<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>14/6/2016</em></strong>
+ <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>21/6/2016</em></strong>
</div>
</td>
<td><em>General</em>
<ul>
- <li></li>
+ <li><!-- JAL---></li>
</ul> <em>Application</em>
<ul>
- <li></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
+ <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
</ul> <em>Applet</em>
<ul>
- <li></li>
+ <li><!-- JAL---></li>
</ul></td>
<td>
<div align="left">
<em>General</em>
<ul>
<li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
+ <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
+ <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
+ <li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
+ <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
+ <li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
+ <li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
+
</ul>
<em>Application</em>
<ul>
- <li></li>
+ <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
+ <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
+ <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
+ <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
+ <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
+ <!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
</ul>
<em>Applet</em>
<ul>
- <li></li>
+ <li><!-- --></li>
</ul>
</div>
</td>
*
* @author jimp
*
- * History: v1.0 revised from original due to refactoring of
- * paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
- * http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview
+ * @version v1.0 revised from original due to refactoring of
+ * paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
+ * http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview <br/>
+ * See also testing URL from fjossinet:<br/>
+ * http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d <br/>
+ * If in doubt, check against the REST client at:
+ * https://github.com/fjossinet/RNA-Science
+ * -Toolbox/blob/master/pyrna/restclient.py
*/
public class Annotate3D
{
- private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d";
+ // also test with
+ // "http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d";
+ private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview";
private static ContentHandler createContentHandler()
{
*
* @return list of columns to display by default
*/
- public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns();
+ public Collection<FTSDataColumnI> getAllDefaultDisplayedFTSDataColumns();
/**
* Return list of FTSDataColumnI objects that can be used to perform a search
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import java.util.ArrayList;
import java.util.Collection;
FTSRestClientI ftsRestClient)
{
this.ftsRestClient = ftsRestClient;
- Collection<FTSDataColumnI> defaultCols = ftsRestClient
- .getAllDefaulDisplayedDataColumns();
-
- structSummaryColumns.addAll(defaultCols);
-
+ if (source.equals(PreferenceSource.STRUCTURE_CHOOSER)
+ || source.equals(PreferenceSource.PREFERENCES))
+ {
+ structSummaryColumns = ((PDBFTSRestClient) ftsRestClient)
+ .getAllDefaultDisplayedStructureDataColumns();
+ }
allFTSDataColumns.addAll(ftsRestClient.getAllFTSDataColumns());
tbl_FTSDataColumnPrefs.setAutoCreateRowSorter(true);
{
case SEARCH_SUMMARY:
data[x++] = new Object[] {
- ftsRestClient.getAllDefaulDisplayedDataColumns()
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.contains(field),
field.getName(), field.getGroup() };
break;
break;
case PREFERENCES:
data[x++] = new Object[] { field.getName(),
- ftsRestClient.getAllDefaulDisplayedDataColumns()
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.contains(field),
structSummaryColumns.contains(field) };
break;
if (currentSource == PreferenceSource.SEARCH_SUMMARY)
{
updatePrefs(ftsRestClient
- .getAllDefaulDisplayedDataColumns(), ftsDataColumn,
+ .getAllDefaultDisplayedFTSDataColumns(), ftsDataColumn,
selected);
}
else if (currentSource == PreferenceSource.STRUCTURE_CHOOSER)
if (col == 1)
{
updatePrefs(ftsRestClient
- .getAllDefaulDisplayedDataColumns(), ftsDataColumn,
+ .getAllDefaultDisplayedFTSDataColumns(), ftsDataColumn,
selected);
}
else if (col == 2)
}
@Override
- public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns()
+ public Collection<FTSDataColumnI> getAllDefaultDisplayedFTSDataColumns()
{
if (defaulDisplayedDataColumns == null
|| defaulDisplayedDataColumns.isEmpty())
txt_search.setEnabled(false);
cmb_searchTarget.setEnabled(false);
previousWantedFields = getFTSRestClient()
- .getAllDefaulDisplayedDataColumns()
+ .getAllDefaultDisplayedFTSDataColumns()
.toArray(new Object[0]);
}
if (sourceTabbedPane.getTitleAt(index).equals(searchTabTitle))
}
return Arrays.equals(getFTSRestClient()
- .getAllDefaulDisplayedDataColumns()
+ .getAllDefaultDisplayedFTSDataColumns()
.toArray(new Object[0]), previousWantedFields) ? false
: true;
String searchTarget = ((FTSDataColumnI) cmb_searchTarget
.getSelectedItem()).getCode();
wantedFields = PDBFTSRestClient.getInstance()
- .getAllDefaulDisplayedDataColumns();
+ .getAllDefaultDisplayedFTSDataColumns();
String searchTerm = decodeSearchTerm(txt_search.getText(),
searchTarget);
}
return instance;
}
+
+ private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
+
+ public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
+ {
+ if (allDefaultDisplayedStructureDataColumns == null
+ || allDefaultDisplayedStructureDataColumns.isEmpty())
+ {
+ allDefaultDisplayedStructureDataColumns = new ArrayList<FTSDataColumnI>();
+ allDefaultDisplayedStructureDataColumns.addAll(super
+ .getAllDefaultDisplayedFTSDataColumns());
+ }
+ return allDefaultDisplayedStructureDataColumns;
+ }
}
.getSelectedItem()).getAltCode();
wantedFields = UniProtFTSRestClient.getInstance()
- .getAllDefaulDisplayedDataColumns();
+ .getAllDefaultDisplayedFTSDataColumns();
String searchTerm = decodeSearchTerm(txt_search.getText(),
searchTarget);
{
long startTime = System.currentTimeMillis();
pdbRestCleint = PDBFTSRestClient.getInstance();
- Collection<FTSDataColumnI> wantedFields = pdbRestCleint
- .getAllDefaulDisplayedDataColumns();
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
discoveredStructuresSet = new LinkedHashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest,
+ getResultTable().setModel(
+ FTSRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
long startTime = System.currentTimeMillis();
pdbRestCleint = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<FTSDataColumnI> wantedFields = pdbRestCleint
- .getAllDefaulDisplayedDataColumns();
+ Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields();
Collection<FTSData> filteredResponse = new HashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- tbl_summary.setModel(FTSRestResponse.getTableModel(
+ getResultTable().setModel(
+ FTSRestResponse.getTableModel(
lastPdbRequest, reorderedStructuresSet));
- FTSRestResponse.configureTableColumn(tbl_summary, wantedFields);
- tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120);
- tbl_summary.getColumn("Ref Sequence").setMinWidth(100);
- tbl_summary.getColumn("Ref Sequence").setMaxWidth(200);
+ FTSRestResponse.configureTableColumn(getResultTable(),
+ wantedFields);
+ getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
+ getResultTable().getColumn("Ref Sequence").setMinWidth(100);
+ getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
// Update table selection model here
- tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+ getResultTable().addRowSelectionInterval(0,
+ filterResponseCount - 1);
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_filter_time", totalTime));
}
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- if (tbl_summary.getSelectedRows().length > 0)
+ if (getResultTable().getSelectedRows().length > 0)
{
btn_view.setEnabled(true);
}
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = tbl_summary.getColumn("PDB Id")
+ int pdbIdColIndex = getResultTable().getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
+ int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
.getModelIndex();
- int[] selectedRows = tbl_summary.getSelectedRows();
+ int[] selectedRows = getResultTable().getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
for (int row : selectedRows)
{
- String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
+ String pdbIdStr = getResultTable().getValueAt(row,
+ pdbIdColIndex)
.toString();
- SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
+ SequenceI selectedSeq = (SequenceI) getResultTable()
+ .getValueAt(row,
refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
{
String searchTerm = txt_search.getText().toLowerCase();
searchTerm = searchTerm.split(":")[0];
- System.out.println(">>>>> search term : " + searchTerm);
+ // System.out.println(">>>>> search term : " + searchTerm);
List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
} catch (ClassNotFoundException q)
{
}
+ StructureViewSettings.setShowSeqFeatures(true);
}
public PDBChain findChain(String id) throws Exception
private JTabbedPane pnl_filter = new JTabbedPane();
- private FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
+ protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
PreferenceSource.STRUCTURE_CHOOSER,
PDBFTSRestClient.getInstance());
protected FTSDataColumnI[] previousWantedFields;
- protected JTable tbl_summary = new JTable()
+ private JTable tbl_summary = new JTable()
{
private boolean inLayout;
}
});
- scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
- scrl_foundStructures
- .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ scrl_foundStructures.setPreferredSize(new Dimension(800, 400));
- scrl_localPDB.setPreferredSize(new Dimension(500, 300));
+ scrl_localPDB.setPreferredSize(new Dimension(800, 400));
scrl_localPDB
.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
btn_cancel.setEnabled(false);
btn_view.setVisible(false);
btn_cancel.setVisible(false);
- previousWantedFields = PDBFTSRestClient.getInstance()
- .getAllDefaulDisplayedDataColumns()
- .toArray(new FTSDataColumnI[0]);
+ previousWantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields().toArray(
+ new FTSDataColumnI[0]);
}
if (sourceTabbedPane.getTitleAt(index)
.equals(foundStructureSummary))
}
};
pnl_filter.addChangeListener(changeListener);
- pnl_filter.setPreferredSize(new Dimension(500, 300));
+ pnl_filter.setPreferredSize(new Dimension(800, 400));
pnl_filter.add(foundStructureSummary, scrl_foundStructures);
pnl_filter.add(configureCols, pdbDocFieldPrefs);
mainFrame.setVisible(true);
mainFrame.setContentPane(this);
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ Desktop.addInternalFrame(mainFrame, frameTitle, 900, 500);
}
public boolean wantedFieldsUpdated()
{
return true;
}
-
- return Arrays.equals(
- PDBFTSRestClient.getInstance()
- .getAllDefaulDisplayedDataColumns()
- .toArray(new FTSDataColumnI[0]),
- previousWantedFields) ? false : true;
+
+ FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields()
+ .toArray(new FTSDataColumnI[0]);
+ return Arrays.equals(currentWantedFields, previousWantedFields) ? false
+ : true;
}
}
}
+ public JTable getResultTable()
+ {
+ return tbl_summary;
+ }
public JComboBox<FilterOption> getCmbFilterOption()
{
return cmb_filterOption;
.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
{
- StructureMapping mapping;
+ StructureMapping siftsMapping;
try
{
- mapping = getStructureMapping(seq, pdbFile, targetChainId, pdb,
- maxChain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(mapping);
+ siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+ pdb, maxChain, sqmpping, maxAlignseq);
+ seqToStrucMapping.add(siftsMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
} catch (SiftsException e)
{
- // e.printStackTrace();
// fall back to NW alignment
System.err.println(e.getMessage());
- seqToStrucMapping.add(getNWMappings(seq, pdbFile,
- targetChainId,
- maxChain, pdb, maxAlignseq));
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ targetChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
}
}
else
{
- try
+ ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ for (PDBChain chain : pdb.getChains())
{
- ArrayList<StructureMapping> tempMapping = new ArrayList<StructureMapping>();
- for (PDBChain chain : pdb.getChains())
+ try
{
- StructureMapping mapping = getStructureMapping(seq, pdbFile,
+ StructureMapping siftsMapping = getStructureMapping(seq,
+ pdbFile,
chain.id, pdb, chain, sqmpping, maxAlignseq);
- tempMapping.add(mapping);
+ foundSiftsMappings.add(siftsMapping);
+ } catch (SiftsException e)
+ {
+ System.err.println(e.getMessage());
}
- seqToStrucMapping.addAll(tempMapping);
- } catch (SiftsException e)
+ }
+ if (!foundSiftsMappings.isEmpty())
{
- // e.printStackTrace();
- // fall back to NW alignment
- System.err.println(e.getMessage());
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
+ seqToStrucMapping.addAll(foundSiftsMappings);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
+ sqmpping);
+ }
+ else
+ {
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
}
}
}
private static final int PDB_ATOM_POS = 1;
- private static final String NOT_FOUND = "Not_Found";
-
private static final String NOT_OBSERVED = "Not_Observed";
- private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
private final static String NEWLINE = System.lineSeparator();
*/
public static File getSiftsFile(String pdbId) throws SiftsException
{
- File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
- + pdbId.toLowerCase() + ".xml.gz");
+ String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
+ + pdbId.toLowerCase() + ".xml.gz";
+ File siftsFile = new File(siftsFileName);
if (siftsFile.exists())
{
// The line below is required for unit testing... don't comment it out!!!
if (isFileOlderThanThreshold(siftsFile,
SiftsSettings.getCacheThresholdInDays()))
{
- // System.out.println("Downloaded file is out of date, hence re-downloading...");
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ File oldSiftsFile = new File(siftsFileName + "_old");
+ siftsFile.renameTo(oldSiftsFile);
+ try
+ {
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ oldSiftsFile.delete();
+ return siftsFile;
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ oldSiftsFile.renameTo(siftsFile);
+ return new File(siftsFileName);
+ }
}
- return siftsFile;
}
- siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ try
+ {
+ siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+ } catch (IOException e)
+ {
+ throw new SiftsException(e.getMessage());
+ }
return siftsFile;
}
* @param pdbId
* @return downloaded SIFTs XML file
* @throws SiftsException
+ * @throws IOException
*/
- public static File downloadSiftsFile(String pdbId) throws SiftsException
+ public static File downloadSiftsFile(String pdbId) throws SiftsException,
+ IOException
{
if (pdbId.contains(".cif"))
{
{
siftsDownloadDir.mkdirs();
}
- try
- {
// System.out.println(">> Download ftp url : " + siftsFileFTPURL);
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
outputStream.close();
inputStream.close();
// System.out.println(">>> File downloaded : " + downloadedSiftsFile);
- } catch (IOException ex)
- {
- throw new SiftsException(ex.getMessage());
- }
return new File(downloadedSiftsFile);
}
public class TestAnnotate3D
{
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void test1GIDbyId() throws Exception
{
// use same ID as standard tests given at
testRNAMLcontent(ids, null);
}
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void testIdVsContent2GIS() throws Exception
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
*
* @throws Exception
*/
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Network" }, enabled = true)
public void testPDBfileVsRNAML() throws Exception
{
PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
testRNAMLcontent(readers, pdbf);
}
- @Test(groups = { "Functional" }, enabled = false)
private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
throws Exception
{
public void getPrimaryKeyColumIndexTest()
{
Collection<FTSDataColumnI> wantedFields = ftsRestClient
- .getAllDefaulDisplayedDataColumns();
+ .getAllDefaultDisplayedFTSDataColumns();
int foundIndex = -1;
try
{
@Test(groups = { "Functional" })
public void getAllDefaulDisplayedDataColumns()
{
- Assert.assertNotNull(ftsRestClient.getAllDefaulDisplayedDataColumns());
- Assert.assertTrue(!ftsRestClient.getAllDefaulDisplayedDataColumns()
+ Assert.assertNotNull(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
+ Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.isEmpty());
- Assert.assertEquals(ftsRestClient.getAllDefaulDisplayedDataColumns()
+ Assert.assertEquals(ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.size(), 7);
}
public void getDataColumnsFieldsAsCommaDelimitedString()
{
Collection<FTSDataColumnI> wantedFields = ftsRestClient
- .getAllDefaulDisplayedDataColumns();
+ .getAllDefaultDisplayedFTSDataColumns();
String actual = ftsRestClient
.getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
Assert.assertEquals(actual,
import java.io.ByteArrayOutputStream;
import java.io.File;
+import java.io.IOException;
import java.io.PrintStream;
import java.util.HashMap;
// Assert that file isn't yet downloaded - if already downloaded, assert it
// is deleted
Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
- File siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
- FileAssert.assertFile(siftsFile);
- SiftsClient.downloadSiftsFile(testPDBId);
+ File siftsFile;
+ try
+ {
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ SiftsClient.downloadSiftsFile(testPDBId);
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
}
@Test(groups = { "Functional" })
git://source.jalview.org / jalview.git / commitdiff