import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
public void testRetrieveAndShowCrossref() throws Exception
{
- List<String> failedDBRetr = new ArrayList<String>();
- List<String> failedXrefMenuItems = new ArrayList<String>();
- List<String> failedProjectRecoveries = new ArrayList<String>();
-
+ List<String> failedDBRetr = new ArrayList<>();
+ List<String> failedXrefMenuItems = new ArrayList<>();
+ List<String> failedProjectRecoveries = new ArrayList<>();
+ // only search for ensembl or Uniprot crossrefs
+ List<String> limit=Arrays.asList(new String[] {
+ DBRefUtils.getCanonicalName("ENSEMBL"),
+ DBRefUtils.getCanonicalName("Uniprot")});
// for every set of db queries
// retrieve db query
// verify presence of expected xrefs
// . codonframes
//
//
- HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
- List<String> keyseq = new ArrayList<String>();
- HashMap<String, File> savedProjects = new HashMap<String, File>();
+ HashMap<String, String> dbtoviewBit = new HashMap<>();
+ List<String> keyseq = new ArrayList<>();
+ HashMap<String, File> savedProjects = new HashMap<>();
- for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
- { "UNIPROT", "P01731" } })
+ for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
{
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
Desktop.instance.closeAll_actionPerformed(null);
// recover stored project
af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
- .get(first).toString(), FormatAdapter.FILE);
+ .get(first).toString(), DataSourceType.FILE);
System.out.println("Recovered view for '" + first + "' from '"
+ savedProjects.get(first).toString() + "'");
dna = af.getViewport().getAlignment().isNucleotide();
ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
seqs, dataset).findXrefSourcesForSequences(dna);
-
+ filterDbRefs(ptypes, limit);
+
// start of pass2: retrieve each cross-ref for fetched or restored
// project.
do // first cross ref and recover crossref loop
// build next key so we an retrieve all views
String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
// perform crossref action, or retrieve stored project
- List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
+ List<AlignmentViewPanel> cra_views = new ArrayList<>();
CrossRefAction cra = null;
if (pass2 == 0)
// recover stored project
AlignFrame af2 = new FileLoader(false)
.LoadFileWaitTillLoaded(savedProjects.get(nextxref)
- .toString(), FormatAdapter.FILE);
+ .toString(), DataSourceType.FILE);
System.out.println("Recovered view for '" + nextxref
+ "' from '" + savedProjects.get(nextxref).toString()
+ "'");
}
}
- HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+ HashMap<String, List<String>> xrptypes = new HashMap<>();
// first save/verify views.
for (AlignmentViewPanel avp : cra_views)
{
nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
for (String xrefdb : xrptypes.get(nextxref))
{
- List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
int q = 0;
String nextnextxref = nextxref + " -> " + xrefdb + "{"
+ q + "}";
AlignFrame af2 = new FileLoader(false)
.LoadFileWaitTillLoaded(
savedProjects.get(nextnextxref)
- .toString(), FormatAdapter.FILE);
+ .toString(),
+ DataSourceType.FILE);
System.out.println("Recovered view for '"
+ nextnextxref + "' from '"
+ savedProjects.get(nextnextxref).toString()
}
}
+ private void filterDbRefs(List<String> ptypes, List<String> limit)
+ {
+ if (limit != null)
+ {
+ int p = 0;
+ while (ptypes.size() > p)
+ {
+ if (!limit.contains(ptypes.get(p)))
+ {
+ ptypes.remove(p);
+ }
+ else
+ {
+ p++;
+ }
+ }
+ }
+ }
+
/**
* wrapper to trap known defect for AH002001 testcase
*
private void assertType(boolean expectProtein,
AlignmentViewPanel alignmentViewPanel, String message)
{
- List<SequenceI> nonType = new ArrayList<SequenceI>();
+ List<SequenceI> nonType = new ArrayList<>();
for (SequenceI sq : alignmentViewPanel.getAlignViewport()
.getAlignment().getSequences())
{