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FormatAdapter throws exception
[jalview.git]
/
src
/
jalview
/
bin
/
JalviewLite.java
diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
a26b9d0
..
c4e17fb
100755
(executable)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-127,8
+127,13
@@
public class JalviewLite extends Applet
}
\r
\r
String format = jalview.io.IdentifyFile.Identify(args[0],"File");
\r
}
\r
\r
String format = jalview.io.IdentifyFile.Identify(args[0],"File");
\r
- SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
\r
-
\r
+ SequenceI[] sequences = null;
\r
+ try{
\r
+ sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
\r
+ }catch(java.io.IOException ex)
\r
+ {
\r
+ ex.printStackTrace();
\r
+ }
\r
if ( (sequences != null) && (sequences.length > 0))
\r
{
\r
AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
\r
if ( (sequences != null) && (sequences.length > 0))
\r
{
\r
AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
\r
@@
-247,8
+252,13
@@
public class JalviewLite extends Applet
public void run()
\r
{
\r
SequenceI[] sequences = null;
\r
public void run()
\r
{
\r
SequenceI[] sequences = null;
\r
- sequences = new AppletFormatAdapter().readFile(file, protocol, format);
\r
-
\r
+ try{
\r
+ sequences = new AppletFormatAdapter().readFile(file, protocol,
\r
+ format);
\r
+ }catch(java.io.IOException ex)
\r
+ {
\r
+ ex.printStackTrace();
\r
+ }
\r
if ((sequences != null) && (sequences.length > 0))
\r
{
\r
currentAlignFrame = new AlignFrame(new Alignment(sequences),
\r
if ((sequences != null) && (sequences.length > 0))
\r
{
\r
currentAlignFrame = new AlignFrame(new Alignment(sequences),
\r
@@
-263,12
+273,11
@@
public class JalviewLite extends Applet
if (treeFile != null)
\r
{
\r
if (treeFile.indexOf("://") == -1)
\r
if (treeFile != null)
\r
{
\r
if (treeFile.indexOf("://") == -1)
\r
- treeFile = getCodeBase() + treeFile;
\r
+ treeFile = getCodeBase() + treeFile;
\r
\r
try
\r
{
\r
\r
try
\r
{
\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
\r
- getCodeBase() + treeFile, "URL");
\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, "URL");
\r
fin.parse();
\r
\r
if (fin.getTree() != null)
\r
fin.parse();
\r
\r
if (fin.getTree() != null)
\r
@@
-276,7
+285,7
@@
public class JalviewLite extends Applet
TreePanel tp = null;
\r
tp = new TreePanel(currentAlignFrame.viewport,
\r
currentAlignFrame.viewport.getAlignment().getSequences(),
\r
TreePanel tp = null;
\r
tp = new TreePanel(currentAlignFrame.viewport,
\r
currentAlignFrame.viewport.getAlignment().getSequences(),
\r
- fin, "FromFile", applet.getCodeBase() + treeFile);
\r
+ fin, "FromFile", treeFile);
\r
addFrame(tp, treeFile, 600, 500);
\r
currentAlignFrame.addTreeMenuItem(tp, treeFile);
\r
}
\r
addFrame(tp, treeFile, 600, 500);
\r
currentAlignFrame.addTreeMenuItem(tp, treeFile);
\r
}
\r