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[jalview.git]
/
src
/
jalview
/
bin
/
Jalview.java
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
64ffd38
..
2b935ed
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-81,8
+81,9
@@
public class Jalview
+ System.getProperty("os.version"));
if (new Platform().isAMac())
{
+ 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");
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
}
ArgsParser aparser = new ArgsParser(args);
}
ArgsParser aparser = new ArgsParser(args);
@@
-94,6
+95,7
@@
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"
.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"
+ "-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"
@@
-178,6
+180,7
@@
public class Jalview
if (!headless)
{
desktop = new Desktop();
if (!headless)
{
desktop = new Desktop();
+ desktop.setInBatchMode(true); // indicate we are starting up
desktop.setVisible(true);
desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
desktop.setVisible(true);
desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
@@
-245,7
+248,7
@@
public class Jalview
{
try
{
{
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));
if (viprotocol == jalview.io.FormatAdapter.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
@@
-330,7
+333,7
@@
public class Jalview
}
}
}
}
- protocol = checkProtocol(file);
+ protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
format = new jalview.io.IdentifyFile().Identify(file, protocol);
format = new jalview.io.IdentifyFile().Identify(file, protocol);
@@
-366,20
+369,20
@@
public class Jalview
data = aparser.getValue("groups", true);
if (data != null)
{
data = aparser.getValue("groups", true);
if (data != null)
{
- af.parseFeaturesFile(data, checkProtocol(data));
+ af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
System.out.println("Added " + data);
}
data = aparser.getValue("features", true);
if (data != null)
{
System.out.println("Added " + data);
}
data = aparser.getValue("features", true);
if (data != null)
{
- af.parseFeaturesFile(data, checkProtocol(data));
+ af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
System.out.println("Added " + data);
}
data = aparser.getValue("annotations", true);
if (data != null)
{
System.out.println("Added " + data);
}
data = aparser.getValue("annotations", true);
if (data != null)
{
- af.loadJalviewDataFile(data);
+ af.loadJalviewDataFile(data, null, null, null);
System.out.println("Added " + data);
}
// set or clear the sortbytree flag.
System.out.println("Added " + data);
}
// set or clear the sortbytree flag.
@@
-397,7
+400,7
@@
public class Jalview
jalview.io.NewickFile fin = null;
try
{
jalview.io.NewickFile fin = null;
try
{
- fin = new jalview.io.NewickFile(data, checkProtocol(data));
+ fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
if (fin != null)
{
af.getViewport().setCurrentTree(
if (fin != null)
{
af.getViewport().setCurrentTree(
@@
-410,7
+413,7
@@
public class Jalview
ex.printStackTrace(System.err);
}
}
ex.printStackTrace(System.err);
}
}
- // todo - load PDB structure to alignment
+ // TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
// (associate with identical sequence in alignment, or a specified
// sequence)
@@
-535,7
+538,7
@@
public class Jalview
startFeatureFetching(getFeatures);
}
}
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())
if (groovyscript != null)
{
if (jalview.bin.Cache.groovyJarsPresent())
@@
-550,8
+553,11
@@
public class Jalview
+ groovyscript);
}
}
+ 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)
+ {
+ desktop.setInBatchMode(false);
+ }
}
private static void startUsageStats(final Desktop desktop)
}
private static void startUsageStats(final Desktop desktop)
@@
-785,17
+791,6
@@
public class Jalview
}
return ff;
}
}
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;
- }
}
/**
}
/**