Node attribute = attributes.getNamedItemNS(XMLConstants.W3C_XML_SCHEMA_INSTANCE_NS_URI, "type"); + + if (attribute != null) + { + String soapencPrefix = argument.lookupPrefix(SOAPConstants.URI_NS_SOAP_ENCODING); + + if (soapencPrefix != null) + { + String type = attribute.getNodeValue(); + + if (type.startsWith(soapencPrefix)) + { + String xsdPrefix = argument.lookupPrefix(XMLConstants.W3C_XML_SCHEMA_NS_URI); + + if (xsdPrefix != null) + { + type = xsdPrefix + type.substring(soapencPrefix.length()); + + attribute.setNodeValue(type); + } + } + } + } + } + Unmarshaller u = MobyMessageContext.getContext().createUnmarshaller(); JAXBElement jel = u.unmarshal(argument, byte[].class); From gordonp at dev.open-bio.org Thu Feb 3 21:38:27 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:38:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032138.p13LcRoM019912@dev.open-bio.org> gordonp Thu Feb 3 16:38:27 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv19880/src/main/ca/ucalgary/seahawk/gui Added Files: FontSizeChangeListener.java Log Message: Added capability to change document font size, for accessibility moby-live/Java/src/main/ca/ucalgary/seahawk/gui FontSizeChangeListener.java,NONE,1.1 From gordonp at dev.open-bio.org Thu Feb 3 21:39:18 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:39:18 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032139.p13LdIex019952@dev.open-bio.org> gordonp Thu Feb 3 16:39:18 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources In directory dev.open-bio.org:/tmp/cvs-serv19920/src/main/ca/ucalgary/seahawk/resources Added Files: SelectFilesBeanShell BinaryFileLoaderBeanShell Log Message: Taverna helper processors to facilitate use of binary input into a Moby workflow moby-live/Java/src/main/ca/ucalgary/seahawk/resources SelectFilesBeanShell,NONE,1.1 BinaryFileLoaderBeanShell,NONE,1.1 From gordonp at dev.open-bio.org Thu Feb 3 21:40:36 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:40:36 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032140.p13Leaji020018@dev.open-bio.org> gordonp Thu Feb 3 16:40:36 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv19982/src/main/ca/ucalgary/seahawk/gui Modified Files: DataImportChoiceDialog.java Log Message: Fixed javadoc and enabled multi-selection (import more than one item to the clipboard at a time) moby-live/Java/src/main/ca/ucalgary/seahawk/gui DataImportChoiceDialog.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/DataImportChoiceDialog.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/DataImportChoiceDialog.java 2010/04/11 02:25:03 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/DataImportChoiceDialog.java 2011/02/03 21:40:36 1.2 @@ -1,11 +1,8 @@ package ca.ucalgary.seahawk.gui; /** - * Generates a preview of a Taverna2 workflow and shows it in a dialog where - * metadata such as title, author, and description can be entered. - * - * Renders the workflow using a remote CGI and asks the user if they want to - * proceed with the export of the workflow. + * Generates a dialog for the user to select what Moby object(s) should be + * imported from the legacy data being pasted into Seahawk. */ import java.awt.*; @@ -42,6 +39,7 @@ // Default select items inheriting from the preferred data type, or choiceList = new JList(this.dataChoices); + choiceList.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); Vector initialSelectionIndices = new Vector(); if(preferredDataType != null && !preferredDataType.getName().equals(MobyTags.MOBYOBJECT)){ for(int i = 0; i < dataChoices.length; i++){ From gordonp at dev.open-bio.org Thu Feb 3 21:42:11 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:42:11 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032142.p13LgAbS020084@dev.open-bio.org> gordonp Thu Feb 3 16:42:10 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv20048/src/main/ca/ucalgary/seahawk/gui Modified Files: FileAndTextTransferHandler.java Log Message: Added ability to export text selections from Seahawk to the clipboard moby-live/Java/src/main/ca/ucalgary/seahawk/gui FileAndTextTransferHandler.java,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FileAndTextTransferHandler.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FileAndTextTransferHandler.java 2010/05/13 16:03:59 1.11 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FileAndTextTransferHandler.java 2011/02/03 21:42:10 1.12 @@ -246,7 +246,14 @@ protected Transferable createTransferable(JComponent c) { if(c instanceof MobyContentPane){ - return new SeahawkTransferable((MobyContentPane) c); + // Can export Moby data (via hyperlink drag) + if(((MobyContentPane) c).isDraggingHyperlink()){ + return new SeahawkTransferable((MobyContentPane) c); + } + // or text selection as string + else{ + return new StringSelection(((MobyContentPane) c).getSelectedText()); + } } else{ return null; From gordonp at dev.open-bio.org Thu Feb 3 21:45:38 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:45:38 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032145.p13LjcT4020152@dev.open-bio.org> gordonp Thu Feb 3 16:45:38 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv20116/src/main/ca/ucalgary/seahawk/gui Modified Files: FilterSearchWidget.java Log Message: Several fixes including ability to not have highlight-as-you-type (can cause freezing), suspending matching when regex has trailing pipe, and search input field that responds to user preference for font size (accessibility) moby-live/Java/src/main/ca/ucalgary/seahawk/gui FilterSearchWidget.java,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java 2010/06/15 22:20:51 1.7 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/FilterSearchWidget.java 2011/02/03 21:45:38 1.8 @@ -4,6 +4,8 @@ import java.awt.Color; import java.awt.Dimension; +import java.awt.Font; +import java.awt.geom.AffineTransform; import java.awt.event.*; import java.net.URL; import java.util.concurrent.*; @@ -15,12 +17,13 @@ * Displays an editable SearchFilter within a MobyContentPane. */ -public class FilterSearchWidget extends JPanel implements ActionListener, DocumentListener{ +public class FilterSearchWidget extends JPanel implements ActionListener, DocumentListener, FontSizeChangeListener{ private FilterSearch currentFilterSearch; private JLabel closeIcon; private JToggleButton caseButton; private JButton inverseButton; // decides whether filter is "if" or "unless" + private JButton applyButton; // used when filter is in "non-interactive" mode private JTextField searchField; private JComboBox docPartOptions; private MobyContentPane contentPane; @@ -28,6 +31,7 @@ public static final String CASE_SENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_sensitive.png"; public static final String CASE_INSENSITIVE_ICON_RESOURCE = "ca/ucalgary/seahawk/resources/images/case_insensitive.png"; + private static final String APPLY_TEXT = "Apply Filter"; private static final String IF_TEXT = "if"; private static final String UNLESS_TEXT = "unless"; private static final String CASE_INSENSITIVE_MSG = "The filter is case insensitive,
click to make case sensitive"; @@ -80,20 +84,41 @@ add(new JLabel("Show data ")); add(inverseButton); add(Box.createRigidArea(new Dimension(5,0))); + searchField = new JTextField(25); + setSearchFieldFontSize(SeahawkOptions.getFontSizeAsDouble()); searchField.setToolTipText("A literal string, or a regular expression"); searchField.getDocument().addDocumentListener(this); add(searchField); + add(Box.createRigidArea(new Dimension(5,0))); add(new JLabel("in")); add(Box.createRigidArea(new Dimension(5,0))); docPartOptions = new JComboBox(); docPartOptions.addActionListener(this); add(docPartOptions); + add(Box.createRigidArea(new Dimension(5,0))); + + if(!SeahawkOptions.isFilterInteractive()){ + // Normally we update any time the user types a letter. + // On some systems this freezes the system randomly, so there is the option to + // type, then press a button to apply the filter... + applyButton = new JButton(APPLY_TEXT); + applyButton.setEnabled(true); + applyButton.addActionListener(this); + add(applyButton); + } add(Box.createHorizontalGlue()); setFilter(null); } + private void setSearchFieldFontSize(double scale){ // Proportion of font compared to default + AffineTransform scaler = new AffineTransform(); + scaler.setToScale(scale, scale); + Font preferredFont = (new JTextField(1)).getFont().deriveFont(scaler); + searchField.setFont(preferredFont); + } + /** * The filter to display as editable right now. */ @@ -104,6 +129,7 @@ inverseButton.setEnabled(false); searchField.setEnabled(false); docPartOptions.setEnabled(false); + if(applyButton != null){applyButton.setEnabled(false);} return; } @@ -119,6 +145,9 @@ docPartOptions.setEnabled(true); docPartOptions.setModel(new DefaultComboBoxModel(fs.getXPathOptions())); docPartOptions.setSelectedItem(fs.getSelectedXPath()); + + if(applyButton != null){applyButton.setEnabled(true);} + currentFilterSearch = fs; // done in this order so no feedback as DocumentEvents while setting fields programmatically } @@ -153,6 +182,14 @@ contentPane.applyFilter(true); return; } + else if(e.getSource() == applyButton){ + StringBuffer sb = currentFilterSearch.getFilterRegex(); + synchronized(searchField){ + sb.replace(0, sb.length(), searchField.getText()); + } + applyFilterWhenSuitable(); + return; + } else if(currentFilterSearch == null || e.getSource() != docPartOptions){ return; } @@ -164,7 +201,7 @@ * Called when the regex has been changed by the user */ public void changedUpdate(DocumentEvent e){ - if(currentFilterSearch == null){ + if(currentFilterSearch == null || !SeahawkOptions.isFilterInteractive() || danglingPipe()){ return; } StringBuffer sb = currentFilterSearch.getFilterRegex(); @@ -175,7 +212,7 @@ } public void insertUpdate(DocumentEvent e){ - if(currentFilterSearch == null){ + if(currentFilterSearch == null || !SeahawkOptions.isFilterInteractive() || danglingPipe()){ return; } StringBuffer sb = currentFilterSearch.getFilterRegex(); @@ -186,7 +223,7 @@ } public void removeUpdate(DocumentEvent e){ - if(currentFilterSearch == null){ + if(currentFilterSearch == null || !SeahawkOptions.isFilterInteractive() || danglingPipe()){ return; } StringBuffer sb = currentFilterSearch.getFilterRegex(); @@ -196,6 +233,22 @@ applyFilterWhenSuitable(); } + // Check if the user is typing a regex and current has a | operator at the end. + // Don't update the matches at this point because of course the empty right side of the regex + // will match between every character, causing hardship for matching and highlight update + // on some machines. + private boolean danglingPipe(){ + String currentText = searchField.getText(); + // Running a regex on a regex to see if there is a trailing unescaped '|'...trippy + if(currentText.matches("(^|.*[^\\\\])(\\\\\\\\)*\\|")){ + searchField.setBackground(Color.YELLOW); + return true; + } + else{ + return false; + } + } + // Waits 600 milliseconds to see if the user is typing a phrase, rather than // filtering for each letter added, which can be slow private void applyFilterWhenSuitable(){ @@ -211,7 +264,7 @@ } catch(Exception e){ logger.log(Level.WARNING, - "Delay less than 400ms on search input due to interrupt", + "Delay less than 500ms on search input due to interrupt", e); } synchronized(sf){ @@ -245,6 +298,12 @@ // else, it's going to be updated soon anyway with the latest string buffer...just return } + public void fontSizeChanged(String size){ + // Data coming in is 110%, etc., convert to decimal scale required by + double scale = Double.parseDouble(size.substring(0, size.length()-1))/100.0; // lop off % sign, convert to ratio + setSearchFieldFontSize(scale); + } + class Closer extends MouseAdapter{ boolean active = false; private FilterSearchWidget widget; From gordonp at dev.open-bio.org Thu Feb 3 21:46:40 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:46:40 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032146.p13Lkee1020218@dev.open-bio.org> gordonp Thu Feb 3 16:46:40 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv20182/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyContentClipboard.java Log Message: Make empty but well-formed clipboard file on startup to avoid exceptions in various widgets like the filter moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentClipboard.java,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java 2010/04/16 20:36:17 1.11 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentClipboard.java 2011/02/03 21:46:40 1.12 @@ -92,6 +92,12 @@ return; } clipboardFile.deleteOnExit(); + try{ + writeClipboardDataToFile(); // Set up empty clipboard doc + } + catch(Exception e){ + logger.log(Level.SEVERE, "Clipboard failed to initialize, cannot write or load temp file", e); + } // The dfeault is to open a new tab when contents is transfered (dropped/pasted) onto the tab, // we want to override that behaviour to a collation for the clipboard @@ -270,7 +276,7 @@ logger.log(Level.FINE, urlContents); MobyDataType targetDataType = null; - if(collection != null){ + if(collection != null && !collection.isEmpty()){ targetDataType = collection.getDataType(); } MobyDataObject[] mobyDataFound = client.getMobyObjects(urlContents, targetDataType); @@ -341,21 +347,24 @@ } } - public void updateDisplay(){ + private void writeClipboardDataToFile() throws Exception{ // Write to temp file + FileOutputStream os = new FileOutputStream(clipboardFile); + MobyDataUtils.toXMLDocument(os, content); + os.close(); + } + + public void updateDisplay(){ try{ - FileOutputStream os = new FileOutputStream(clipboardFile); - MobyDataUtils.toXMLDocument(os, content); - os.close(); + writeClipboardDataToFile(); gotoURL(clipboardFile.toURI().toURL(), false); - } - catch(Exception e){ + tabbedPane.setTitleAt(tabbedPane.indexOfComponent(this), CLIPBOARD_TAB_NAME + + ": " + getResponseType(content)); + contentGUI.setVisible(true); + } catch(Exception e){ logger.log(Level.SEVERE, "Clipboard failed to update the display, cannot write or load temp file", e); return; } - tabbedPane.setTitleAt(tabbedPane.indexOfComponent(this), CLIPBOARD_TAB_NAME + - ": " + getResponseType(content)); - contentGUI.setVisible(true); } /** From gordonp at dev.open-bio.org Thu Feb 3 21:47:57 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:47:57 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032147.p13LlvQl020284@dev.open-bio.org> gordonp Thu Feb 3 16:47:57 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv20248/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyContentGUI.java Log Message: Implement font resizing, and singleton application launching moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentGUI.java,1.23,1.24 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java,v retrieving revision 1.23 retrieving revision 1.24 diff -u -r1.23 -r1.24 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java 2010/05/13 16:13:21 1.23 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentGUI.java 2011/02/03 21:47:57 1.24 @@ -26,6 +26,7 @@ import org.biomoby.shared.data.*; import org.biomoby.shared.parser.MobyTags; +import ca.ucalgary.util.*; import ca.ucalgary.seahawk.util.*; import ca.ucalgary.seahawk.services.MobyClient; @@ -36,7 +37,7 @@ * @author Paul Gordon (gordonp at ucalgary.ca) */ -public class MobyContentGUI extends JFrame implements ActionListener, ComponentListener, KeyListener, MobyRequestEventHandler, MouseListener{ +public class MobyContentGUI extends JFrame implements ActionListener, ComponentListener, KeyListener, MobyRequestEventHandler, MouseListener, FontSizeChangeListener, ArgumentListener{ // Variables used to coordinate component finding with the unit test cases public final static String BACK_BUTTON_NAME = "MCGbackButton"; @@ -248,7 +249,7 @@ tabbedPane.add(clipboard); clipboard.init(); - settingsGUI = new SeahawkOptionsGUI(this); + settingsGUI = new SeahawkOptionsGUI(this, this); // params are frame owner, font change listener } public Acme.Serve.Serve getServletContainer(){ @@ -1189,15 +1190,17 @@ new Thread(){ public void run(){ for(;;) { - renderSplashFrame(g); - splash.update(); try { + renderSplashFrame(g); + splash.update(); Thread.sleep(100); } - catch(InterruptedException e) { + catch(Exception e) { } if(killSplash.tryAcquire()){ - splash.close(); + // Okay, we don't need to close the splash screen + // because it autocloses when a Java Window is shown. + //splash.close(); return; } } @@ -1277,6 +1280,24 @@ gui.loadPaneFromURL(startURL, true); } } + SingletonApplication.setArgumentListener(gui); + } + + // Called when user attempts to launch Seahawk again while its running + public void processArgument(String arg){ + try{ + loadPaneFromURL(new URL(arg), true); + } + catch(Exception e){ + System.err.println("Could not load "+arg+" as a URL, trying as a file"); + try{ + File f = new File(arg); + loadPaneFromURL(f.toURI().toURL(), true); + } catch(Exception fe){ + logger.error("Could not load "+arg+" as a URL or file: "+fe.getMessage()); + e.printStackTrace(); + } + } } protected static void cacheOntologies(){ @@ -1314,4 +1335,11 @@ public JLabel getStatusComponent() { return status; } + + public void fontSizeChanged(String fontSize) { + // Update font in all Seahawk-generated documents + for(int i = 0; i < tabbedPane.getTabCount(); i++){ + ((MobyContentPane) tabbedPane.getComponentAt(i)).setFontSize(fontSize); + } + } } From gordonp at dev.open-bio.org Thu Feb 3 21:49:01 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:49:01 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032149.p13Ln1mG020350@dev.open-bio.org> gordonp Thu Feb 3 16:49:01 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv20314/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyContentHelpPane.java Log Message: Tiny fix so fot resizing can happen properly (requires help document URL be in history) moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentHelpPane.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentHelpPane.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentHelpPane.java 2010/03/29 19:55:22 1.5 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentHelpPane.java 2011/02/03 21:49:01 1.6 @@ -68,7 +68,7 @@ } } - gotoURL(helpHTMLURL, false); + gotoURL(helpHTMLURL, true); editorPane.scrollToReference("start"); // use anchor at top of doc: pane scrolls to bottom normally... } From gordonp at dev.open-bio.org Thu Feb 3 21:50:51 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:50:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032150.p13LopH7020516@dev.open-bio.org> gordonp Thu Feb 3 16:50:50 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv20460/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyContentPane.java Log Message: Fixes for font resizing, copying of data from Seahawk to the clipboard moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.33,1.34 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java,v retrieving revision 1.33 retrieving revision 1.34 diff -u -r1.33 -r1.34 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java 2010/05/13 16:12:19 1.33 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java 2011/02/03 21:50:50 1.34 @@ -31,9 +31,11 @@ import javax.swing.text.SimpleAttributeSet; import javax.swing.text.DefaultHighlighter; import javax.swing.text.Highlighter; +import javax.swing.text.MutableAttributeSet; import javax.swing.text.Style; import javax.swing.text.StyleConstants; import javax.swing.text.StyledDocument; +import javax.swing.text.html.CSS; import javax.swing.text.html.HTML; import javax.swing.text.html.HTMLDocument; @@ -81,6 +83,7 @@ /** The name of the param in the stylesheet that will hold the Moby doc URL for XPointer usage */ public final static String XSL_DOC_SOURCE_PARAM = "sourceURL"; + public final static String XSL_DOC_FONTSIZE_PARAM = "fontSize"; private JScrollPane scrollPane; protected JTabbedPane tabbedPane; @@ -110,6 +113,7 @@ private Map jobXPtrs = null; // Map private List origStyles = null; private boolean firstDocRendering = true; + private String tempFontSize = null; // Next two items used for service wrapping private JMenuItem createServicePopupItem; @@ -485,6 +489,20 @@ } /** + * Used to temporarily change the font size of the displayed document. + * Normally the SeahawkOptions values are used. + * + * @param fontSize an absolute or relative font size as per HTML's basefont size specification. If null, document default size is used. + */ + public synchronized void setFontSize(String fontSize){ + tempFontSize = fontSize == null ? "100%" : fontSize; + gotoURL(getCurrentURL(), false); + // Also notify filter widget since the text input field will need resizing + filterSearchWidget.fontSizeChanged(tempFontSize); + tempFontSize = null; + } + + /** * This is the URLLoader callback method the MOBY data fetcher * will call when MOBY XML data is ready to be seen. */ @@ -534,7 +552,12 @@ } // Tell the stylesheet the URL of the moby data (it will create xpointers to it) - contentGUI.getTransformer().setParameter(XSL_DOC_SOURCE_PARAM, url.toString()); + contentGUI.getTransformer().setParameter(XSL_DOC_SOURCE_PARAM, + url.toString()); + //String fontSize = tempFontSize != null ? tempFontSize : SeahawkOptions.getFontSize(); + //System.err.println("Font size for XML doc will be "+fontSize); + //contentGUI.getTransformer().setParameter(XSL_DOC_FONTSIZE_PARAM, + // fontSize); // Do the actual transformation String htmlContents = "[Seahawk Internal Error]"; try{ @@ -542,6 +565,9 @@ contentGUI.getTransformer().transform(new StreamSource(url.openStream()), new StreamResult(stringWriter)); htmlContents = stringWriter.toString(); + if(htmlContents == null || htmlContents.length() == 0){ + htmlContents = "[Empty]"; + } // NOTE: If you switch the registry in the middle of using Seahawk, // the following might fail on documents in the history, as they were // encoded according to a different registry than the current value of @@ -549,7 +575,9 @@ // registries, there has to be a way to note the source registry for the data in the // document (preferred), or we must maintain a hash of the document:registry mappings // for the session. - htmlContents = HTMLUtils.encapsulateBinaryData(url, htmlContents, SeahawkOptions.getRegistry()); + else{ + htmlContents = HTMLUtils.encapsulateBinaryData(url, htmlContents, SeahawkOptions.getRegistry()); + } } catch(TransformerException te){ status.setText("Sorry! Could not transform the MOBY data into presentation form"); @@ -710,6 +738,16 @@ e.printStackTrace(); } + // Adjust font size if necessary in HTML docs + if((tempFontSize != null || !SeahawkOptions.getFontSize().equals("100%")) && + editorPane.getDocument() instanceof HTMLDocument){ + HTMLDocument doc = (HTMLDocument) editorPane.getDocument(); + MutableAttributeSet attr = new SimpleAttributeSet(); + String fontSize = tempFontSize != null ? tempFontSize : SeahawkOptions.getFontSize(); + doc.getStyleSheet().addCSSAttribute(attr, CSS.Attribute.FONT_SIZE, fontSize); + doc.setCharacterAttributes(0, editorPane.getDocument().getLength(), attr, false); + } + setCursor(new Cursor(Cursor.DEFAULT_CURSOR)); if(addToHistory){ @@ -854,6 +892,7 @@ * PBE recorder. */ public void exportDone(String valuePasted, String transformRuleURI){ + System.err.println("Export done, notifying wrapping servlet (if any)"); if(cgiServlet != null && cgiServlet.getRecorder() != null && (cgiServlet.getRecorder() instanceof PBERecorder)){ ((PBERecorder) cgiServlet.getRecorder()).dataCopied(getDraggedData(), valuePasted, transformRuleURI); } @@ -1124,6 +1163,8 @@ public void hyperlinkUpdate(HyperlinkEvent he){ URL targetURL = he.getURL(); if(he.getEventType() == HyperlinkEvent.EventType.ACTIVATED){ + overHyperlink = true; + lastHyperlinkHovered = targetURL; // Internal moby pseudo-URL if(targetURL == null){ String desc = he.getDescription(); @@ -1554,6 +1595,9 @@ } FilterSearch filter = filterHistory.get(getCurrentURL()); + if(getCurrentDoc() == null){ + return; + } filterableNodes = DataUtils.findFilteredNodes(getCurrentDoc(), filter, filterableNodes, filteredData, jobXPtrs, currentSelectedData, currentSelectionXPath, apply); @@ -1660,7 +1704,7 @@ javax.swing.text.Element el = d.getElement(filterable); String fragment = d.getText(el.getStartOffset(), el.getEndOffset() - el.getStartOffset()); - Matcher matcher = p.matcher(fragment); + Matcher matcher = p.matcher(fragment.trim()); while (matcher.find()) { // Only count match if not already highlighted in a containing filterable node // todo: in future, avoid looking in text bits already checked, for efficiency @@ -1880,6 +1924,10 @@ return; } else{ // keep track of the previous selection so we can use it once it's gone + if(dragging){ //if a hyperlink is being dragged, don't highlight too + System.err.println("Ignoring highlight while dragging hyperlink"); + return; + } oldMark = mark; oldDot = dot; } @@ -1904,13 +1952,29 @@ tab.getDisplay().setText("Use the file/globe icon at the bottom of this window to load data," + "or drag'n'drop/paste data from your desktop or Web browser."); } + // Ctrl+C copy of selection if any + if(e.getKeyCode() == KeyEvent.VK_C && e.isControlDown() && selectedTextData != null){ + getTransferHandler().exportToClipboard(this, + Toolkit.getDefaultToolkit().getSystemClipboard(), + TransferHandler.COPY); + } } public void keyReleased(KeyEvent e){} public void keyTyped(KeyEvent e){} + public boolean isDraggingHyperlink(){ + return dragging; + } + + public String getSelectedText(){ + return selectedTextData; + } + public void paste(){ - getTransferHandler().importData(this, Toolkit.getDefaultToolkit().getSystemClipboard().getContents(this)); + if(!dragging){ //don't allow drag onto self... + getTransferHandler().importData(this, Toolkit.getDefaultToolkit().getSystemClipboard().getContents(this)); + } } public void mouseDragged(MouseEvent e){ @@ -1919,13 +1983,14 @@ dragging = true; // so we don't export many times in a row while dragging lastHyperlinkDragged = lastHyperlinkHovered; status.setText("Drop the hyperlink onto a Web form field to populate it"); - getTransferHandler().exportToClipboard(this, - Toolkit.getDefaultToolkit().getSystemClipboard(), - TransferHandler.COPY); + System.err.println("Dragging initiated via mouseDragged for "+lastHyperlinkDragged); + //getTransferHandler().exportToClipboard(this, + // Toolkit.getDefaultToolkit().getSystemClipboard(), + // TransferHandler.COPY); getTransferHandler().exportAsDrag(this, e, TransferHandler.COPY); } else if(!dragging){ - //System.err.println("Dragging with no hyperlink activated"); + System.err.println("Dragging with no hyperlink activated"); } } @@ -1935,18 +2000,24 @@ // mouse button being down here. if(overHyperlink && (e.getModifiersEx() & MouseEvent.BUTTON1_DOWN_MASK) == MouseEvent.BUTTON1_DOWN_MASK){ //System.err.println("Got wonky drag"); - lastHyperlinkDragged = lastHyperlinkHovered; status.setText("Drop the hyperlink onto a Web form field to populate it"); - //System.err.println("Dragging "+lastHyperlinkDragged); - getTransferHandler().exportAsDrag(this, e, TransferHandler.COPY); + if(lastHyperlinkDragged != lastHyperlinkHovered){ + System.err.println("Dragging initiated via mouseMoved for "+lastHyperlinkDragged); + lastHyperlinkDragged = lastHyperlinkHovered; + //getTransferHandler().exportToClipboard(this, + // Toolkit.getDefaultToolkit().getSystemClipboard(), + // TransferHandler.COPY); + getTransferHandler().exportAsDrag(this, e, TransferHandler.COPY); + } } else if(dragging){ + System.err.println("Dragging stopped...no mouse down on mouseMoved"); dragging = false; } } public void lostOwnership(Clipboard clipboard, Transferable contents){ - //System.err.println("Lost clipboard ownership"); + System.err.println("Lost clipboard ownership"); } } From gordonp at dev.open-bio.org Thu Feb 3 21:52:05 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:52:05 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032152.p13Lq5W0020642@dev.open-bio.org> gordonp Thu Feb 3 16:52:05 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv20606/src/main/ca/ucalgary/seahawk/gui Modified Files: SeahawkOptionsGUI.java Log Message: Added support for disabling highlight-while-typing (may cause freezing), and font resizing moby-live/Java/src/main/ca/ucalgary/seahawk/gui SeahawkOptionsGUI.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkOptionsGUI.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkOptionsGUI.java 2007/12/06 18:47:31 1.6 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkOptionsGUI.java 2011/02/03 21:52:05 1.7 @@ -34,8 +34,12 @@ private JTextField converterPortTextField; private JTextField cacheExpiryTextField; private JFileChooser cacheDirFileChooser; + private JComboBox fontComboBox; + private String[] fontSizes = new String[]{"50%","75%","90%","100%","110%","125%","150%","200%"}; + private FontSizeChangeListener fontSizeChangeListener; private JCheckBox sendReferrerCheckBox; + private JCheckBox filterInteractiveCheckBox; private JButton resetButton; private JButton okButton; @@ -49,14 +53,15 @@ /** * @param owner the frame that launches this dialog */ - public SeahawkOptionsGUI(Frame owner){ + public SeahawkOptionsGUI(Frame owner, FontSizeChangeListener listener){ super(owner, DIALOG_TITLE, DIALOG_MODAL); // Custom handling of window close operation setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); addWindowListener(this); + fontSizeChangeListener = listener; - // The dreaded GridBagLayout... + // The dreaded GridBagLayout...see http://madbean.com/anim/totallygridbag/ GridBagLayout gridbag = new GridBagLayout(); GridBagConstraints c = new GridBagConstraints(); c.fill = GridBagConstraints.BOTH; @@ -72,6 +77,16 @@ registryNames[i] = CUSTOM_REGISTRY_SYNONYM; c.insets = new Insets(3,2,3,2); + + // Font size widget + + //........................................ + //c.gridx = 0; + //c.gridy = 4; + //c.gridwidth = 5; + //JSeparator line = new JSeparator(); + //add(line, c); + //........................................ c.gridwidth = 2; @@ -185,20 +200,50 @@ //........................................ c.gridx = 0; c.gridy = 7; - c.gridwidth = 4; + c.gridwidth = 2; c.gridheight = 1; sendReferrerCheckBox = new JCheckBox("Send referrer data to services"); add(sendReferrerCheckBox, c); + c.gridx = 2; + c.gridwidth = 2; + c.gridheight = 1; + filterInteractiveCheckBox = new JCheckBox("Highlight filter matches while typing"); + add(filterInteractiveCheckBox, c); //........................................ + c.gridx = 0; c.gridy = 8; c.gridwidth = 5; line = new JSeparator(); add(line, c); - //........................................ + c.gridx = 0; c.gridy = 9; c.gridwidth = 2; + c.weightx = 0.0; + c.weighty = 0.0; + c.fill = GridBagConstraints.HORIZONTAL; + label = new JLabel("Document Font Size:", JLabel.RIGHT); + add(label, c); + c.gridx = 2; + c.gridwidth = 1; + + adjustFontSizesIfNecessary(); + fontComboBox = new JComboBox(fontSizes); + fontComboBox.setSelectedItem(SeahawkOptions.getFontSize()); // do this here to avoid unnecessary callback + fontComboBox.addActionListener(this); + add(fontComboBox, c); + + //........................................ + c.gridx = 0; + c.gridy = 10; + c.gridwidth = 5; + line = new JSeparator(); + add(line, c); + + c.gridy = 11; + c.gridx = 0; + c.gridwidth = 2; label = new JLabel("Cache expiry (in hours)", JLabel.RIGHT); add(label, c); @@ -232,10 +277,54 @@ pack(); } + // If the value of the user preferred font size is not one of the standard presets + // (e.g. they set it manually in the config file), + // add that custom value to the list of options. + private void adjustFontSizesIfNecessary(){ + String currentFontSize = SeahawkOptions.getFontSize(); + double currentSizeDouble = convertFontSizeToDouble(currentFontSize); + for(String presetChoice: fontSizes){ + if(convertFontSizeToDouble(presetChoice) == currentSizeDouble){ + SeahawkOptions.setFontSize(presetChoice); // avoids confusion in parts of app looking for 100%, not 100.000% etc. + return; // it's an existing choice + } + } + + // If we got here, it's a custom value + System.err.println("Inserting custom value (" + currentFontSize + ") into font size choices"); + String[] newFontSizes = new String[fontSizes.length+1]; + // Insertion of custom value into ordered presets list assumes existing font sizes and ordered small to large + boolean customValuePlaced = false; + for(int i = 0; i < fontSizes.length; i++){ + if(customValuePlaced){ + newFontSizes[i+1] = fontSizes[i]; + } + else if(currentSizeDouble < convertFontSizeToDouble(fontSizes[i])){ + newFontSizes[i] = currentFontSize; + customValuePlaced = true; + i--; + } + else{ + newFontSizes[i] = fontSizes[i]; // verbatim 'cause custom value not encountered yet + } + } + // Bigger than any preset? append to new list + if(!customValuePlaced){ + newFontSizes[fontSizes.length] = currentFontSize; + } + fontSizes = newFontSizes; + } + + // "100%" -> 100.0 + private double convertFontSizeToDouble(String fontSize){ + return Double.parseDouble(fontSize.substring(0, fontSize.length()-1)); // lop off % sign + } + public void actionPerformed(ActionEvent event){ Object source = event.getSource(); if(source == cancelButton){ setCurrentValues(); + updateDocumentFont(SeahawkOptions.getFontSize()); setVisible(false); } else if(source == okButton){ @@ -257,6 +346,9 @@ else if(source == registryComboBox){ updateRegistryFields(); } + else if(source == fontComboBox){ + updateDocumentFont(fontComboBox.getSelectedItem().toString()); + } } /** @@ -279,8 +371,9 @@ converterHostTextField.setText(""+SeahawkOptions.getDocConverterHost()); converterPortTextField.setText(""+SeahawkOptions.getDocConverterPort()); sendReferrerCheckBox.setSelected(SeahawkOptions.getSendReferrerPolicy()); + filterInteractiveCheckBox.setSelected(SeahawkOptions.isFilterInteractive()); cacheExpiryTextField.setText(""+SeahawkOptions.getCacheExpiry()); - cacheDirFileChooser.setSelectedFile(SeahawkOptions.getTempDir()); + cacheDirFileChooser.setSelectedFile(SeahawkOptions.getTempDir()); } private void saveSettings(){ @@ -350,6 +443,15 @@ SeahawkOptions.setDocConverterHost(converterHostTextField.getText().trim()); SeahawkOptions.setSendReferrerPolicy(sendReferrerCheckBox.isSelected()); SeahawkOptions.setCacheExpiry(expiry); + if(filterInteractiveCheckBox.isSelected() != SeahawkOptions.isFilterInteractive()){ + JOptionPane.showMessageDialog(null, + "Please restart Seahawk to fully apply the filter behaviour change.", + "Filter behaviour change requires restart", + JOptionPane.INFORMATION_MESSAGE); + } + SeahawkOptions.setFilterInteractive(filterInteractiveCheckBox.isSelected()); + SeahawkOptions.setFontSize(fontComboBox.getSelectedItem().toString()); + updateDocumentFont(fontComboBox.getSelectedItem().toString()); // Saves the new values to a file, so they will perpetuate themselves between sessions if(!SeahawkOptions.saveSettings()){ @@ -377,6 +479,12 @@ setVisible(false); } + private void updateDocumentFont(String fontSize){ + if(fontSizeChangeListener != null){ + fontSizeChangeListener.fontSizeChanged(fontSize); + } + } + private void updateRegistryFields(){ // Update all the registry fields if the name switches String selectedRegistryName = registryComboBox.getSelectedItem().toString(); @@ -446,7 +554,7 @@ JFrame frame = new JFrame("test"); frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); - SeahawkOptionsGUI dialog = new SeahawkOptionsGUI(frame); + SeahawkOptionsGUI dialog = new SeahawkOptionsGUI(frame, null); frame.pack(); frame.setVisible(true); From gordonp at dev.open-bio.org Thu Feb 3 21:54:51 2011 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 3 Feb 2011 16:54:51 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <201102032154.p13Lsp92020752@dev.open-bio.org> gordonp Thu Feb 3 16:54:51 EST 2011 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources In directory dev.open-bio.org:/tmp/cvs-serv20716/src/main/ca/ucalgary/seahawk/resources Modified Files: mobyBuilderRules.xml Log Message: New and improved protein recognition rule moby-live/Java/src/main/ca/ucalgary/seahawk/resources mobyBuilderRules.xml,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml 2010/04/11 02:20:46 1.11 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml 2011/02/03 21:54:51 1.12 @@ -55,8 +55,8 @@