/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.io;
import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.io.vamsas.DatastoreItem;
import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
-import jalview.util.UrlLink;
-
import java.io.IOException;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
+import java.util.List;
import java.util.Vector;
import java.util.jar.JarInputStream;
import java.util.jar.JarOutputStream;
import uk.ac.vamsas.objects.utils.Properties;
/*
- *
+ *
* static {
* org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
* "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
- *
+ *
*/
/*
- * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
+ * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
*/
public class VamsasAppDatastore
{
else
{
// first find the alignment sequence to associate this with.
- SequenceI jvalsq = null;
- Enumeration jval = av.getAlignment().getSequences()
- .elements();
- while (jval.hasMoreElements())
+ for (SequenceI jvalsq : av.getAlignment().getSequences())
{
- jvalsq = (SequenceI) jval.nextElement();
// saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
// sref, aa[i]);
if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
* creates/syncs the jvalsq from the alignment sequence
*/
private boolean syncFromAlignmentSequence(AlignmentSequence valseq,
- char valGapchar, char gapChar, Vector dsseqs)
+ char valGapchar, char gapChar, List<SequenceI> dsseqs)
{
boolean modal = false;
/**
* list of alignment views created when updating Jalview from document.
*/
- private Vector newAlignmentViews = new Vector();
+ private final Vector newAlignmentViews = new Vector();
/**
* update local jalview view settings from the stored appdata (if any)
jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
{
+ @Override
public String getFilename()
{
return "Jalview Vamsas Document Client Data";
}
+ @Override
public JarInputStream getJarInputStream() throws IOException
{
jalview.bin.Cache.log
jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
{
+ @Override
public String getFilename()
{
return "Jalview Vamsas Document User Data";
}
+ @Override
public JarInputStream getJarInputStream() throws IOException
{
jalview.bin.Cache.log
if (mappings != null && mappings.length > 0)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).addMappings(mappings);
+ .getStructureSelectionManager(Desktop.instance)
+ .addMappings(mappings);
}
}
}
Object vobject = jv2vobj.remove(oldjvobject);
if (vobject == null)
{
+ // NOTE: this happens if user deletes object in one session then updates
+ // from another client
throw new Error(
"IMPLEMENTATION ERROR: old jalview object is not bound ! ("
+ oldjvobject + ")");
// ///LOAD DATASET
DataSet dataset = root.getDataSet(_ds);
int i, iSize = dataset.getSequenceCount();
- Vector dsseqs;
+ List<SequenceI> dsseqs;
jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
int jremain = 0;
if (jdataset == null)
SequenceI[] seqs = new SequenceI[dsseqs.size()];
for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
{
- seqs[i] = (SequenceI) dsseqs.elementAt(i);
- dsseqs.setElementAt(null, i);
+ seqs[i] = dsseqs.get(i);
+ dsseqs.set(i, null);
}
jdataset = new jalview.datamodel.Alignment(seqs);
Cache.log.debug("New vamsas dataset imported into jalview.");
SequenceI[] seqs = new SequenceI[dsseqs.size()];
for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
{
- seqs[i] = (SequenceI) dsseqs.elementAt(i);
- dsseqs.setElementAt(null, i);
+ seqs[i] = dsseqs.get(i);
+ dsseqs.set(i, null);
}
jal = new jalview.datamodel.Alignment(seqs);
Cache.log.debug("New vamsas alignment imported into jalview "
git://source.jalview.org / jalview.git / blobdiff