git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
8d056f6
)
parseResult takes the title as string. usually null
author
amwaterhouse
<Andrew Waterhouse>
Wed, 8 Feb 2006 15:27:00 +0000
(15:27 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 8 Feb 2006 15:27:00 +0000
(15:27 +0000)
src/jalview/gui/SequenceFetcher.java
patch
|
blob
|
history
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
6d49d12
..
498489d
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-194,7
+194,7
@@
public class SequenceFetcher
for (int i = 0; i < reply.length; i++)
\r
result.append(reply[i] + "\n");
\r
\r
for (int i = 0; i < reply.length; i++)
\r
result.append(reply[i] + "\n");
\r
\r
- parseResult(result.toString());
\r
+ parseResult(result.toString(), null);
\r
}
\r
}
\r
else if (database.getSelectedItem().equals("PDB"))
\r
}
\r
}
\r
else if (database.getSelectedItem().equals("PDB"))
\r
@@
-210,7
+210,7
@@
public class SequenceFetcher
\r
\r
if (result.length()>0)
\r
\r
\r
if (result.length()>0)
\r
- parseResult(result.toString());
\r
+ parseResult(result.toString(), null);
\r
}
\r
else if( database.getSelectedItem().equals("PFAM"))
\r
{
\r
}
\r
else if( database.getSelectedItem().equals("PFAM"))
\r
{
\r
@@
-221,7
+221,7
@@
public class SequenceFetcher
);
\r
\r
if(result.length()>0)
\r
);
\r
\r
if(result.length()>0)
\r
- parseResult( result.toString() );
\r
+ parseResult( result.toString(), textfield.getText().toUpperCase() );
\r
\r
}catch(java.io.IOException ex)
\r
{ result = null; }
\r
\r
}catch(java.io.IOException ex)
\r
{ result = null; }
\r
@@
-272,7
+272,7
@@
public class SequenceFetcher
}
\r
\r
//Then read in the features and apply them to the dataset
\r
}
\r
\r
//Then read in the features and apply them to the dataset
\r
- SequenceI[] sequence = parseResult(result.toString());
\r
+ SequenceI[] sequence = parseResult(result.toString(), null);
\r
for (int i = 0; i < entries.size(); i++)
\r
{
\r
UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
\r
for (int i = 0; i < entries.size(); i++)
\r
{
\r
UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
\r
@@
-336,23
+336,28
@@
public class SequenceFetcher
return result;
\r
}
\r
\r
return result;
\r
}
\r
\r
- SequenceI[] parseResult(String result)
\r
+ SequenceI[] parseResult(String result, String title)
\r
{
\r
String format = IdentifyFile.Identify(result, "Paste");
\r
SequenceI[] sequences = null;
\r
\r
if (FormatAdapter.formats.contains(format))
\r
{
\r
{
\r
String format = IdentifyFile.Identify(result, "Paste");
\r
SequenceI[] sequences = null;
\r
\r
if (FormatAdapter.formats.contains(format))
\r
{
\r
- sequences = new FormatAdapter().readFile(result.toString(), "Paste",
\r
- format);
\r
+ sequences = null;
\r
+ try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
\r
+ format);}
\r
+ catch(Exception ex){}
\r
+
\r
if (sequences != null && sequences.length > 0)
\r
{
\r
if (alignFrame == null)
\r
{
\r
AlignFrame af = new AlignFrame(new Alignment(sequences));
\r
af.currentFileFormat = format;
\r
if (sequences != null && sequences.length > 0)
\r
{
\r
if (alignFrame == null)
\r
{
\r
AlignFrame af = new AlignFrame(new Alignment(sequences));
\r
af.currentFileFormat = format;
\r
+ if(title==null)
\r
+ title = "Retrieved from " + database.getSelectedItem();
\r
Desktop.addInternalFrame(af,
\r
Desktop.addInternalFrame(af,
\r
- "Retrieved from " + database.getSelectedItem(),
\r
+ title,
\r
AlignFrame.NEW_WINDOW_WIDTH,
\r
AlignFrame.NEW_WINDOW_HEIGHT);
\r
af.statusBar.setText("Successfully pasted alignment file");
\r
AlignFrame.NEW_WINDOW_WIDTH,
\r
AlignFrame.NEW_WINDOW_HEIGHT);
\r
af.statusBar.setText("Successfully pasted alignment file");
\r
@@
-370,7
+375,7
@@
public class SequenceFetcher
alignFrame.viewport.alignment.addSequence(sequences[i]);
\r
\r
////////////////////////////
\r
alignFrame.viewport.alignment.addSequence(sequences[i]);
\r
\r
////////////////////////////
\r
- //Datset needs extension;
\r
+ //Dataset needs extension;
\r
/////////////////////////////
\r
Sequence ds = new Sequence(sequences[i].getName(),
\r
AlignSeq.extractGaps("-. ",
\r
/////////////////////////////
\r
Sequence ds = new Sequence(sequences[i].getName(),
\r
AlignSeq.extractGaps("-. ",
\r