X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=76f9958edbff61d13ed65164149cfde6fd439c28;hb=bb7c8e1f39eca07ec0bc544df298ee58f109b011;hp=39c0a5bfb4b306a15b518a5c72404b5fb25fbeca;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 39c0a5b..76f9958 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,9 +20,6 @@
*/
package jalview.bin;
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
@@ -40,7 +37,6 @@ import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
@@ -67,6 +63,9 @@ import java.util.Vector;
import javax.swing.UIManager;
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
/**
* Main class for Jalview Application
*
@@ -176,8 +175,11 @@ public class Jalview
*
* @param args
* open filename
+ * @throws InterruptedException
+ * @throws IOException
*/
public static void main(String[] args)
+ throws IOException, InterruptedException
{
instance = new Jalview();
instance.doMain(args);
@@ -185,8 +187,10 @@ public class Jalview
/**
* @param args
+ * @throws InterruptedException
+ * @throws IOException
*/
- void doMain(String[] args)
+ void doMain(String[] args) throws IOException, InterruptedException
{
System.setSecurityManager(null);
System.out.println("Java version: "
@@ -511,16 +515,10 @@ public class Jalview
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty.getColour(af
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
.getViewport().getAlignment(), data);
- if (cs == null)
- {
- UserColourScheme ucs = new UserColourScheme("white");
- ucs.parseAppletParameter(data);
- cs = ucs;
- }
- else
+ if (cs != null)
{
System.out.println("CMD [-color " + data
+ "] executed successfully!");
@@ -585,18 +583,14 @@ public class Jalview
data = aparser.getValue("tree", true);
if (data != null)
{
- jalview.io.NewickFile fin = null;
try
{
System.out.println("CMD [-tree " + data
+ "] executed successfully!");
- fin = new NewickFile(data,
+ NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
- if (fin != null)
- {
- af.getViewport().setCurrentTree(
- af.ShowNewickTree(fin, data).getTree());
- }
+ af.getViewport().setCurrentTree(
+ af.showNewickTree(nf, data).getTree());
} catch (IOException ex)
{
System.err.println("Couldn't add tree " + data);
@@ -979,7 +973,7 @@ public class Jalview
}
try
{
- Map vbinding = new HashMap();
+ Map vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
@@ -1046,7 +1040,7 @@ public class Jalview
+ nickname + "|" + url);
if (source == null)
{
- source = new Vector();
+ source = new Vector<>();
}
source.addElement(nickname);
}
@@ -1064,7 +1058,7 @@ public class Jalview
System.out.println("adding source '" + data + "'");
if (source == null)
{
- source = new Vector();
+ source = new Vector<>();
}
source.addElement(data);
}