import jalview.io.AppletFormatAdapter;
/**
- * Main class for Jalview Application
+ * Main class for Jalview Application <br>
* <br>
- * <br>start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
- *
+ * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ *
* @author $author$
* @version $Revision$
*/
/**
* main class for Jalview application
- *
- * @param args open <em>filename</em>
+ *
+ * @param args
+ * open <em>filename</em>
*/
public static void main(String[] args)
{
- System.out.println("Java version: " + System.getProperty("java.version"));
+ System.out.println("Java version: "
+ + System.getProperty("java.version"));
System.out.println(System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
if (aparser.contains("help") || aparser.contains("h"))
{
- System.out.println(
- "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
- + "-nodisplay\tRun Jalview without User Interface.\n"
- +
- "-props FILE\tUse the given Jalview properties file instead of users default.\n"
- +
- "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
- +
- "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
- +
- "-features FILE\tUse the given file to mark features on the alignment.\n"
- + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
- + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
- + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
- + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
- + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
- + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
- + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
- + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
- + "-png FILE\tCreate PNG image FILE from alignment.\n"
- +
- "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
- + "-eps FILE\tCreate EPS file FILE from alignment."
- + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
- + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ System.out
+ .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ + "-nodisplay\tRun Jalview without User Interface.\n"
+ + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+ + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
+ + "-features FILE\tUse the given file to mark features on the alignment.\n"
+ + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+ + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+ + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+ + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
+ + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ + "-png FILE\tCreate PNG image FILE from alignment.\n"
+ + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ + "-eps FILE\tCreate EPS file FILE from alignment."
+ + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
+ + "-noquestionnaire\tTurn off questionnaire check."
+ + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
+ + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
+ + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
System.exit(0);
}
- Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!
+ Cache.loadProperties(aparser.getValue("props")); // must do this before
+ // anything else!
if (aparser.contains("nodisplay"))
{
System.setProperty("java.awt.headless", "true");
}
if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ && System.getProperty("java.awt.headless").equals("true"))
{
headless = true;
}
try
{
Cache.initLogger();
- }
- catch (java.lang.NoClassDefFoundError error)
+ } catch (java.lang.NoClassDefFoundError error)
{
error.printStackTrace();
- System.out.println(
- "\nEssential logging libraries not found."
- + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ System.out
+ .println("\nEssential logging libraries not found."
+ + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
System.exit(0);
}
try
{
- UIManager.setLookAndFeel(
- UIManager.getSystemLookAndFeelClassName()
- // UIManager.getCrossPlatformLookAndFeelClassName()
- //"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
- //"javax.swing.plaf.metal.MetalLookAndFeel"
- //"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
- //"com.sun.java.swing.plaf.motif.MotifLookAndFeel"
-
- );
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()
+ // UIManager.getCrossPlatformLookAndFeelClassName()
+ // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
+ // "javax.swing.plaf.metal.MetalLookAndFeel"
+ // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
+ // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
+
+ );
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
if (!headless)
{
desktop = new Desktop();
desktop.setVisible(true);
desktop.discoverer.start();
- String url = aparser.getValue("questionnaire");
- if (url != null)
- {
- // Start the desktop questionnaire prompter with the specified questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
- desktop.checkForQuestionnaire(url);
- }
- else
+ if (!aparser.contains("noquestionnaire"))
{
- if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ String url = aparser.getValue("questionnaire");
+ if (url != null)
{
- // Start the desktop questionnaire prompter with the specified questionnaire
- // String defurl = "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; //
- String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug("Starting questionnaire with default url: " + defurl);
- desktop.checkForQuestionnaire(defurl);
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ Cache.log.debug("Starting questionnaire url at " + url);
+ desktop.checkForQuestionnaire(url);
+ }
+ else
+ {
+ if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ {
+ // Start the desktop questionnaire prompter with the specified
+ // questionnaire
+ // String defurl =
+ // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+ // //
+ String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+ Cache.log.debug("Starting questionnaire with default url: "
+ + defurl);
+ desktop.checkForQuestionnaire(defurl);
+ }
}
}
-
}
String file = null, protocol = null, format = null, data = null;
jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
-
+ Vector getFeatures = null; // vector of das source nicknames to fetch features from
+ // loading is done.
file = aparser.getValue("open");
if (file == null && desktop == null)
if (!file.startsWith("http://"))
{
- if (! (new java.io.File(file)).exists())
+ if (!(new java.io.File(file)).exists())
{
System.out.println("Can't find " + file);
if (headless)
}
protocol = checkProtocol(file);
-
+
format = new jalview.io.IdentifyFile().Identify(file, protocol);
-
- AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
if (af == null)
{
{
data.replaceAll("%20", " ");
- jalview.schemes.ColourSchemeI cs =
- jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().
- getAlignment(), data);
+ jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+ .getColour(af.getViewport().getAlignment(), data);
if (cs == null)
{
- jalview.schemes.UserColourScheme ucs
- = new jalview.schemes.UserColourScheme("white");
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ "white");
ucs.parseAppletParameter(data);
cs = ucs;
}
if (data != null)
{
jalview.io.NewickFile fin = null;
- try {
+ try
+ {
fin = new jalview.io.NewickFile(data, checkProtocol(data));
- if (fin!=null)
+ if (fin != null)
{
- af.getViewport().setCurrentTree(af.ShowNewickTree(fin, data).getTree());
+ af.getViewport().setCurrentTree(
+ af.ShowNewickTree(fin, data).getTree());
System.out.println("Added tree " + data);
}
- }
- catch (IOException ex)
+ } catch (IOException ex)
{
- System.err.println("Couldn't add tree "+data);
+ System.err.println("Couldn't add tree " + data);
ex.printStackTrace(System.err);
}
}
-
+ getFeatures = checkDasArguments(aparser);
+ if (af != null && getFeatures!=null)
+ {
+ startFeatureFetching(getFeatures);
+ // need to block until fetching is complete.
+ while (af.operationInProgress())
+ {
+ // wait around until fetching is finished.
+ try {
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+
+ }
+ }
+ }
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
if (af.saveAlignment(file, format))
{
- System.out.println("Written alignment in " + format +
- " format to " + file);
+ System.out.println("Written alignment in " + format
+ + " format to " + file);
}
else
{
- System.out.println("Error writing file " + file + " in " + format +
- " format!!");
+ System.out.println("Error writing file " + file + " in " + format
+ + " format!!");
}
}
System.out.println("Unknown arg: " + aparser.nextValue());
}
}
-
+ AlignFrame startUpAlframe = null;
// We'll only open the default file if the desktop is visible.
// And the user
- //////////////////////
- if (
- !headless
- && file == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
- )
+ // ////////////////////
+ if (!headless && file == null
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
-
file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- "http://www.jalview.org/examples/exampleFile_2_3.jar");
+ "http://www.jalview.org/examples/exampleFile_2_3.jar");
protocol = "File";
format = new jalview.io.IdentifyFile().Identify(file, protocol);
}
- fileLoader.LoadFile(file, protocol, format);
-
+ startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
+ format);
+ getFeatures = checkDasArguments(aparser);
+ }
+ // Once all loading is done. Retrieve features.
+ if (getFeatures!=null)
+ {
+ if (startUpAlframe!=null)
+ {
+ startFeatureFetching(getFeatures);
+ }
+ }
+ }
+ /**
+ * Check commandline for any das server definitions or any fetchfrom switches
+ * @return vector of DAS source nicknames to retrieve from
+ */
+ private static Vector checkDasArguments(ArgsParser aparser)
+ {
+ Vector source=null;
+ String data;
+ String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
+ while ((data = aparser.getValue("dasserver"))!=null)
+ {
+ String nickname = null;
+ String url = null;
+ int pos = data.indexOf('=');
+ if (pos > 0)
+ {
+ nickname = data.substring(0, pos);
+ }
+ url = data.substring(pos + 1);
+ if (url != null && url.startsWith("http:"))
+ {
+ if (nickname == null)
+ {
+ nickname = url;
+ }
+ if (locsources==null)
+ {
+ locsources="";
+ } else {
+ locsources+="\t";
+ }
+ locsources=locsources+nickname+"|"+url;
+ System.err
+ .println("NOTE! dasserver parameter not yet really supported (got args of "
+ + nickname + "|" + url);
+ if (source==null)
+ {
+ source = new Vector();
+ }
+ source.addElement(nickname);
+ }
+ } // loop until no more server entries are found.
+ if (locsources!=null && locsources.indexOf('|')>-1)
+ {
+ Cache.log.debug("Setting local source list in properties file to:\n"+locsources);
+ Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
}
+ while ((data = aparser.getValue("fetchfrom"))!=null)
+ {
+ System.out.println("adding source '"+data+"'");
+ if (source==null)
+ {
+ source = new Vector();
+ }
+ source.addElement(data);
+ }
+ return source;
}
+ /**
+ * start a feature fetcher for every alignment frame
+ * @param dasSources
+ */
+ private static void startFeatureFetching(final Vector dasSources)
+ {
+ AlignFrame afs[] = Desktop.getAlignframes();
+ if (afs==null || afs.length==0)
+ {
+ return;
+ }
+ for (int i = 0; i<afs.length; i++)
+ {
+ final AlignFrame af = afs[i];
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run()
+ {
+ af.featureSettings_actionPerformed(null);
+ af.featureSettings.fetchDasFeatures(dasSources);
+ }
+ });
+ }
+ }
private static String checkProtocol(String file)
{
- String protocol = jalview.io.FormatAdapter.FILE;
+ String protocol = jalview.io.FormatAdapter.FILE;
- if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
- {
- protocol = jalview.io.FormatAdapter.URL;
- }
- return protocol;
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ {
+ protocol = jalview.io.FormatAdapter.URL;
+ }
+ return protocol;
}
}
+
+/**
+ * Notes: this argParser does not distinguish between parameter switches,
+ * parameter values and argument text. If an argument happens to be identical
+ * to a parameter, it will be taken as such (even though it didn't have a '-' prefixing it).
+ *
+ * @author Andrew Waterhouse and JBP documented.
+ *
+ */
class ArgsParser
{
Vector vargs = null;
+
public ArgsParser(String[] args)
{
vargs = new Vector();
vargs.addElement(arg);
}
}
-
+ /**
+ * check for and remove first occurence of arg+parameter in arglist.
+ * @param arg
+ * @return return the argument following the given arg if arg was in list.
+ */
public String getValue(String arg)
{
int index = vargs.indexOf(arg);
}
return ret;
}
-
+ /**
+ * check for and remove first occurence of arg in arglist.
+ * @param arg
+ * @return true if arg was present in argslist.
+ */
public boolean contains(String arg)
{
if (vargs.contains(arg))
git://source.jalview.org / jalview.git / commitdiff