X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1eeda9850f0f8db3d16df111d0aef88a6a2681be;hb=743a0473c959092ec7c80bdb8169a541d33657cd;hp=5bb5e9808f3a1af061b8f570fe6cc489f6acd18c;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5bb5e98..1eeda98 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -22,6 +22,7 @@ package jalview.bin;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.io.BioJsHTMLOutput;
import jalview.io.HtmlSvgOutput;
import jalview.util.MessageManager;
import jalview.util.Platform;
@@ -45,12 +46,11 @@ import java.security.CodeSource;
import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
/**
* Main class for Jalview Application
@@ -67,6 +67,7 @@ public class Jalview
// grab all the rights we can the JVM
Policy.setPolicy(new Policy()
{
+ @Override
public PermissionCollection getPermissions(CodeSource codesource)
{
Permissions perms = new Permissions();
@@ -74,6 +75,7 @@ public class Jalview
return (perms);
}
+ @Override
public void refresh()
{
}
@@ -93,23 +95,6 @@ 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");
- // try
- // {
- // UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
- // .getLookAndFeel());
- // System.out
- // .println("--------------------------------------------> in here");
- // } catch (UnsupportedLookAndFeelException e)
- // {
- // // TODO Auto-generated catch block
- // e.printStackTrace();
- // }
- // }
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
@@ -125,7 +110,14 @@ public class Jalview
System.setProperty("java.awt.headless", "true");
headless = true;
}
- Cache.loadProperties(aparser.getValue("props")); // must do this before
+ String usrPropsFile = aparser.getValue("props");
+ Cache.loadProperties(usrPropsFile); // must do this before
+ if (usrPropsFile != null)
+ {
+ System.out.println("CMD [-props " + usrPropsFile
+ + "] executed successfully!");
+ }
+
// anything else!
final String jabawsUrl = aparser.getValue("jabaws");
@@ -134,6 +126,8 @@ public class Jalview
try
{
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println("CMD [-jabaws " + jabawsUrl
+ + "] executed successfully!");
} catch (MalformedURLException e)
{
System.err.println("Invalid jabaws parameter: " + jabawsUrl
@@ -185,7 +179,7 @@ public class Jalview
} catch (Exception ex)
{
}
- if (new Platform().isAMac())
+ if (Platform.isAMac())
{
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
"Jalview");
@@ -194,10 +188,10 @@ public class Jalview
{
UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
.getLookAndFeel());
- } catch (UnsupportedLookAndFeelException e)
+ } catch (Throwable e)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ System.err.println("Failed to set QuaQua look and feel: "
+ + e.toString());
}
}
@@ -211,6 +205,11 @@ public class Jalview
{
startUsageStats(desktop);
}
+ else
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
@@ -220,6 +219,8 @@ public class Jalview
// questionnaire
Cache.log.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
}
else
{
@@ -238,11 +239,20 @@ public class Jalview
}
}
}
+ else
+ {
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
desktop.checkForNews();
}
+ if (!isHeadlessMode())
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
+
String file = null, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+ jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
Vector getFeatures = null; // vector of das source nicknames to fetch
// features from
// loading is done.
@@ -348,10 +358,11 @@ public class Jalview
{
if (!headless)
{
- desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
+ desktop.setProgressBar(MessageManager
+ .getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
- System.out.println("Opening file: " + file);
+ System.out.println("CMD [-open " + file + "] executed successfully!");
if (!file.startsWith("http://"))
{
@@ -367,7 +378,7 @@ public class Jalview
protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new jalview.io.IdentifyFile().identify(file, protocol);
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
@@ -377,7 +388,7 @@ public class Jalview
}
else
{
-
+ Desktop.setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
@@ -393,8 +404,11 @@ public class Jalview
ucs.parseAppletParameter(data);
cs = ucs;
}
-
- System.out.println("colour is " + data);
+ else
+ {
+ System.out.println("CMD [-color " + data
+ + "] executed successfully!");
+ }
af.changeColour(cs);
}
@@ -404,34 +418,53 @@ public class Jalview
{
af.parseFeaturesFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD groups[-" + data
+ + "] executed successfully!");
}
data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-features " + data
+ + "] executed successfully!");
}
data = aparser.getValue("annotations", true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-annotations " + data
+ + "] executed successfully!");
}
// set or clear the sortbytree flag.
if (aparser.contains("sortbytree"))
{
af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
+ {
+ System.out.println("CMD [-sortbytree] executed successfully!");
+ }
}
if (aparser.contains("no-annotation"))
{
af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ System.out.println("CMD no-annotation executed successfully!");
+ }
}
if (aparser.contains("nosortbytree"))
{
af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
+ {
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
+ }
}
data = aparser.getValue("tree", true);
if (data != null)
@@ -439,13 +472,14 @@ public class Jalview
jalview.io.NewickFile fin = null;
try
{
+ System.out.println("CMD [-tree " + data
+ + "] executed successfully!");
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)
{
@@ -484,8 +518,10 @@ public class Jalview
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, af });
+ executeGroovyScript(groovyscript, new Object[] { desktop, af });
+
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
}
else
{
@@ -532,8 +568,10 @@ public class Jalview
}
else if (format.equalsIgnoreCase("eps"))
{
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
+ File outputFile = new java.io.File(file);
+ System.out.println("Creating EPS file: "
+ + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
continue;
}
@@ -590,7 +628,7 @@ public class Jalview
}
else
{
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ format = new jalview.io.IdentifyFile().identify(file, protocol);
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
@@ -615,8 +653,8 @@ public class Jalview
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, startUpAlframe });
+ executeGroovyScript(groovyscript, new Object[] { desktop,
+ startUpAlframe });
}
else
{
@@ -653,6 +691,7 @@ public class Jalview
+ "-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"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ "-png FILE\tCreate PNG image FILE from alignment.\n"
+ "-svg FILE\tCreate SVG image FILE from alignment.\n"
@@ -691,6 +730,7 @@ public class Jalview
+ "\n\n(you can enable or disable usage tracking in the preferences)",
new Runnable()
{
+ @Override
public void run()
{
Cache.log
@@ -700,6 +740,7 @@ public class Jalview
}
}, new Runnable()
{
+ @Override
public void run()
{
Cache.log.debug("Not enabling Google Tracking.");
@@ -820,17 +861,16 @@ public class Jalview
* = new Binding(); binding.setVariable("input", "world");
* gse.run("hello.groovy", binding);
*/
- Class[] bspec;
+ Class>[] bspec;
Object[] binding;
int blen = ((jalviewContext[0] == null) ? 0 : 1)
+ ((jalviewContext[1] == null) ? 0 : 1);
- String cnames[] = new String[]
- { "Jalview", "currentAlFrame" };
+ 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();
+ Map vbinding = new HashMap();
for (int jc = 0; jc < jalviewContext.length; jc++)
{
if (jalviewContext[jc] != null)
@@ -847,8 +887,8 @@ public class Jalview
blen++;
}
}
- Class gbindingc = cl.loadClass("groovy.lang.Binding");
- Constructor gbcons;
+ Class> gbindingc = cl.loadClass("groovy.lang.Binding");
+ Constructor> gbcons;
Object gbinding;
try
{
@@ -858,23 +898,23 @@ public class Jalview
{
// old style binding config - using series of string/object values to
// setVariable.
- gbcons = gbindingc.getConstructor(null);
- gbinding = gbcons.newInstance(null);
+ gbcons = gbindingc.getConstructor();
+ gbinding = gbcons.newInstance();
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 } }); // .toString() } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
- { String.class, gbindingc });
- run.invoke(gse, new Object[]
- { sfile.toString(), gbinding });
+
+ 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 } }); // .toString()
+ // } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[] {
+ String.class, gbindingc });
+ run.invoke(gse, new Object[] { sfile.toString(), gbinding });
success = true;
} catch (Exception e)
{
@@ -939,6 +979,8 @@ public class Jalview
}
source.addElement(nickname);
}
+ System.out.println("CMD [-dasserver " + data
+ + "] executed successfully!");
} // loop until no more server entries are found.
if (locsources != null && locsources.indexOf('|') > -1)
{
@@ -966,7 +1008,7 @@ public class Jalview
private static FeatureFetcher startFeatureFetching(final Vector dasSources)
{
FeatureFetcher ff = new FeatureFetcher();
- AlignFrame afs[] = Desktop.getAlignframes();
+ AlignFrame afs[] = Desktop.getAlignFrames();
if (afs == null || afs.length == 0)
{
return null;
@@ -977,6 +1019,16 @@ public class Jalview
}
return ff;
}
+
+ public static boolean isHeadlessMode()
+ {
+ String isheadless = System.getProperty("java.awt.headless");
+ if (isheadless != null && isheadless.equalsIgnoreCase("true"))
+ {
+ return true;
+ }
+ return false;
+ }
}
/**
@@ -991,6 +1043,7 @@ public class Jalview
class rnabuttonlistener implements ActionListener
{
+ @Override
public void actionPerformed(ActionEvent arg0)
{
System.out.println("Good idea ! ");
@@ -1000,6 +1053,7 @@ class rnabuttonlistener implements ActionListener
class pbuttonlistener implements ActionListener
{
+ @Override
public void actionPerformed(ActionEvent arg0)
{
@@ -1120,6 +1174,7 @@ class FeatureFetcher
new Thread(new Runnable()
{
+ @Override
public void run()
{
synchronized (us)
@@ -1128,7 +1183,8 @@ class FeatureFetcher
running++;
}
- af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
af.featureSettings_actionPerformed(null);
af.featureSettings.fetchDasFeatures(dasSources, true);
af.setProgressBar(null, id);
@@ -1145,4 +1201,4 @@ class FeatureFetcher
return queued == 0 && running == 0;
}
-};
+}