import jalview.gui.WebserviceInfo;
import jalview.io.packed.DataProvider;
import jalview.io.packed.JalviewDataset;
+import jalview.io.packed.JalviewDataset.AlignmentSet;
import jalview.io.packed.ParsePackedSet;
import jalview.io.packed.SimpleDataProvider;
import jalview.io.packed.DataProvider.JvDataType;
public RestJobThread(RestClient restClient)
{
- super();
+ super(restClient.af, null, restClient._input,
+ restClient.service.postUrl);
this.restClient = restClient; // may not be needed
// Test Code
// minimal job - submit given input and parse result onto alignment as
* annotation/features.
*/
/**
- * alignments. New alignments are added to dataset, and subsequently
- * annotated/visualised accordingly. 1. New alignment frame created for new
- * alignment. Decide if any vis settings should be inherited from old
- * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to
- * alignment as below:
+ * alignment panels derived from each alignment set returned by service.
*/
+ ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>();
/**
- * annotation update to original/newly created context alignment: 1.
- * identify alignment where annotation is to be loaded onto. 2. Add
- * annotation, excluding any duplicates. 3. Ensure annotation is visible on
- * alignment - honouring ordering given by file.
+ * current pane being worked with
*/
+ jalview.gui.AlignmentPanel destPanel;
/**
- * features updated to original or newly created context alignment: 1.
- * Features are(or were already) added to dataset. 2. Feature settings
- * modified to ensure all features are displayed - honouring any ordering
- * given by result file. Consider merging action with the code used by the
- * DAS fetcher to update alignment views with new info.
+ * when false, zeroth pane is panel derived from input deta.
*/
- /**
- * Seq associated data files (PDB files). 1. locate seq association in
- * current dataset/alignment context and add file as normal - keep handle of
- * any created ref objects. 2. decide if new data should be displayed : PDB
- * display: if alignment has PDB display already, should new pdb files be
- * aligned to it ?
- *
- */
- jalview.gui.AlignmentPanel destPanel = null;
+ boolean newAlignment = false;
if (merge)
{
if (!restClient.isAlignmentModified())
{
destPanel = destPanel.alignFrame.newView(false);
}
+ // add the destination panel to frame zero of result panel set
+ destPanels.add(destPanel);
}
}
- if (destPanel == null)
+ if (destPanels.size()==0)
{
- Object[] idat = input.getAlignmentAndColumnSelection(restClient.av.getGapCharacter());
+ Object[] idat = input.getAlignmentAndColumnSelection(restClient.av
+ .getGapCharacter());
AlignFrame af = new AlignFrame((AlignmentI) idat[0],
(ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
AlignFrame.DEFAULT_HEIGHT);
destPanel = af.alignPanel;
// create totally new alignment from stashed data/results
+ newAlignment = true;
}
- else
+ // Now process results, adding/creating new views as necessary.
{
+ boolean hsepjobs = restClient.service.isHseparable();
+ boolean vsepjobs = restClient.service.isVseparable();
+ // total number of distinct alignment sets generated by job set.
+ int totalSets = 0, numAlSets = 0;
for (int j = 0; j < jobs.length; j++)
{
RestJob rj = (RestJob) jobs[j];
- if (rj.jvresultobj!=null && rj.jvresultobj.length>0) {
- // transfer results onto panel
-
+ if (rj.hasResults())
+ {
+ JalviewDataset rset = rj.context;
+ numAlSets = rset.hasAlignments() ? 0 : rset.getAl().size();
+ if (numAlSets > 0)
+ {
+ for (int als = 0; als < numAlSets; als++)
+ {
+ // gather data from context
+ if (vsepjobs)
+ {
+ // todo: merge data from each group/sequence onto whole
+ // alignment
+ }
+ else
+ {
+ if (hsepjobs)
+ {
+ // map single result back on to all visible region of original alignment
+ if (als==0 && rj.isInputContextModified())
+ {
+ // transfer features, annotation, groups, etc, from input context to align panel derived from input data
+ new jalview.datamodel.Alignment(new jalview.datamodel.SequenceI[] {null}).getAlignmentAnnotation();
+ }
+
+ }
+ else
+ {
+ // map result onto visible contigs.
+ AlignmentSet alset = rset.getAl().get(als);
+ if (als>0 )
+ if (als == 0)
+ {
+
+ // alignment is added straight to
+ }
+ }
+ }
+ }
+ }
}
+ // transfer results onto panel
+
}
+ /**
+ * alignments. New alignments are added to dataset, and subsequently
+ * annotated/visualised accordingly. 1. New alignment frame created for
+ * new alignment. Decide if any vis settings should be inherited from old
+ * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to
+ * alignment as below:
+ */
+ /**
+ * annotation update to original/newly created context alignment: 1.
+ * identify alignment where annotation is to be loaded onto. 2. Add
+ * annotation, excluding any duplicates. 3. Ensure annotation is visible
+ * on alignment - honouring ordering given by file.
+ */
+ /**
+ * features updated to original or newly created context alignment: 1.
+ * Features are(or were already) added to dataset. 2. Feature settings
+ * modified to ensure all features are displayed - honouring any ordering
+ * given by result file. Consider merging action with the code used by the
+ * DAS fetcher to update alignment views with new info.
+ */
+ /**
+ * Seq associated data files (PDB files). 1. locate seq association in
+ * current dataset/alignment context and add file as normal - keep handle
+ * of any created ref objects. 2. decide if new data should be displayed :
+ * PDB display: if alignment has PDB display already, should new pdb files
+ * be aligned to it ?
+ *
+ */
+
}
- destPanel.adjustAnnotationHeight();
-
+ // destPanel.adjustAnnotationHeight();
}
git://source.jalview.org / jalview.git / commitdiff