/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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.
+ * Jalview 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 3 of the License, or (at your option) any later version.
*
- * 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
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.bin;
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",true);
- file = aparser.getValue("open",true);
+ groovyscript = aparser.getValue("groovy", true);
+ file = aparser.getValue("open", true);
if (file == null && desktop == null)
{
// session at the user's leisure.
Cache.log
.info("Skipping Push for import of data into existing vamsas session."); // TODO:
- // enable
- // this
- // when
- // debugged
+ // enable
+ // this
+ // when
+ // debugged
// desktop.getVamsasApplication().push_update();
}
}
return;
}
- data = aparser.getValue("colour",true);
+ data = aparser.getValue("colour", true);
if (data != null)
{
data.replaceAll("%20", " ");
}
// Must maintain ability to use the groups flag
- data = aparser.getValue("groups",true);
+ data = aparser.getValue("groups", true);
if (data != null)
{
af.parseFeaturesFile(data, checkProtocol(data));
System.out.println("Added " + data);
}
- data = aparser.getValue("features",true);
+ data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data, checkProtocol(data));
System.out.println("Added " + data);
}
- data = aparser.getValue("annotations",true);
+ data = aparser.getValue("annotations", true);
if (data != null)
{
af.loadJalviewDataFile(data);
{
af.getViewport().setSortByTree(false);
}
- data = aparser.getValue("tree",true);
+ data = aparser.getValue("tree", true);
if (data != null)
{
jalview.io.NewickFile fin = null;
ex.printStackTrace(System.err);
}
}
- // todo - load PDB structure to alignment
- // (associate with identical sequence in alignment, or a specified sequence)
-
-
+ // todo - load PDB structure to alignment
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
+
getFeatures = checkDasArguments(aparser);
if (af != null && getFeatures != null)
{
FeatureFetcher ff = startFeatureFetching(getFeatures);
- if (ff!=null)
+ if (ff != null)
while (!ff.allFinished() || af.operationInProgress())
{
// wait around until fetching is finished.
- try
- {
- Thread.sleep(100);
- } catch (Exception e)
- {
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception e)
+ {
+ }
}
- }
getFeatures = null; // have retrieved features - forget them now.
}
if (groovyscript != null)
getFeatures = checkDasArguments(aparser);
// extract groovy arguments before anything else.
}
- // If the user has specified features to be retrieved,
+ // If the user has specified features to be retrieved,
// or a groovy script to be executed, do them if they
- // haven't been done already
+ // haven't been done already
// fetch features for the default alignment
if (getFeatures != null)
{
startFeatureFetching(getFeatures);
}
}
- // execute a groovy script.
+ // execute a groovy script.
if (groovyscript != null)
{
if (jalview.bin.Cache.groovyJarsPresent())
"USAGESTATS",
"Jalview Usage Statistics",
"Do you want to help make Jalview better by enabling "
- +"the collection of usage statistics with Google Analytics ?"
- +"\n\n(you can enable or disable usage tracking in the preferences)",
+ + "the collection of usage statistics with Google Analytics ?"
+ + "\n\n(you can enable or disable usage tracking in the preferences)",
new Runnable()
{
public void run()
Vector source = null;
String data;
String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
- while ((data = aparser.getValue("dasserver",true)) != null)
+ while ((data = aparser.getValue("dasserver", true)) != null)
{
String nickname = null;
String url = null;
+ locsources);
Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
}
- while ((data = aparser.getValue("fetchfrom",true)) != null)
+ while ((data = aparser.getValue("fetchfrom", true)) != null)
{
System.out.println("adding source '" + data + "'");
if (source == null)
}
return ff;
}
+
private static String checkProtocol(String file)
{
String protocol = jalview.io.FormatAdapter.FILE;
{
return getValue(arg, false);
}
+
public String getValue(String arg, boolean utf8decode)
{
int index = vargs.indexOf(arg);
- String dc=null,ret = null;
+ String dc = null, ret = null;
if (index != -1)
{
ret = vargs.elementAt(index + 1).toString();
vargs.removeElementAt(index);
vargs.removeElementAt(index);
- if (utf8decode && ret!=null)
+ if (utf8decode && ret != null)
{
- try {
- dc = URLDecoder.decode(ret,"UTF-8");
+ try
+ {
+ dc = URLDecoder.decode(ret, "UTF-8");
ret = dc;
} catch (Exception e)
{
}
}
+
/**
* keep track of feature fetching tasks.
+ *
* @author JimP
- *
+ *
*/
-class FeatureFetcher {
+class FeatureFetcher
+{
/*
- * TODO: generalise to track all jalview events to orchestrate batch processing events.
+ * TODO: generalise to track all jalview events to orchestrate batch
+ * processing events.
*/
- private int queued=0;
- private int running=0;
+ private int queued = 0;
+
+ private int running = 0;
+
public FeatureFetcher()
{
-
+
}
+
public void addFetcher(final AlignFrame af, final Vector dasSources)
{
- final long id = System.currentTimeMillis();
+ final long id = System.currentTimeMillis();
queued++;
- final FeatureFetcher us=this;
+ final FeatureFetcher us = this;
new Thread(new Runnable()
{
public void run()
{
- synchronized (us) {
- queued--;
- running++;
+ synchronized (us)
+ {
+ queued--;
+ running++;
}
-
+
af.setProgressBar("DAS features being retrieved...", id);
af.featureSettings_actionPerformed(null);
af.featureSettings.fetchDasFeatures(dasSources, true);
af.setProgressBar(null, id);
- synchronized (us) {
- running --;
+ synchronized (us)
+ {
+ running--;
}
}
}).start();
}
- public synchronized boolean allFinished() {
- return queued==0 && running==0;
+
+ public synchronized boolean allFinished()
+ {
+ return queued == 0 && running == 0;
}
};
git://source.jalview.org / jalview.git / blobdiff