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Hidden tabs and vamsas refs for beta release
author
amwaterhouse
<Andrew Waterhouse>
Thu, 17 Nov 2005 18:18:55 +0000
(18:18 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 17 Nov 2005 18:18:55 +0000
(18:18 +0000)
src/jalview/gui/AlignFrame.java
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|
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src/jalview/gui/Desktop.java
patch
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blob
|
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src/jalview/gui/SequenceFetcher.java
patch
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src/jalview/gui/SequenceRenderer.java
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diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
65b9a08
..
74f081b
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-98,7
+98,7
@@
public class AlignFrame
// remove(tabbedPane);
\r
getContentPane().add(alignPanel, BorderLayout.CENTER);
\r
\r
// remove(tabbedPane);
\r
getContentPane().add(alignPanel, BorderLayout.CENTER);
\r
\r
- setGUINucleotide(al.isNucleotide());
\r
+
\r
\r
// tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
\r
\r
\r
// tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
\r
\r
@@
-127,8
+127,12
@@
public class AlignFrame
}
\r
});
\r
\r
}
\r
});
\r
\r
- if(Desktop.desktop!=null)
\r
+
\r
+ if (Desktop.desktop != null)
\r
+ {
\r
addServiceListeners();
\r
addServiceListeners();
\r
+ setGUINucleotide(al.isNucleotide());
\r
+ }
\r
}
\r
\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */
\r
}
\r
\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */
\r
@@
-2492,7
+2496,7
@@
public class AlignFrame
// TODO: group services by location as well as function.
\r
}
\r
\r
// TODO: group services by location as well as function.
\r
}
\r
\r
- public void vamsasStore_actionPerformed(ActionEvent e)
\r
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
\r
{
\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
getProperty("LAST_DIRECTORY"));
\r
{
\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
getProperty("LAST_DIRECTORY"));
\r
@@
-2509,7
+2513,7
@@
public class AlignFrame
//vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
}
\r
//vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
}
\r
- }
\r
+ }*/
\r
\r
public void featureSettings_actionPerformed(ActionEvent e)
\r
{
\r
\r
public void featureSettings_actionPerformed(ActionEvent e)
\r
{
\r
diff --git
a/src/jalview/gui/Desktop.java
b/src/jalview/gui/Desktop.java
index
cc720fe
..
8323320
100755
(executable)
--- a/
src/jalview/gui/Desktop.java
+++ b/
src/jalview/gui/Desktop.java
@@
-550,7
+550,7
@@
public class Desktop extends jalview.jbgui.GDesktop
}
}
}
}
- public void vamsasLoad_actionPerformed(ActionEvent e)
+ /* public void vamsasLoad_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
getProperty("LAST_DIRECTORY"));
{
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
getProperty("LAST_DIRECTORY"));
@@
-569,7
+569,7
@@
public class Desktop extends jalview.jbgui.GDesktop
);
}
);
}
- }
+ }*/
public void inputSequence_actionPerformed(ActionEvent e)
public void inputSequence_actionPerformed(ActionEvent e)
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
4fa215f
..
adadf14
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-127,6
+127,7
@@
public class SequenceFetcher
\r
public void run()
\r
{
\r
\r
public void run()
\r
{
\r
+ String error = null;
\r
StringBuffer result = new StringBuffer();
\r
if (database.getSelectedItem().equals("Uniprot")
\r
|| database.getSelectedItem().equals("EMBL")
\r
StringBuffer result = new StringBuffer();
\r
if (database.getSelectedItem().equals("Uniprot")
\r
|| database.getSelectedItem().equals("EMBL")
\r
@@
-160,13
+161,11
@@
public class SequenceFetcher
}
\r
}catch(Exception ex)// Problem parsing PDB file
\r
{
\r
}
\r
}catch(Exception ex)// Problem parsing PDB file
\r
{
\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
- "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem(),
\r
- "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
\r
+ error = "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem();
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
- if (result.length() > 0)
\r
+ if (result.length() > 0 && error!=null)
\r
{
\r
String format = IdentifyFile.Identify(result.toString(), "Paste");
\r
SequenceI[] sequences = null;
\r
{
\r
String format = IdentifyFile.Identify(result.toString(), "Paste");
\r
SequenceI[] sequences = null;
\r
@@
-228,9
+227,9
@@
public class SequenceFetcher
\r
}
\r
else
\r
\r
}
\r
else
\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
- "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem(),
\r
- "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
\r
+ error = "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem();
\r
+
\r
+
\r
\r
}
\r
}
\r
\r
}
\r
}
\r
@@
-240,6
+239,11
@@
public class SequenceFetcher
ok.setEnabled(true);
\r
cancel.setEnabled(true);
\r
frame.setTitle("Sequence Fetcher");
\r
ok.setEnabled(true);
\r
cancel.setEnabled(true);
\r
frame.setTitle("Sequence Fetcher");
\r
+
\r
+ if(error!=null)
\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
+ error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
\r
+
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
f70a9fa
..
e95ca02
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-86,7
+86,8
@@
public class SequenceRenderer
\r
graphics = bi.getGraphics();
\r
\r
\r
graphics = bi.getGraphics();
\r
\r
- bi.setRGB(0,0, initialCol.getRGB());
\r
+ if(initialCol!=null)
\r
+ bi.setRGB(0,0, initialCol.getRGB());
\r
\r
allGroups = av.alignment.findAllGroups(seq);
\r
\r
\r
allGroups = av.alignment.findAllGroups(seq);
\r
\r