X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=859b6f544219f4a933e78ac503db3f7ba9d1e503;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=624ac582c723569dea6e1fc998201a1e0870088b;hpb=bd6ce583c00bc78edfc027df4e6b7cc9180ff9d0;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 624ac58..859b6f5 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,20 +1,20 @@
/*
- * 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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
@@ -25,6 +25,7 @@ import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.lang.reflect.Constructor;
+import java.net.URI;
import java.net.URL;
import java.net.URLDecoder;
import java.security.AllPermission;
@@ -37,7 +38,7 @@ import java.util.*;
import javax.swing.*;
import jalview.gui.*;
-import jalview.io.AppletFormatAdapter;
+import jalview.util.Platform;
/**
* Main class for Jalview Application
@@ -80,6 +81,12 @@ public class Jalview
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ if (new Platform().isAMac())
+ {
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ }
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
@@ -90,6 +97,7 @@ public class Jalview
.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"
+ + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\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"
@@ -121,6 +129,11 @@ public class Jalview
+ "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
System.exit(0);
}
+ if (aparser.contains("nodisplay") || aparser.contains("nogui") || aparser.contains("headless"))
+ {
+ System.setProperty("java.awt.headless", "true");
+ headless=true;
+ }
Cache.loadProperties(aparser.getValue("props")); // must do this before
// anything else!
String defs = aparser.getValue("setprop");
@@ -140,16 +153,12 @@ public class Jalview
}
defs = aparser.getValue("setprop");
}
- if (aparser.contains("nodisplay"))
- {
- System.setProperty("java.awt.headless", "true");
- }
if (System.getProperty("java.awt.headless") != null
&& System.getProperty("java.awt.headless").equals("true"))
{
headless = true;
}
-
+ System.setProperty("http.agent", "Jalview Desktop/"+Cache.getDefault("VERSION", "Unknown"));
try
{
Cache.initLogger();
@@ -166,22 +175,17 @@ public class Jalview
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());
} catch (Exception ex)
{
}
+
if (!headless)
{
desktop = new Desktop();
+ desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
- desktop.discoverer.start();
+ desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
{
startUsageStats(desktop);
@@ -213,6 +217,7 @@ public class Jalview
}
}
}
+ desktop.checkForNews();
}
String file = null, protocol = null, format = null, data = null;
@@ -223,8 +228,8 @@ public class Jalview
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)
{
@@ -247,7 +252,8 @@ public class Jalview
{
try
{
- String viprotocol = Jalview.checkProtocol(vamsasImport);
+ String viprotocol = jalview.io.AppletFormatAdapter
+ .checkProtocol(vamsasImport);
if (viprotocol == jalview.io.FormatAdapter.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
@@ -307,17 +313,23 @@ public class Jalview
// 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();
}
}
}
+ long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
{
+ if (!headless)
+ {
+ desktop.setProgressBar("Processing commandline arguments...",
+ progress = System.currentTimeMillis());
+ }
System.out.println("Opening file: " + file);
if (!file.startsWith("http://"))
@@ -332,7 +344,7 @@ public class Jalview
}
}
- protocol = checkProtocol(file);
+ protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
format = new jalview.io.IdentifyFile().Identify(file, protocol);
@@ -341,158 +353,164 @@ public class Jalview
if (af == null)
{
System.out.println("error");
- return;
}
-
- data = aparser.getValue("colour",true);
- if (data != null)
+ else
{
- data.replaceAll("%20", " ");
-
- jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
- .getColour(af.getViewport().getAlignment(), data);
- if (cs == null)
+ data = aparser.getValue("colour", true);
+ if (data != null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
- ucs.parseAppletParameter(data);
- cs = ucs;
- }
+ data.replaceAll("%20", " ");
- System.out.println("colour is " + data);
- af.changeColour(cs);
- }
+ jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+ .getColour(af.getViewport().getAlignment(), data);
- // Must maintain ability to use the groups flag
- data = aparser.getValue("groups",true);
- if (data != null)
- {
- af.parseFeaturesFile(data, checkProtocol(data));
- System.out.println("Added " + data);
- }
- data = aparser.getValue("features",true);
- if (data != null)
- {
- af.parseFeaturesFile(data, checkProtocol(data));
- System.out.println("Added " + data);
- }
-
- data = aparser.getValue("annotations",true);
- if (data != null)
- {
- af.loadJalviewDataFile(data);
- System.out.println("Added " + data);
- }
- // set or clear the sortbytree flag.
- if (aparser.contains("sortbytree"))
- {
- af.getViewport().setSortByTree(true);
- }
- if (aparser.contains("nosortbytree"))
- {
- af.getViewport().setSortByTree(false);
- }
- data = aparser.getValue("tree",true);
- if (data != null)
- {
- jalview.io.NewickFile fin = null;
- try
- {
- fin = new jalview.io.NewickFile(data, checkProtocol(data));
- if (fin != null)
+ if (cs == null)
{
- af.getViewport().setCurrentTree(
- af.ShowNewickTree(fin, data).getTree());
- System.out.println("Added tree " + data);
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ "white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
}
- } catch (IOException ex)
- {
- System.err.println("Couldn't add tree " + data);
- ex.printStackTrace(System.err);
- }
- }
- // 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)
- while (!ff.allFinished() || af.operationInProgress())
- {
- // wait around until fetching is finished.
- try
- {
- Thread.sleep(100);
- } catch (Exception e)
- {
- }
+ System.out.println("colour is " + data);
+ af.changeColour(cs);
}
- getFeatures = null; // have retrieved features - forget them now.
- }
- if (groovyscript != null)
- {
- // 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())
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue("groups", true);
+ if (data != null)
{
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, desktop);
+ af.parseFeaturesFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ System.out.println("Added " + data);
}
- else
+ data = aparser.getValue("features", true);
+ if (data != null)
{
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
- + groovyscript);
+ af.parseFeaturesFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ System.out.println("Added " + data);
}
- groovyscript = null;
- }
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
- {
- format = aparser.nextValue();
- file = aparser.nextValue();
- if (format.equalsIgnoreCase("png"))
+ data = aparser.getValue("annotations", true);
+ if (data != null)
{
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
+ af.loadJalviewDataFile(data, null, null, null);
+ System.out.println("Added " + data);
}
- else if (format.equalsIgnoreCase("imgMap"))
+ // set or clear the sortbytree flag.
+ if (aparser.contains("sortbytree"))
{
- af.createImageMap(new java.io.File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
+ af.getViewport().setSortByTree(true);
}
- else if (format.equalsIgnoreCase("eps"))
+ if (aparser.contains("nosortbytree"))
{
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
- continue;
+ af.getViewport().setSortByTree(false);
}
+ data = aparser.getValue("tree", true);
+ if (data != null)
+ {
+ jalview.io.NewickFile fin = null;
+ try
+ {
+ fin = new jalview.io.NewickFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ if (fin != null)
+ {
+ af.getViewport().setCurrentTree(
+ af.ShowNewickTree(fin, data).getTree());
+ System.out.println("Added tree " + data);
+ }
+ } catch (IOException ex)
+ {
+ System.err.println("Couldn't add tree " + data);
+ ex.printStackTrace(System.err);
+ }
+ }
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
- if (af.saveAlignment(file, format))
+ getFeatures = checkDasArguments(aparser);
+ if (af != null && getFeatures != null)
{
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ FeatureFetcher ff = startFeatureFetching(getFeatures);
+ if (ff != null)
+ while (!ff.allFinished() || af.operationInProgress())
+ {
+ // wait around until fetching is finished.
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception e)
+ {
+
+ }
+ }
+ getFeatures = null; // have retrieved features - forget them now.
}
- else
+ if (groovyscript != null)
{
- System.out.println("Error writing file " + file + " in " + format
- + " format!!");
+ // 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);
+ executeGroovyScript(groovyscript, new Object[]
+ { desktop, af });
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
+ }
+ groovyscript = null;
}
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ format = aparser.nextValue();
+ file = aparser.nextValue();
- }
+ if (format.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new java.io.File(file));
+ imageName = (new java.io.File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new java.io.File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ System.out.println("Creating EPS file: " + file);
+ af.createEPS(new java.io.File(file));
+ continue;
+ }
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
+ if (af.saveAlignment(file, format))
+ {
+ System.out.println("Written alignment in " + format
+ + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + format + " format!!");
+ }
+
+ }
+
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
+ }
}
}
AlignFrame startUpAlframe = null;
@@ -502,8 +520,18 @@ public class Jalview
if (!headless && file == null && vamsasImport == 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");
+ file = jalview.bin.Cache.getDefault(
+ "STARTUP_FILE",
+ jalview.bin.Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org")
+ + "/examples/exampleFile_2_7.jar");
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ {
+ // hardwire upgrade of the startup file
+ file.replace("_2_3.jar", "_2_7.jar");
+ // and remove the stale setting
+ jalview.bin.Cache.removeProperty("STARTUP_FILE");
+ }
protocol = "File";
@@ -526,9 +554,9 @@ public class Jalview
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)
{
@@ -537,13 +565,14 @@ public class Jalview
startFeatureFetching(getFeatures);
}
}
- // execute a groovy script.
+ // Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, desktop);
+ executeGroovyScript(groovyscript, new Object[]
+ { desktop, startUpAlframe });
}
else
{
@@ -552,8 +581,15 @@ public class Jalview
+ groovyscript);
}
}
-
- // Once all other stuff is done, execute any groovy scripts (in order)
+ // and finally, turn off batch mode indicator - if the desktop still exists
+ if (desktop != null)
+ {
+ if (progress != -1)
+ {
+ desktop.setProgressBar(null, progress);
+ }
+ desktop.setInBatchMode(false);
+ }
}
private static void startUsageStats(final Desktop desktop)
@@ -566,8 +602,8 @@ public class Jalview
"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()
@@ -584,7 +620,7 @@ public class Jalview
Cache.log.info("Not enabling Google Tracking.");
}
}, null, true);
- SwingUtilities.invokeLater(prompter);
+ desktop.addDialogThread(prompter);
}
/**
@@ -597,22 +633,29 @@ public class Jalview
* 'Jalview' object.
*/
private static void executeGroovyScript(String groovyscript,
- Object jalviewContext)
+ Object[] jalviewContext)
{
if (jalviewContext == null)
{
System.err
.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
}
- File sfile = null;
+ /**
+ * for scripts contained in files
+ */
+ File tfile = null;
+ /**
+ * script's URI
+ */
+ URL sfile = null;
if (groovyscript.trim().equals("STDIN"))
{
// read from stdin into a tempfile and execute it
try
{
- sfile = File.createTempFile("jalview", "groovy");
+ tfile = File.createTempFile("jalview", "groovy");
PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(sfile)));
+ new FileOutputStream(tfile)));
BufferedReader br = new BufferedReader(
new java.io.InputStreamReader(System.in));
String line = null;
@@ -627,30 +670,56 @@ public class Jalview
} catch (Exception ex)
{
System.err.println("Failed to read from STDIN into tempfile "
- + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+ + ((tfile == null) ? "(tempfile wasn't created)" : tfile
.toString()));
ex.printStackTrace();
return;
}
+ try
+ {
+ sfile = tfile.toURI().toURL();
+ } catch (Exception x)
+ {
+ System.err
+ .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ + tfile.toURI());
+ x.printStackTrace();
+ return;
+ }
}
else
{
- sfile = new File(groovyscript);
- }
- if (!sfile.exists())
- {
- System.err.println("File '" + groovyscript + "' does not exist.");
- return;
- }
- if (!sfile.canRead())
- {
- System.err.println("File '" + groovyscript + "' cannot be read.");
- return;
- }
- if (sfile.length() < 1)
- {
- System.err.println("File '" + groovyscript + "' is empty.");
- return;
+ try
+ {
+ sfile = new URI(groovyscript).toURL();
+ } catch (Exception x)
+ {
+ tfile = new File(groovyscript);
+ if (!tfile.exists())
+ {
+ System.err.println("File '" + groovyscript + "' does not exist.");
+ return;
+ }
+ if (!tfile.canRead())
+ {
+ System.err.println("File '" + groovyscript + "' cannot be read.");
+ return;
+ }
+ if (tfile.length() < 1)
+ {
+ System.err.println("File '" + groovyscript + "' is empty.");
+ return;
+ }
+ try
+ {
+ sfile = tfile.getAbsoluteFile().toURI().toURL();
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to create a file URL for "
+ + tfile.getAbsoluteFile());
+ return;
+ }
+ }
}
boolean success = false;
try
@@ -666,25 +735,61 @@ public class Jalview
* = new Binding(); binding.setVariable("input", "world");
* gse.run("hello.groovy", binding);
*/
- ClassLoader cl = jalviewContext.getClass().getClassLoader();
+ Class[] bspec;
+ Object[] binding;
+ int blen = ((jalviewContext[0] == null) ? 0 : 1)
+ + ((jalviewContext[1] == null) ? 0 : 1);
+ String cnames[] = new String[]
+ { "Jalview", "currentAlFrame" };
+ bspec = new Class[blen * 2];
+ binding = new Object[blen * 2];
+ blen = 0;
+ ClassLoader cl = null;
+ Map vbinding = new Hashtable();
+ for (int jc = 0; jc < jalviewContext.length; jc++)
+ {
+ if (jalviewContext[jc] != null)
+ {
+ if (cl == null)
+ {
+ cl = jalviewContext[jc].getClass().getClassLoader();
+ }
+ bspec[blen * 2] = String.class;
+ bspec[blen * 2 + 1] = Object.class;
+ binding[blen * 2] = cnames[jc];
+ binding[blen * 2 + 1] = jalviewContext[jc];
+ vbinding.put(cnames[jc], jalviewContext[jc]);
+ blen++;
+ }
+ }
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 });
+ Constructor gbcons;
+ Object gbinding;
+ try
+ {
+ gbcons = gbindingc.getConstructor(Map.class);
+ gbinding = gbcons.newInstance(vbinding);
+ } catch (NoSuchMethodException x)
+ {
+ // old style binding config - using series of string/object values to
+ // setVariable.
+ gbcons = gbindingc.getConstructor(null);
+ gbinding = gbcons.newInstance(null);
+ java.lang.reflect.Method setvar = gbindingc.getMethod(
+ "setVariable", bspec);
+ setvar.invoke(gbinding, binding);
+ }
+ ;
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() } });
+ { sfile } }); // .toString() } });
java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
{ String.class, gbindingc });
run.invoke(gse, new Object[]
- { sfile.getName(), gbinding });
+ { sfile.toString(), gbinding });
success = true;
} catch (Exception e)
{
@@ -697,7 +802,7 @@ public class Jalview
{
// delete temp file that we made - but only if it was successfully
// executed
- sfile.delete();
+ tfile.delete();
}
}
@@ -711,7 +816,7 @@ public class Jalview
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;
@@ -756,7 +861,7 @@ public class Jalview
+ 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)
@@ -787,16 +892,6 @@ public class Jalview
}
return ff;
}
- private static String checkProtocol(String file)
- {
- String protocol = jalview.io.FormatAdapter.FILE;
-
- if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
- {
- protocol = jalview.io.FormatAdapter.URL;
- }
- return protocol;
- }
}
/**
@@ -836,19 +931,21 @@ class ArgsParser
{
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)
{
@@ -889,48 +986,59 @@ class ArgsParser
}
}
+
/**
* 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;
}
};