/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.lang.reflect.Constructor;
-import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.net.URLDecoder;
+ "\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");
}
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();
}
}
}
+ desktop.checkForNews();
}
String file = null, protocol = null, format = null, data = null;
{
try
{
- String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport);
+ String viprotocol = jalview.io.AppletFormatAdapter
+ .checkProtocol(vamsasImport);
if (viprotocol == jalview.io.FormatAdapter.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
}
}
- long progress=-1;
+ long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
{
if (!headless)
{
- desktop.setProgressBar("Processing commandline arguments...", progress=System.currentTimeMillis());
+ desktop.setProgressBar("Processing commandline arguments...",
+ progress = System.currentTimeMillis());
}
System.out.println("Opening file: " + file);
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, jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
- }
- data = aparser.getValue("features", true);
- if (data != null)
- {
- af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
- }
-
- data = aparser.getValue("annotations", true);
- if (data != null)
- {
- af.loadJalviewDataFile(data, null, null, null);
- 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, jalview.io.AppletFormatAdapter.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(s) to alignment JAL-629
- // (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, new Object[] {desktop,af});
+ 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;
if (!headless && file == null && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_7.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
+ file.replace("_2_3.jar", "_2_7.jar");
+ // and remove the stale setting
jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
-
+
protocol = "File";
if (file.indexOf("http:") > -1)
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[] { desktop, startUpAlframe});
+ executeGroovyScript(groovyscript, new Object[]
+ { desktop, startUpAlframe });
}
else
{
// and finally, turn off batch mode indicator - if the desktop still exists
if (desktop != null)
{
- if (progress!=-1) {
+ if (progress != -1)
+ {
desktop.setProgressBar(null, progress);
}
desktop.setInBatchMode(false);
Cache.log.info("Not enabling Google Tracking.");
}
}, null, true);
- SwingUtilities.invokeLater(prompter);
+ desktop.addDialogThread(prompter);
}
/**
ex.printStackTrace();
return;
}
- try {
+ try
+ {
sfile = tfile.toURI().toURL();
} catch (Exception x)
{
- System.err.println("Unexpected Malformed URL Exception for temporary file created from STDIN: "+tfile.toURI());
+ System.err
+ .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ + tfile.toURI());
x.printStackTrace();
return;
}
System.err.println("File '" + groovyscript + "' is empty.");
return;
}
- try {
- sfile = tfile.getAbsoluteFile().toURI().toURL();
+ try
+ {
+ sfile = tfile.getAbsoluteFile().toURI().toURL();
} catch (Exception ex)
{
- System.err.println("Failed to create a file URL for "+tfile.getAbsoluteFile());
+ System.err.println("Failed to create a file URL for "
+ + tfile.getAbsoluteFile());
return;
}
}
git://source.jalview.org / jalview.git / blobdiff