+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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.List;
import java.util.Map;
-import java.util.Map.Entry;
import java.util.Set;
import java.util.Vector;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
-import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.io.packed.DataProvider;
import jalview.io.packed.JalviewDataset;
-import jalview.io.packed.ParsePackedSet;
-import jalview.io.packed.SimpleDataProvider;
-import jalview.io.packed.DataProvider.JvDataType;
import jalview.ws.AWsJob;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.SeqGroupIndexVector;
*/
int[] origviscontig;
- private AlignmentI contextAl=null;
+ private AlignmentI contextAl = null;
/**
* create a rest job using data bounded by the given start/end column.
// get sequences for the alignmentI
// get groups trimmed to alignment columns
// get any annotation trimmed to start/end columns, too.
-
+ squniq = jalview.analysis.SeqsetUtils.uniquify(
+ _input.getSequencesArray(), true);
// prepare input
// form alignment+groups+annotation,preprocess and then record references
// for formatters
ArrayList<InputType> alinp = new ArrayList<InputType>();
int paramsWithData = 0;
+ // TODO: JAL-715 - generalise the following validation logic for all
+ // parameter types
// we cheat for moment - since we know a-priori what data is available and
// what inputs we have implemented so far
for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet())
}
else
{
- // TODO: move validation of input data to SeqGroupIndexVector
- if ((prm.getValue() instanceof SeqGroupIndexVector)
- && (_input.getGroups() != null && _input.getGroups()
- .size() >= prm.getValue().min))
+ if (prm.getValue() instanceof SeqGroupIndexVector
+ && _input.getGroups() != null
+ && _input.getGroups().size() >= -1 + prm.getValue().min)
{
+ // the test above is not rigorous but fixes JAL-1298, since
+ // submission will fail if the partition set doesn't contain at
+ // least one partition
alinp.add(prm.getValue());
- } else {
- statMessage=("Not enough groups defined on the alignment - need at least "+prm.getValue().min);
+ }
+ else
+ {
+ statMessage = ("Not enough groups defined on the alignment - need at least " + prm
+ .getValue().min);
}
}
}
_input.setDataset(null);
}
dsForIO = _input.getDataset();
- if (contextAl==null)
+ if (contextAl == null)
{
contextAl = _input;
}
validInput = false;
}
}
-
+
boolean validInput = false;
@Override
if (context == null)
{
context = new JalviewDataset(dsForIO, null, squniq, null);
- if (contextAl!=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()) {
+ // 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)
+ // 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);
}
-
+
}
return context;
}
* context used to parse results from service
*/
JalviewDataset context = null;
+
protected boolean parsedResults = false;
- protected boolean validJvresults=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. Use hasResults to test if results were added to context.
+ * 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
{
- if (!parsedResults) {
- parsedResults=true;
+ 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
+ * @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 contextAl != null && validJvresults
+ && context.getAl().get(0).isModified();
}
/**
*
- * @return true if the ID/metadata for the input sequences were saved and sequence IDs renamed.
+ * @return true if the ID/metadata for the input sequences were saved and
+ * sequence IDs renamed.
*/
public boolean isInputUniquified()
{
}
/**
- * Return map between ordering of alignment submitted as input, and ordering of alignment as provided by user
+ * 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++)
+ 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
+ // 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;
git://source.jalview.org / jalview.git / blobdiff