/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
+ * 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/>.
+ * 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 jalview.util.MessageManager;
import java.io.IOException;
import java.util.Enumeration;
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
{
{
Cache.log.debug(
"Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(
- "Overwriting vamsas id binding."));
+ + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
if (vbound.getV_parent() != null
&& dataset != vbound.getV_parent())
{
- throw new Error(
- "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences"));
// This occurs because the dataset for the alignment we are
// trying to
}
{
boolean modified = false;
// check existing sequences in local and in document.
- Vector docseqs = new Vector(alignment
- .getAlignmentSequenceAsReference());
+ Vector docseqs = new Vector(
+ alignment.getAlignmentSequenceAsReference());
for (int i = 0; i < jal.getHeight(); i++)
{
modified |= syncToAlignmentSequence(jal.getSequenceAt(i),
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)
if (aa[i].annotations[a].secondaryStructure != ' ')
{
Glyph ss = new Glyph();
- ss
- .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
- ss
- .setContent(String
- .valueOf(aa[i].annotations[a].secondaryStructure));
+ ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ ss.setContent(String
+ .valueOf(aa[i].annotations[a].secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
an.setGroup(Integer.toString(aa[i].graphGroup));
if (aa[i].threshold != null && aa[i].threshold.displayed)
{
- an
- .addProperty(Properties.newProperty(THRESHOLD,
- Properties.FLOATTYPE, ""
- + aa[i].threshold.value));
+ an.addProperty(Properties.newProperty(THRESHOLD,
+ Properties.FLOATTYPE, "" + aa[i].threshold.value));
if (aa[i].threshold.label != null)
{
an.addProperty(Properties.newProperty(THRESHOLD
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.getViewPort().getSequenceSetId().equals(
- av.getSequenceSetId()))
+ if (tp.getViewPort().getSequenceSetId()
+ .equals(av.getSequenceSetId()))
{
DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
jal, alignment);
* 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;
else
{
alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq
- .getSequence().replace(valGapchar, gapChar), (int) valseq
- .getStart(), (int) valseq.getEnd());
+ .getSequence().replace(valGapchar, gapChar),
+ (int) valseq.getStart(), (int) valseq.getEnd());
Vobject datsetseq = (Vobject) valseq.getRefid();
if (datsetseq != null)
{
// we only write an annotation where it really exists.
Glyph ss = new Glyph();
- ss
- .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
ss.setContent(String
.valueOf(alan.annotations[a].secondaryStructure));
ae.addGlyph(ss);
/**
* 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
};
if (dojvsync)
{
- fromxml.LoadJalviewAlign(jprovider);
+ fromxml.loadJalviewAlign(jprovider);
}
} catch (Exception e)
{
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 (dojvsync)
{
- fromxml.LoadJalviewAlign(jarstream);
+ fromxml.loadJalviewAlign(jarstream);
}
} catch (Exception e)
{
if (mappings != null && mappings.length > 0)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().addMappings(mappings);
+ .getStructureSelectionManager(Desktop.instance)
+ .addMappings(mappings);
}
}
}
Object vobject = jv2vobj.remove(oldjvobject);
if (vobject == null)
{
- throw new Error(
- "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
- + oldjvobject + ")");
+ // NOTE: this happens if user deletes object in one session then updates
+ // from another client
+ throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
}
if (newjvobject != null)
{
jxml.setSkipList(skipList);
if (dojvsync)
{
- jxml.SaveState(new JarOutputStream(cappdata
+ jxml.saveState(new JarOutputStream(cappdata
.getClientOutputStream()));
}
{
// TODO raise GUI warning if user requests it.
jalview.bin.Cache.log
- .error(
- "Couldn't update jalview client application data. Giving up - local settings probably lost.",
+ .error("Couldn't update jalview client application data. Giving up - local settings probably lost.",
e);
}
}
// ///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.");
AlignmentSequence valseq = alignment.getAlignmentSequence(i);
jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
- dsseqs)
- && alseq != null)
+ dsseqs) && alseq != null)
{
// updated to sequence from the document
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 "
.toString());
av = alignFrame.getViewport();
newAlignmentViews.addElement(av);
- String title = alignment.getProvenance().getEntry(
- alignment.getProvenance().getEntryCount() - 1)
+ String title = alignment
+ .getProvenance()
+ .getEntry(
+ alignment.getProvenance().getEntryCount() - 1)
.getAction();
if (alignment.getPropertyCount() > 0)
{
{
if (glyphs[g]
.getDict()
- .equals(
- uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
+ .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
{
ss = glyphs[g].getContent();
AeContent[HASSECSTR] = true;
}
else if (glyphs[g]
.getDict()
- .equals(
- uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
+ .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
{
Cache.log.debug("ignoring hydrophobicity glyph marker.");
AeContent[HASHPHOB] = true;
if (colour == null)
{
anot[row][pos] = new jalview.datamodel.Annotation(
- (dc != null) ? dc : "", desc, (ss != null) ? ss
- .charAt(0) : ' ', val);
+ (dc != null) ? dc : "", desc,
+ (ss != null) ? ss.charAt(0) : ' ', val);
}
else
{
anot[row][pos] = new jalview.datamodel.Annotation(
- (dc != null) ? dc : "", desc, (ss != null) ? ss
- .charAt(0) : ' ', val, colour);
+ (dc != null) ? dc : "", desc,
+ (ss != null) ? ss.charAt(0) : ' ', val, colour);
}
}
else
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
}
} catch (Exception e)
{
- throw new Exception("Couldn't store sequence mappings for " + title,
- e);
+ throw new Exception(MessageManager.formatMessage("exception.couldnt_store_sequence_mappings", new String[]{title}),e);
}
}
git://source.jalview.org / jalview.git / blobdiff