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Retrieves PFAM alignments
author
amwaterhouse
<Andrew Waterhouse>
Fri, 3 Feb 2006 17:44:33 +0000
(17:44 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 3 Feb 2006 17:44:33 +0000
(17:44 +0000)
src/jalview/gui/SequenceFetcher.java
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diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
0884d44
..
6d49d12
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-44,6
+44,7
@@
public class SequenceFetcher
database.addItem("EMBL");
\r
database.addItem("EMBLCDS");
\r
database.addItem("PDB");
\r
database.addItem("EMBL");
\r
database.addItem("EMBLCDS");
\r
database.addItem("PDB");
\r
+ database.addItem("PFAM");
\r
\r
try
\r
{
\r
\r
try
\r
{
\r
@@
-64,8
+65,7
@@
public class SequenceFetcher
\r
private String getFrameTitle()
\r
{
\r
\r
private String getFrameTitle()
\r
{
\r
- return ( (alignFrame == null) ? "New " : "Additional ") +
\r
- "Sequence Fetcher (WSDBfetch@EBI)";
\r
+ return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
\r
}
\r
\r
private void jbInit()
\r
}
\r
\r
private void jbInit()
\r
@@
-142,7
+142,6
@@
public class SequenceFetcher
\r
public void ok_actionPerformed(ActionEvent e)
\r
{
\r
\r
public void ok_actionPerformed(ActionEvent e)
\r
{
\r
- frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");
\r
database.setEnabled(false);
\r
textfield.setEnabled(false);
\r
ok.setEnabled(false);
\r
database.setEnabled(false);
\r
textfield.setEnabled(false);
\r
ok.setEnabled(false);
\r
@@
-158,7
+157,6
@@
public class SequenceFetcher
textfield.setEnabled(true);
\r
ok.setEnabled(true);
\r
close.setEnabled(true);
\r
textfield.setEnabled(true);
\r
ok.setEnabled(true);
\r
close.setEnabled(true);
\r
- frame.setTitle(getFrameTitle());
\r
}
\r
\r
public void run()
\r
}
\r
\r
public void run()
\r
@@
-214,13
+212,27
@@
public class SequenceFetcher
if (result.length()>0)
\r
parseResult(result.toString());
\r
}
\r
if (result.length()>0)
\r
parseResult(result.toString());
\r
}
\r
+ else if( database.getSelectedItem().equals("PFAM"))
\r
+ {
\r
+ try{
\r
+ result.append(new FastaFile(
\r
+ "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
\r
+ + textfield.getText().toUpperCase(), "URL").print()
\r
+ );
\r
+
\r
+ if(result.length()>0)
\r
+ parseResult( result.toString() );
\r
+
\r
+ }catch(java.io.IOException ex)
\r
+ { result = null; }
\r
+ }
\r
\r
if (result == null || result.length() == 0)
\r
showErrorMessage("Error retrieving " + textfield.getText()
\r
+ " from " + database.getSelectedItem());
\r
\r
if (result == null || result.length() == 0)
\r
showErrorMessage("Error retrieving " + textfield.getText()
\r
+ " from " + database.getSelectedItem());
\r
- else
\r
- textfield.setText("");
\r
+
\r
resetDialog();
\r
resetDialog();
\r
+ return;
\r
}
\r
\r
void getUniprotFile(String id)
\r
}
\r
\r
void getUniprotFile(String id)
\r
@@
-433,9
+445,11
@@
public class SequenceFetcher
\r
void showErrorMessage(String error)
\r
{
\r
\r
void showErrorMessage(String error)
\r
{
\r
+ resetDialog();
\r
JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
error, "Error Retrieving Data",
\r
JOptionPane.WARNING_MESSAGE);
\r
JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
error, "Error Retrieving Data",
\r
JOptionPane.WARNING_MESSAGE);
\r
+ return;
\r
}
\r
}
\r
\r
}
\r
}
\r
\r