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Throw exception if pdb result size is zero
author
amwaterhouse
<Andrew Waterhouse>
Wed, 4 Apr 2007 13:06:15 +0000
(13:06 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 4 Apr 2007 13:06:15 +0000
(13:06 +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
6687020
..
0ea13a2
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-195,7
+195,7
@@
extends JPanel implements Runnable
else if (database.getSelectedItem().equals("EMBL")
|| database.getSelectedItem().equals("EMBLCDS"))
{
else if (database.getSelectedItem().equals("EMBL")
|| database.getSelectedItem().equals("EMBLCDS"))
{
- String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
+ String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
? jalview.datamodel.DBRefSource.EMBLCDS
: jalview.datamodel.DBRefSource.EMBL;
? jalview.datamodel.DBRefSource.EMBLCDS
: jalview.datamodel.DBRefSource.EMBL;
@@
-213,7
+213,7
@@
extends JPanel implements Runnable
jalview.datamodel.xdb.embl.EmblFile efile=null;
if (reply != null && reply.exists())
{
jalview.datamodel.xdb.embl.EmblFile efile=null;
if (reply != null && reply.exists())
{
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
}
if (efile!=null) {
for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
}
if (efile!=null) {
for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
@@
-246,7
+246,7
@@
extends JPanel implements Runnable
if (seqs!=null && seqs.length>0) {
if (parseResult(new Alignment(seqs), null, null)!=null)
result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
if (seqs!=null && seqs.length>0) {
if (parseResult(new Alignment(seqs), null, null)!=null)
result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
- }
+ }
}
else if (database.getSelectedItem().equals("PDB"))
{
}
else if (database.getSelectedItem().equals("PDB"))
{
@@
-447,7
+447,7
@@
extends JPanel implements Runnable
entry.getProperty().put("chains",
pdbchain.id
+ "=" + sq.getStart()
entry.getProperty().put("chains",
pdbchain.id
+ "=" + sq.getStart()
- + "-" + sq.getEnd());
+ + "-" + sq.getEnd());
sq.getDatasetSequence().addPDBId(entry);
*/
// Add PDB DB Refs
sq.getDatasetSequence().addPDBId(entry);
*/
// Add PDB DB Refs
@@
-460,6
+460,11
@@
extends JPanel implements Runnable
result.addElement(sq.deriveSequence());
}
}
result.addElement(sq.deriveSequence());
}
}
+
+ if (result.size() < 1)
+ {
+ throw new Exception("WsDBFetch for PDB id resulted in zero result size");
+ }
}
catch (Exception ex) // Problem parsing PDB file
{
}
catch (Exception ex) // Problem parsing PDB file
{
@@
-468,6
+473,8
@@
extends JPanel implements Runnable
database.getSelectedItem(), ex);
return null;
}
database.getSelectedItem(), ex);
return null;
}
+
+
SequenceI[] results = new SequenceI[result.size()];
for (int i = 0, j = result.size(); i < j; i++)
{
SequenceI[] results = new SequenceI[result.size()];
for (int i = 0, j = result.size(); i < j; i++)
{