/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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
+ Vector getFeatures = null; // vector of das source nicknames to fetch
+ // features from
// loading is done.
- String groovyscript = null; // script to execute after all loading is completed one way or another
+ String groovyscript = null; // script to execute after all loading is
+ // completed one way or another
// extract groovy argument and execute if necessary
groovyscript = aparser.getValue("groovy");
file = aparser.getValue("open");
}
}
getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures!=null)
+ if (af != null && getFeatures != null)
{
- startFeatureFetching(getFeatures);
+ startFeatureFetching(getFeatures);
// need to block until fetching is complete.
while (af.operationInProgress())
{
// wait around until fetching is finished.
- try {
+ try
+ {
Thread.sleep(10);
} catch (Exception e)
{
-
+
}
}
}
- if (groovyscript!=null)
+ if (groovyscript != null)
{
- // Execute the groovy script after we've done all the rendering stuff
+ // Execute the groovy script after we've done all the rendering stuff
// and before any images or figures are generated.
if (jalview.bin.Cache.groovyJarsPresent())
{
- System.out.println("Executing script "+groovyscript);
+ System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, desktop);
- } else {
- System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
}
groovyscript = null;
}
// extract groovy arguments before anything else.
}
// Once all loading is done. Retrieve features.
- if (getFeatures!=null)
+ if (getFeatures != null)
{
- if (startUpAlframe!=null)
+ if (startUpAlframe != null)
{
startFeatureFetching(getFeatures);
}
}
- if (groovyscript!=null)
+ if (groovyscript != null)
{
if (jalview.bin.Cache.groovyJarsPresent())
{
- System.out.println("Executing script "+groovyscript);
+ System.out.println("Executing script " + groovyscript);
executeGroovyScript(groovyscript, desktop);
- } else {
- System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
}
}
// Once all other stuff is done, execute any groovy scripts (in order)
}
+
/**
* Locate the given string as a file and pass it to the groovy interpreter.
- * @param groovyscript the script to execute
- * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object.
+ *
+ * @param groovyscript
+ * the script to execute
+ * @param jalviewContext
+ * the Jalview Desktop object passed in to the groovy binding
+ * as the 'Jalview' object.
*/
- private static void executeGroovyScript(String groovyscript, Object jalviewContext)
+ private static void executeGroovyScript(String groovyscript,
+ Object jalviewContext)
{
- if (jalviewContext==null)
+ if (jalviewContext == null)
{
- System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
+ System.err
+ .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
}
File sfile = null;
if (groovyscript.trim().equals("STDIN"))
{
// read from stdin into a tempfile and execute it
- try {
+ try
+ {
sfile = File.createTempFile("jalview", "groovy");
- PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(sfile)));
- BufferedReader br = new BufferedReader(new java.io.InputStreamReader(System.in));
- String line=null;
- while ((line=br.readLine())!=null)
+ PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(sfile)));
+ BufferedReader br = new BufferedReader(
+ new java.io.InputStreamReader(System.in));
+ String line = null;
+ while ((line = br.readLine()) != null)
{
- outfile.write(line+"\n");
+ outfile.write(line + "\n");
}
br.close();
outfile.flush();
outfile.close();
-
+
} catch (Exception ex)
{
- System.err.println("Failed to read from STDIN into tempfile "+((sfile==null) ? "(tempfile wasn't created)" : sfile.toString()));
+ System.err.println("Failed to read from STDIN into tempfile "
+ + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+ .toString()));
ex.printStackTrace();
return;
}
- } else {
+ }
+ else
+ {
sfile = new File(groovyscript);
}
if (!sfile.exists())
{
- System.err.println("File '"+groovyscript+"' does not exist.");
+ System.err.println("File '" + groovyscript + "' does not exist.");
return;
}
if (!sfile.canRead())
{
- System.err.println("File '"+groovyscript+"' cannot be read.");
+ System.err.println("File '" + groovyscript + "' cannot be read.");
return;
}
- if (sfile.length()<1)
+ if (sfile.length() < 1)
{
- System.err.println("File '"+groovyscript+"' is empty.");
+ System.err.println("File '" + groovyscript + "' is empty.");
return;
}
boolean success = false;
- try {
- /* The following code performs the GroovyScriptEngine invocation using reflection,
- * and is equivalent to this fragment from the embedding groovy documentation on
- * the groovy site:
- * <code>
- import groovy.lang.Binding;
- import groovy.util.GroovyScriptEngine;
-
- String[] roots = new String[] { "/my/groovy/script/path" };
- GroovyScriptEngine gse = new GroovyScriptEngine(roots);
- Binding binding = new Binding();
- binding.setVariable("input", "world");
- gse.run("hello.groovy", binding);
- * </code>
- */
- ClassLoader cl = jalviewContext.getClass().getClassLoader();
- Class gbindingc = cl.loadClass("groovy.lang.Binding");
- Constructor gbcons = gbindingc.getConstructor(null);
- Object gbinding = gbcons.newInstance(null);
- java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} );
- setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext});
- Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
- Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class } ); // String[].class });
- Object gse = gseccons.newInstance(new Object[] { new URL[] { sfile.toURL() } }); // .toString() } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
- run.invoke(gse, new Object[] { sfile.getName(), gbinding });
- success = true;
+ try
+ {
+ /*
+ * The following code performs the GroovyScriptEngine invocation using
+ * reflection, and is equivalent to this fragment from the embedding
+ * groovy documentation on the groovy site: <code> import
+ * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
+ *
+ * String[] roots = new String[] { "/my/groovy/script/path" };
+ * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding =
+ * new Binding(); binding.setVariable("input", "world");
+ * gse.run("hello.groovy", binding); </code>
+ */
+ ClassLoader cl = jalviewContext.getClass().getClassLoader();
+ Class gbindingc = cl.loadClass("groovy.lang.Binding");
+ Constructor gbcons = gbindingc.getConstructor(null);
+ Object gbinding = gbcons.newInstance(null);
+ java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
+ new Class[]
+ { String.class, Object.class });
+ setvar.invoke(gbinding, new Object[]
+ { "Jalview", jalviewContext });
+ Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+ Constructor gseccons = gsec.getConstructor(new Class[]
+ { URL[].class }); // String[].class });
+ Object gse = gseccons.newInstance(new Object[]
+ { new URL[]
+ { sfile.toURL() } }); // .toString() } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
+ { String.class, gbindingc });
+ run.invoke(gse, new Object[]
+ { sfile.getName(), gbinding });
+ success = true;
} catch (Exception e)
{
- System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
+ System.err.println("Exception Whilst trying to execute file " + sfile
+ + " as a groovy script.");
e.printStackTrace(System.err);
-
+
}
if (success && groovyscript.equals("STDIN"))
{
- // delete temp file that we made - but only if it was successfully executed
+ // delete temp file that we made - but only if it was successfully
+ // executed
sfile.delete();
}
}
+
/**
* 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;
+ Vector source = null;
String data;
String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
- while ((data = aparser.getValue("dasserver"))!=null)
+ while ((data = aparser.getValue("dasserver")) != null)
{
String nickname = null;
String url = null;
{
nickname = url;
}
- if (locsources==null)
+ if (locsources == null)
+ {
+ locsources = "";
+ }
+ else
{
- locsources="";
- } else {
- locsources+="\t";
+ locsources += "\t";
}
- locsources=locsources+nickname+"|"+url;
+ locsources = locsources + nickname + "|" + url;
System.err
.println("NOTE! dasserver parameter not yet really supported (got args of "
+ nickname + "|" + url);
- if (source==null)
+ if (source == null)
{
source = new Vector();
}
source.addElement(nickname);
}
} // loop until no more server entries are found.
- if (locsources!=null && locsources.indexOf('|')>-1)
+ if (locsources != null && locsources.indexOf('|') > -1)
{
- Cache.log.debug("Setting local source list in properties file to:\n"+locsources);
+ 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)
+ while ((data = aparser.getValue("fetchfrom")) != null)
{
- System.out.println("adding source '"+data+"'");
- if (source==null)
+ System.out.println("adding source '" + data + "'");
+ if (source == null)
{
source = new Vector();
}
}
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)
+ if (afs == null || afs.length == 0)
{
return;
}
- for (int i = 0; i<afs.length; i++)
+ for (int i = 0; i < afs.length; i++)
{
final AlignFrame af = afs[i];
- SwingUtilities.invokeLater(new Runnable() {
+ SwingUtilities.invokeLater(new Runnable()
+ {
public void run()
- {
+ {
af.featureSettings_actionPerformed(null);
af.featureSettings.fetchDasFeatures(dasSources);
}
/**
* 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).
+ * 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
{
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.
*/
}
return ret;
}
+
/**
* check for and remove first occurence of arg in arglist.
+ *
* @param arg
* @return true if arg was present in argslist.
*/
git://source.jalview.org / jalview.git / blobdiff