X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=fcee9e1f35b2719dc7ef82162277802e604bc33a;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=0fe16645fc85cd09e4c7b740d85fdb438cf7c9a0;hpb=10e637daad8983c41db8679baabea5563d7371f4;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0fe1664..fcee9e1 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
@@ -20,6 +20,14 @@
*/
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;
+import jalview.ws.jws2.Jws2Discoverer;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.BufferedReader;
@@ -45,13 +53,6 @@ import java.util.Vector;
import javax.swing.UIManager;
import javax.swing.UnsupportedLookAndFeelException;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.io.HtmlSvgOutput;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
/**
* Main class for Jalview Application
*
@@ -93,23 +94,6 @@ 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 +109,14 @@ 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 +125,8 @@ 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
@@ -211,6 +204,11 @@ public class Jalview
{
startUsageStats(desktop);
}
+ else
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
@@ -220,6 +218,8 @@ 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 +238,20 @@ 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 +357,11 @@ 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://"))
{
@@ -377,7 +387,7 @@ public class Jalview
}
else
{
-
+ Desktop.setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
@@ -393,8 +403,11 @@ 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 +417,53 @@ 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 +471,14 @@ 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 +517,10 @@ 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 +567,10 @@ 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;
}
@@ -615,8 +652,8 @@ 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 +690,7 @@ 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"
@@ -824,8 +862,7 @@ public class Jalview
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;
@@ -866,15 +903,15 @@ public class Jalview
}
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 });
+ 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 +976,8 @@ 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)
{
@@ -977,6 +1016,16 @@ 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;
+ }
}
/**
@@ -1128,7 +1177,8 @@ 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 +1195,4 @@ class FeatureFetcher
return queued == 0 && running == 0;
}
-};
+}