/*
- * 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 2.9)
+ * Copyright (C) 2015 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 jalview.viewmodel.AlignmentViewport;
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.Set;
import java.util.Vector;
import java.util.jar.JarInputStream;
import java.util.jar.JarOutputStream;
-import uk.ac.vamsas.client.*;
-import uk.ac.vamsas.objects.core.*;
+import uk.ac.vamsas.client.IClientAppdata;
+import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation;
+import uk.ac.vamsas.objects.core.AnnotationElement;
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DataSetAnnotations;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Glyph;
+import uk.ac.vamsas.objects.core.Local;
+import uk.ac.vamsas.objects.core.MapType;
+import uk.ac.vamsas.objects.core.Mapped;
+import uk.ac.vamsas.objects.core.Property;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.RangeAnnotation;
+import uk.ac.vamsas.objects.core.RangeType;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.core.VAMSAS;
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
{
private void buildSkipList()
{
skipList = new Hashtable();
- AlignFrame[] al = Desktop.getAlignframes();
+ AlignFrame[] al = Desktop.getAlignFrames();
for (int f = 0; al != null && f < al.length; f++)
{
skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug(
- "Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(
- "Overwriting vamsas id binding."));
+ Cache.log
+ .debug("Warning? Overwriting existing vamsas id binding for "
+ + vobj.getVorbaId(),
+ new Exception(
+ MessageManager
+ .getString("exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
&& 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.");
+ 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);
* @return true if alignment associated with this view will be stored in
* document.
*/
- public boolean alignmentWillBeSkipped(AlignViewport av)
+ public boolean alignmentWillBeSkipped(AlignmentViewport av)
{
return (!av.getAlignment().isAligned());
}
- private void addToSkipList(AlignViewport av)
+ private void addToSkipList(AlignmentViewport av)
{
if (skipList == null)
{
* 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);
an.addProperty(Properties.newProperty(THRESHOLD,
Properties.FLOATTYPE, "" + alan.getThreshold().value));
if (alan.getThreshold().label != null)
+ {
an.addProperty(Properties.newProperty(THRESHOLD + "Name",
Properties.STRINGTYPE, "" + alan.getThreshold().label));
+ }
}
((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
bindjvvobj(alan, an);
end = start;
start = t;
}
- return new int[]
- { start, end, pol < 0 ? 1 : 0 };
+ return new int[] { start, end, pol < 0 ? 1 : 0 };
}
/**
/**
* 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)
{
// sync,
// and if any contain more than one view, then remove the one generated by
// document update.
- AlignViewport views[], av = null;
+ AlignmentViewport views[], av = null;
AlignFrame af = null;
Iterator newviews = newAlignmentViews.iterator();
while (newviews.hasNext())
{
- av = (AlignViewport) newviews.next();
+ av = (AlignmentViewport) newviews.next();
af = Desktop.getAlignFrameFor(av);
// TODO implement this : af.getNumberOfViews
String seqsetidobj = av.getSequenceSetId();
// to the align frames.
boolean gathered = false;
String newviewid = null;
- AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames();
+ Set<AlignedCodonFrame> mappings = av.getAlignment()
+ .getCodonFrames();
for (int i = 0; i < views.length; i++)
{
if (views[i] != av)
{
// ensure sequence mappings from vamsas document view still
// active
- if (mappings != null && mappings.length > 0)
+ if (mappings != null)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().addMappings(mappings);
+ .getStructureSelectionManager(Desktop.instance)
+ .registerMappings(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.");
uk.ac.vamsas.objects.core.Alignment alignment = dataset
.getAlignment(al);
// TODO check this handles multiple views properly
- AlignViewport av = findViewport(alignment);
+ AlignmentViewport av = findViewport(alignment);
jalview.datamodel.AlignmentI jal = null;
if (av != null)
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)
{
return newAlignmentViews.size();
}
- public AlignViewport findViewport(Alignment alignment)
+ public AlignmentViewport findViewport(Alignment alignment)
{
- AlignViewport av = null;
- AlignViewport[] avs = Desktop
+ AlignmentViewport av = null;
+ AlignmentViewport[] avs = Desktop
.getViewports((String) getvObj2jv(alignment));
if (avs != null)
{
// may not quite cope with this (without binding an array of annotations to
// a vamsas alignment annotation)
// summary flags saying what we found over the set of annotation rows.
- boolean[] AeContent = new boolean[]
- { false, false, false, false, false };
+ boolean[] AeContent = new boolean[] { false, false, false, false, false };
int[] rangeMap = getMapping(annotation);
jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
{ new jalview.datamodel.Annotation[rangeMap.length],
{
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
anot[1][i].description = anot[1][i].description + " (after)";
}
}
- return new Object[]
- { AeContent, rangeMap, anot[0], anot[1] };
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
}
else
{
// no annotations to parse. Just return an empty annotationElement[]
// array.
- return new Object[]
- { AeContent, rangeMap, anot[0], anot[1] };
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
}
// return null;
}
Cache.log.warn("Failed to parse threshold property");
}
if (val != null)
+ {
if (gl == null)
{
gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
{
gl.value = val.floatValue();
}
+ }
}
else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
{
if (gl == null)
+ {
gl = new GraphLine(0, "", java.awt.Color.black);
+ }
gl.label = props[p].getContent();
}
}
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
// could do a polarity for pos range too. and pass back indication of
// discontinuities.
int pos = dseta.getPos(0).getI();
- se = new int[]
- { pos, pos };
+ se = new int[] { pos, pos };
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
throw new Error(
- "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
* initialise a range type object from a set of start/end inclusive intervals
*
* @param mrt
- * @param range
+ * @param ranges
*/
- private void initRangeType(RangeType mrt, int[] range)
+ private void initRangeType(RangeType mrt, List<int[]> ranges)
{
- for (int i = 0; i < range.length; i += 2)
+ for (int[] range : ranges)
{
Seg vSeg = new Seg();
- vSeg.setStart(range[i]);
- vSeg.setEnd(range[i + 1]);
+ vSeg.setStart(range[0]);
+ vSeg.setEnd(range[1]);
mrt.addSeg(vSeg);
}
}
return vobj2jv;
}
- public void storeSequenceMappings(AlignViewport viewport, String title)
+ public void storeSequenceMappings(AlignmentViewport viewport, String title)
throws Exception
{
- AlignViewport av = viewport;
+ AlignmentViewport av = viewport;
try
{
jalview.datamodel.AlignmentI jal = av.getAlignment();
}
// Store any sequence mappings.
- if (av.getAlignment().getCodonFrames() != null
- && av.getAlignment().getCodonFrames().length > 0)
+ Set<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
+ if (cframes != null)
{
- jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment()
- .getCodonFrames();
- for (int cf = 0; cf < cframes.length; cf++)
+ for (AlignedCodonFrame acf : cframes)
{
- if (cframes[cf].getdnaSeqs() != null
- && cframes[cf].getdnaSeqs().length > 0)
+ if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
{
- jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
- jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
+ jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
+ jalview.datamodel.Mapping[] mps = acf.getProtMappings();
for (int smp = 0; smp < mps.length; smp++)
{
uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);
}
} 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