/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
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;
import java.util.Vector;
import javax.swing.UIManager;
+import javax.swing.UnsupportedLookAndFeelException;
/**
* Main class for Jalview Application <br>
}
/**
- * Put protein=true for get a protein example
- */
- private static boolean protein = false;
-
- /**
* main class for Jalview application
*
* @param args
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");
- }
+ // 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;
} catch (Exception ex)
{
}
+ 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());
+ } catch (UnsupportedLookAndFeelException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
if (!headless)
{
{
af.getViewport().setSortByTree(true);
}
+ if (aparser.contains("no-annotation"))
+ {
+ af.getViewport().setShowAnnotation(false);
+ }
if (aparser.contains("nosortbytree"))
{
af.getViewport().setSortByTree(false);
System.out.println("Creating SVG image: " + file);
continue;
}
+ else if (format.equalsIgnoreCase("html"))
+ {
+ File imageFile = new java.io.File(file);
+ imageName = imageFile.getName();
+ new HtmlSvgOutput(new java.io.File(file), af.alignPanel);
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
else if (format.equalsIgnoreCase("imgMap"))
{
af.createImageMap(new java.io.File(file), imageName);
// ////////////////////
if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
- && protein == true)
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
file = jalview.bin.Cache.getDefault(
"STARTUP_FILE",
+ "-blc FILE\tCreate alignment file FILE in BLC 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"
+ + "-html FILE\tCreate HTML file from alignment.\n"
+ "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
public void run()
{
Cache.log
- .info("Initialising googletracker for usage stats.");
+ .debug("Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
Cache.log.debug("Tracking enabled.");
}
{
public void run()
{
- Cache.log.info("Not enabling Google Tracking.");
+ Cache.log.debug("Not enabling Google Tracking.");
}
}, null, true);
desktop.addDialogThread(prompter);