+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
package jalview.ws.rest;
import java.io.IOException;
+import java.sql.ResultSet;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Hashtable;
import java.util.Set;
import java.util.Vector;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
}
else
{
+ // TODO: move validation of input data to SeqGroupIndexVector
if ((prm.getValue() instanceof SeqGroupIndexVector)
&& (_input.getGroups() != null && _input.getGroups()
- .size() > 0))
+ .size() >= prm.getValue().min))
{
alinp.add(prm.getValue());
+ } else {
+ statMessage=("Not enough groups defined on the alignment - need at least "+prm.getValue().min);
}
}
}
validInput = false;
}
}
-
+
boolean validInput = false;
@Override
public boolean hasResults()
{
- return gotresult;
+ return gotresult && (parsedResults ? validJvresults : true);
}
@Override
context = new JalviewDataset(dsForIO, null, squniq, null);
if (contextAl!=null)
{
+ // TODO devise way of merging new annotation onto (identical) existing annotation that was used as input
+ // delete all input annotation
+ if (contextAl.getAlignmentAnnotation()!=null) {
+ for (AlignmentAnnotation alan: contextAl.getAlignmentAnnotation()) {
+ contextAl.deleteAnnotation(alan);
+ }
+ }
+ // TODO devise way of merging new groups onto (identical) existing groups when they were used as input to service
+ // delete all existing groups
+ if (contextAl.getGroups()!=null)
+ {
+ contextAl.deleteAllGroups();
+ }
context.addAlignment(contextAl);
}
* context used to parse results from service
*/
JalviewDataset context = null;
-
+ protected boolean parsedResults = false;
+ protected boolean validJvresults=false;
Object[] jvresultobj = null;
-
/**
* process the results obtained from the server into jalview datamodel objects
- * ready to be merged/added to the users' view.
+ * ready to be merged/added to the users' view. Use hasResults to test if results were added to context.
*/
public void parseResultSet() throws Exception, Error
{
- jvresultobj = resSet.parseResultSet();
+ if (!parsedResults) {
+ parsedResults=true;
+ jvresultobj = resSet.parseResultSet();
+ validJvresults = true;
+ }
+ }
+
+ /**
+ *
+ * @return true if job has an input alignment and it was annotated when results were parsed
+ */
+ public boolean isInputContextModified()
+ {
+ return contextAl!=null && validJvresults && context.getAl().get(0).isModified();
+ }
+
+ /**
+ *
+ * @return true if the ID/metadata for the input sequences were saved and sequence IDs renamed.
+ */
+ public boolean isInputUniquified()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ /**
+ * Return map between ordering of alignment submitted as input, and ordering of alignment as provided by user
+ * @return int[sequence index in submitted data]==sequence index in input.
+ */
+ public int[] getOrderMap()
+ {
+ SequenceI[] contseq = contextAl.getSequencesArray();
+ int map[] = new int[contseq.length];
+ for (int i=0;i<contseq.length;i++)
+ {
+ // TODO: optimise for large N - build a lookup hash for IDs returning order, and then lookup each sequ's original order
+ map[i] = inputOrder.getOrder().indexOf(contseq[i]);
+ }
+ return map;
}
}