*
*/
-public class VamsasDatastore {
+public class VamsasDatastore
+{
Entry provEntry = null;
// AlignViewport av;
IdentityHashMap jv2vobj;
public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,
- IdentityHashMap jv2vobj, Entry provEntry) {
- this.cdoc = cdoc;
+ IdentityHashMap jv2vobj, Entry provEntry)
+ {
+ this.cdoc = cdoc;
this.vobj2jv = vobj2jv;
this.jv2vobj = jv2vobj;
this.provEntry = provEntry;
/**
* @return the Vobject bound to Jalview datamodel object
*/
- protected Vobject getjv2vObj(Object jvobj) {
+ protected Vobject getjv2vObj(Object jvobj)
+ {
if (jv2vobj.containsKey(jvobj))
- return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
+ {
+ return cdoc.getObject( (VorbaId) jv2vobj.get(jvobj));
+ }
return null;
}
* @param vobj
* @return Jalview datamodel object bound to the vamsas document object
*/
- protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {
+ protected Object getvObj2jv(org.vamsas.client.Vobject vobj)
+ {
VorbaId id = vobj.getVorbaId();
if (id == null)
{
id = cdoc.registerObject(vobj);
Cache.log
- .debug("Registering new object and returning null for getvObj2jv");
+ .debug("Registering new object and returning null for getvObj2jv");
return null;
}
if (vobj2jv.containsKey(vobj.getVorbaId()))
+ {
return vobj2jv.get(vobj.getVorbaId());
+ }
return null;
}
- protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {
+ protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj)
+ {
VorbaId id = vobj.getVorbaId();
if (id == null)
{
id = cdoc.registerObject(vobj);
- if (id==null || vobj.getVorbaId()==null)
- Cache.log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);
+ if (id == null || vobj.getVorbaId() == null)
+ {
+ Cache.log.error("Failed to get id for " +
+ (vobj.isRegisterable() ? "registerable" :
+ "unregisterable") + " object " + vobj);
+ }
}
- 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."));
+ 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."));
}
- else if (jv2vobj.containsKey(jvobj) && !((VorbaId)jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
+ else if (jv2vobj.containsKey(jvobj) &&
+ ! ( (VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug("Warning? Overwriting existing jalview object binding for "+jvobj, new Exception("Overwriting jalview object binding."));
+ Cache.log.debug(
+ "Warning? Overwriting existing jalview object binding for " + jvobj,
+ new Exception("Overwriting jalview object binding."));
}
/* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to bindjvvobj"));
- }*/
+ }*/
// we just update the hash's regardless!
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
* @param av alignViewport to be stored
* @param aFtitle title for alignment
*/
- public void storeVAMSAS(AlignViewport av, String aFtitle) {
+ public void storeVAMSAS(AlignViewport av, String aFtitle)
+ {
try
{
jalview.datamodel.AlignmentI jal = av.getAlignment();
// flag.
// this *will* break when alignment contains both nucleotide and amino
// acid sequences.
- String dict = jal.isNucleotide() ? org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+ String dict = jal.isNucleotide() ?
+ org.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
: org.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
for (int i = 0; i < jal.getHeight(); i++)
{
for (int sf = 0; sf < sfSize; sf++)
{
- jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq
- .getSequenceFeatures()[sf];
+ jalview.datamodel.SequenceFeature feature = (jalview.datamodel.
+ SequenceFeature) sq
+ .getSequenceFeatures()[sf];
DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature);
if (dsa == null)
// contain more residues than were originally referenced - we must
// then make a number of dataset sequence entries
System.out
- .println("update dataset sequence database references.");
+ .println("update dataset sequence database references.");
}
}
alignment = new Alignment();
bindjvvobj(av, alignment);
if (alignment.getProvenance() == null)
+ {
alignment.setProvenance(new Provenance());
+ }
addProvenance(alignment.getProvenance(), "added"); // TODO: insert some
// sensible source
// here
else
{
System.out
- .println("update edited alignment to new alignment in document.");
+ .println("update edited alignment to new alignment in document.");
}
}
// ////////////////////////////////////////////
// SAVE Alignment Sequence Features
- for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
+ for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize;
+ i++)
{
AlignmentSequence valseq;
SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
- .getAlignmentSequence(i));
+ .getAlignmentSequence(i));
if (alseq != null && alseq.getSequenceFeatures() != null)
{
jalview.datamodel.SequenceFeature[] features = alseq
- .getSequenceFeatures();
+ .getSequenceFeatures();
for (int f = 0; f < features.length; f++)
{
if (features[f] != null)
{
- AlignmentSequenceAnnotation valseqf = (AlignmentSequenceAnnotation) getjv2vObj(features[i]);
+ AlignmentSequenceAnnotation valseqf = (
+ AlignmentSequenceAnnotation) getjv2vObj(features[i]);
if (valseqf == null)
{
- valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
- new AlignmentSequenceAnnotation(), features[i]);
+ valseqf = (AlignmentSequenceAnnotation)
+ getDSAnnotationFromJalview(
+ new AlignmentSequenceAnnotation(), features[i]);
if (valseqf.getProvenance() == null)
{
valseqf.setProvenance(new Provenance());
if (jal.getAlignmentAnnotation() != null)
{
jalview.datamodel.AlignmentAnnotation[] aa = jal
- .getAlignmentAnnotation();
+ .getAlignmentAnnotation();
java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
// alignment columns to
// sequence positions.
}
if (aa[i].sequenceRef != null)
{
- org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
- org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[i]);
+ org.vamsas.objects.core.AlignmentSequence alsref = (org.vamsas.
+ objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
+ org.vamsas.objects.core.AlignmentSequenceAnnotation an = (org.
+ vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[
+ i]);
int[] gapMap = null;
if (AlSeqMaps.containsKey(aa[i].sequenceRef))
{
// map from alignment position to sequence position.
int[] sgapMap = aa[i].sequenceRef.gapMap();
for (int a = 0; a < sgapMap.length; a++)
+ {
gapMap[sgapMap[a]] = a;
+ }
}
if (an == null)
{
vSeg.setInclusive(true);
vSeg.setEnd(gapMap.length);
an.addSeg(vSeg);
- an.setType("jalview:SecondaryStructurePrediction");// TODO: better fix this rough guess ;)
+ an.setType("jalview:SecondaryStructurePrediction"); // TODO: better fix this rough guess ;)
alsref.addAlignmentSequenceAnnotation(an);
- bindjvvobj(aa[i],an);
+ bindjvvobj(aa[i], an);
// LATER: much of this is verbatim from the alignmentAnnotation
// method below. suggests refactoring to make rangeAnnotation the
// base class
an.setDescription(aa[i].description);
if (aa[i].graph > 0)
+ {
an.setGraph(true); // aa[i].graph);
+ }
else
+ {
an.setGraph(false);
+ }
an.setLabel(aa[i].label);
an.setProvenance(dummyProvenance()); // get provenance as user
// created, or jnet, or
ae.setDescription(aa[i].annotations[a].description);
ae.addGlyph(new Glyph());
ae.getGlyph(0)
- .setContent(aa[i].annotations[a].displayCharacter); // assume
+ .setContent(aa[i].annotations[a].displayCharacter); // assume
// jax-b
// takes
// care
// of
// utf8
// translation
- if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+ if (aa[i].graph !=
+ jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+ {
ae.addValue(aa[i].annotations[a].value);
- ae.setPosition(gapMap[a]+1); // position w.r.t. AlignmentSequence
+ }
+ ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
// symbols
if (aa[i].annotations[a].secondaryStructure != ' ')
{
// we only write an annotation where it really exists.
Glyph ss = new Glyph();
ss
- .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ .setDict(org.vamsas.objects.utils.GlyphDictionary.
+ PROTEIN_SS_3STATE);
ss.setContent(String
- .valueOf(aa[i].annotations[a].secondaryStructure));
+ .valueOf(aa[i].annotations[a].
+ secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
{
// verify existing alignment sequence annotation is up to date
System.out
- .println("make new alignment sequence annotation if modification has happened.");
+ .println(
+ "make new alignment sequence annotation if modification has happened.");
}
}
}
else
{
// add Alignment Annotation
- org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
+ org.vamsas.objects.core.AlignmentAnnotation an = (org.vamsas.
+ objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
if (an == null)
{
an = new org.vamsas.objects.core.AlignmentAnnotation();
vSeg.setEnd(jal.getWidth());
an.addSeg(vSeg);
if (aa[i].graph > 0)
+ {
an.setGraph(true); // aa[i].graph);
+ }
an.setLabel(aa[i].label);
an.setProvenance(dummyProvenance());
- if (aa[i].graph!=aa[i].NO_GRAPH) {
+ if (aa[i].graph != aa[i].NO_GRAPH)
+ {
an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
// originally we
- // were going to
- // store
- // graphGroup in
- // the Jalview
- // specific
- // bits.
+ // were going to
+ // store
+ // graphGroup in
+ // the Jalview
+ // specific
+ // bits.
an.setGraph(true);
- } else {
+ }
+ else
+ {
an.setGraph(false);
}
AnnotationElement ae;
for (int a = 0; a < aa[i].annotations.length; a++)
{
- if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ if ( (aa[i] == null) || (aa[i].annotations[a] == null))
{
continue;
}
ae.setDescription(aa[i].annotations[a].description);
ae.addGlyph(new Glyph());
ae.getGlyph(0)
- .setContent(aa[i].annotations[a].displayCharacter); // assume
+ .setContent(aa[i].annotations[a].displayCharacter); // assume
// jax-b
// takes
// care
// utf8
// translation
ae.addValue(aa[i].annotations[a].value);
- ae.setPosition(a+1);
+ ae.setPosition(a + 1);
if (aa[i].annotations[a].secondaryStructure != ' ')
{
Glyph ss = new Glyph();
ss
- .setDict(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ .setDict(org.vamsas.objects.utils.GlyphDictionary.
+ PROTEIN_SS_3STATE);
ss.setContent(String
- .valueOf(aa[i].annotations[a].secondaryStructure));
+ .valueOf(aa[i].annotations[a].
+ secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
}
- if (aa[i].editable) {
+ if (aa[i].editable)
+ {
//an.addProperty(newProperty("jalview:editable", null, "true"));
an.setModifiable(true);
}
- if (aa[i].graph!=jalview.datamodel.AlignmentAnnotation.NO_GRAPH) {
+ if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+ {
an.setGraph(true);
an.setGroup(Integer.toString(aa[i].graphGroup));
- an.addProperty(newProperty("jalview:graphType",null,
- ((aa[i].graph==jalview.datamodel.AlignmentAnnotation.BAR_GRAPH) ? "BAR_GRAPH" : "LINE_GRAPH")));
+ an.addProperty(newProperty("jalview:graphType", null,
+ ( (aa[i].graph ==
+ jalview.datamodel.AlignmentAnnotation.
+ BAR_GRAPH) ? "BAR_GRAPH" :
+ "LINE_GRAPH")));
/** and on and on..
vProperty=new Property();
if (an.getModifiable())
{
// verify annotation - update (perhaps)
- Cache.log.info("update alignment sequence annotation. not yet implemented.");
+ Cache.log.info(
+ "update alignment sequence annotation. not yet implemented.");
}
else
{
else
{
System.out
- .println("Add modified tree as new tree in document.");
+ .println("Add modified tree as new tree in document.");
}
}
}
}
- private Property newProperty(String name, String type, String content) {
- Property vProperty=new Property();
+ private Property newProperty(String name, String type, String content)
+ {
+ Property vProperty = new Property();
vProperty.setName(name);
- if (type!=null)
+ if (type != null)
+ {
vProperty.setType(type);
+ }
else
+ {
vProperty.setType("String");
+ }
vProperty.setContent(content);
return vProperty;
}
* @return
*/
private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
- SequenceFeature feature) {
+ SequenceFeature feature)
+ {
dsa.setType(feature.getType());
Seg vSeg = new Seg();
vSeg.setStart(feature.getBegin());
{
Link vLink = new Link();
if (sep > 0)
+ {
vLink.setContent(link.substring(0, sep - 1));
+ }
else
+ {
vLink.setContent("");
+ }
vLink.setHref(link.substring(sep + 1)); // TODO: validate href.
dsa.addLink(vLink);
}
* @param tp
* @return
*/
- private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) {
+ private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
+ {
Provenance prov = new Provenance();
prov.addEntry(new Entry());
- prov.getEntry(0).setAction("imported "+tp.getTitle());
+ prov.getEntry(0).setAction("imported " + tp.getTitle());
prov.getEntry(0).setUser(provEntry.getUser());
prov.getEntry(0).setApp(provEntry.getApp());
prov.getEntry(0).setDate(provEntry.getDate());
// the document.
// vInput.setObjRef(getjv2vObj(jal));
vInput.setObjRef(getjv2vObj(tp.getViewPort()));
- prov.getEntry(0).setAction("created "+tp.getTitle());
+ prov.getEntry(0).setAction("created " + tp.getTitle());
prov.getEntry(0).addInput(vInput);
vInput.setName("jalview:seqdist");
prov.getEntry(0).addParam(new Param());
int ranges[] = tp.getTree().seqData.getVisibleContigs();
// VisibleContigs are with respect to alignment coordinates. Still need offsets
- int start= tp.getTree().seqData.getAlignmentOrigin();
+ int start = tp.getTree().seqData.getAlignmentOrigin();
for (int r = 0; r < ranges.length; r += 2)
{
Seg visSeg = new Seg();
- visSeg.setStart(1+start+ranges[r]);
- visSeg.setEnd(start+ranges[r + 1]);
+ visSeg.setStart(1 + start + ranges[r]);
+ visSeg.setEnd(start + ranges[r + 1]);
visSeg.setInclusive(true);
vInput.addSeg(visSeg);
}
* @return Object[] { AlignmentView, AlignmentI - reference alignment for
* input }
*/
- private Object[] recoverInputData(Provenance tp) {
+ private Object[] recoverInputData(Provenance tp)
+ {
for (int pe = 0; pe < tp.getEntryCount(); pe++)
{
if (tp.getEntry(pe).getInputCount() > 0)
{
if (tp.getEntry(pe).getInputCount() > 1)
+ {
Cache.log.warn("Ignoring additional input spec in provenance entry "
- + tp.getEntry(pe).toString());
+ + tp.getEntry(pe).toString());
+ }
// LATER: deal sensibly with multiple inputs.
Input vInput = tp.getEntry(pe).getInput(0);
if (vInput.getObjRef() instanceof org.vamsas.objects.core.Alignment)
{
// recover an AlignmentView for the input data
- AlignViewport javport = (AlignViewport) getvObj2jv((org.vamsas.client.Vobject) vInput
+ AlignViewport javport = (AlignViewport) getvObj2jv( (org.vamsas.
+ client.Vobject) vInput
.getObjRef());
jalview.datamodel.AlignmentI jal = javport.getAlignment();
- jalview.datamodel.CigarArray view = javport.getAlignment().getCompactAlignment();
+ jalview.datamodel.CigarArray view = javport.getAlignment().
+ getCompactAlignment();
int from = 1, to = jal.getWidth();
- int offset=0; // deleteRange modifies its frame of reference
+ int offset = 0; // deleteRange modifies its frame of reference
for (int r = 0, s = vInput.getSegCount(); r < s; r++)
{
Seg visSeg = vInput.getSeg(r);
- int se[] = getSegRange(visSeg,true); // jalview doesn't do bidirection alignments yet.
+ int se[] = getSegRange(visSeg, true); // jalview doesn't do bidirection alignments yet.
if (to < se[1])
+ {
Cache.log.warn("Ignoring invalid segment in InputData spec.");
+ }
else
{
if (se[0] > from)
{
- view.deleteRange(offset+from-1, offset+se[0] - 2);
- offset-=se[0]-from;
+ view.deleteRange(offset + from - 1, offset + se[0] - 2);
+ offset -= se[0] - from;
}
from = se[1] + 1;
}
}
if (from < to)
{
- view.deleteRange(offset+from-1, offset+to-1); // final deletion - TODO: check off by
+ view.deleteRange(offset + from - 1, offset + to - 1); // final deletion - TODO: check off by
// one for to
}
- return new Object[] { new AlignmentView(view), jal };
+ return new Object[]
+ {
+ new AlignmentView(view), jal};
}
}
}
* @param ensureDirection when true - always ensure start is less than end.
* @return int[] { start, end, direction} where direction==1 for range running from end to start.
*/
- private int[] getSegRange(Seg visSeg, boolean ensureDirection) {
+ private int[] getSegRange(Seg visSeg, boolean ensureDirection)
+ {
boolean incl = visSeg.getInclusive();
// adjust for inclusive flag.
int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
// region.
int start = visSeg.getStart() + (incl ? 0 : pol);
int end = visSeg.getEnd() + (incl ? 0 : -pol);
- if (ensureDirection && pol==-1)
+ if (ensureDirection && pol == -1)
{
// jalview doesn't deal with inverted ranges, yet.
int t = end;
end = start;
start = t;
}
- return new int[] { start, end, pol<0 ? 1 : 0 };
+ return new int[]
+ {
+ start, end, pol < 0 ? 1 : 0};
}
/**
* @param annotation
* @return true if annotation is not to be stored in document
*/
- private boolean isJalviewOnly(AlignmentAnnotation annotation) {
+ private boolean isJalviewOnly(AlignmentAnnotation annotation)
+ {
return annotation.label.equals("Quality")
- || annotation.label.equals("Conservation")
- || annotation.label.equals("Consensus");
+ || annotation.label.equals("Conservation")
+ || annotation.label.equals("Consensus");
}
+
/**
* This will return the first AlignFrame viewing AlignViewport av.
* It will break if there are more than one AlignFrames viewing a particular av.
* @param av
* @return alignFrame for av
*/
- public AlignFrame getAlignFrameFor(AlignViewport av) {
+ public AlignFrame getAlignFrameFor(AlignViewport av)
+ {
if (Desktop.desktop != null)
{
javax.swing.JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int t = 0; t < frames.length; t++)
{
- if (frames[t] instanceof AlignFrame) {
- if (((AlignFrame) frames[t]).getViewport()==av)
+ if (frames[t] instanceof AlignFrame)
+ {
+ if ( ( (AlignFrame) frames[t]).getViewport() == av)
+ {
return (AlignFrame) frames[t];
+ }
}
}
}
return null;
}
- public void updateToJalview() {
+
+ public void updateToJalview()
+ {
VAMSAS _roots[] = cdoc.getVamsasRoots();
- for (int _root = 0; _root<_roots.length; _root++) {
+ for (int _root = 0; _root < _roots.length; _root++)
+ {
VAMSAS root = _roots[_root];
- boolean newds=false;
- for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {
+ boolean newds = false;
+ for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
+ {
// ///////////////////////////////////
// ///LOAD DATASET
DataSet dataset = root.getDataSet(_ds);
int i, iSize = dataset.getSequenceCount();
Vector dsseqs;
- jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
- int jremain=0;
- if (jdataset==null) {
+ jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment)
+ getvObj2jv(dataset);
+ int jremain = 0;
+ if (jdataset == null)
+ {
Cache.log.debug("Initialising new jalview dataset fields");
- newds=true;
- dsseqs=new Vector();
- } else {
+ newds = true;
+ dsseqs = new Vector();
+ }
+ else
+ {
Cache.log.debug("Update jalview dataset from vamsas.");
- jremain=jdataset.getHeight();
- dsseqs=jdataset.getSequences();
+ jremain = jdataset.getHeight();
+ dsseqs = jdataset.getSequences();
}
// TODO: test sequence merging - we preserve existing non vamsas
// sequences but add in any new vamsas ones, and don't yet update any
// sequence attributes
- for (i = 0; i < iSize ; i++)
+ for (i = 0; i < iSize; i++)
{
Sequence vdseq = dataset.getSequence(i);
jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq);
- if (dsseq!=null) {
+ if (dsseq != null)
+ {
if (!dsseq.getSequence().equals(vdseq.getSequence()))
- throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
+ {
+ throw new Error(
+ "Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
+ }
jremain--;
- } else {
+ }
+ else
+ {
dsseq = new jalview.datamodel.Sequence(
dataset.getSequence(i).getName(),
dataset.getSequence(i).getSequence(),
dataset.getSequence(i).getStart(),
- dataset.getSequence(i).getEnd() );
+ dataset.getSequence(i).getEnd());
dsseq.setDescription(dataset.getSequence(i).getDescription());
bindjvvobj(dsseq, dataset.getSequence(i));
dsseq.setVamsasId(dataset.getSequence(i).getVorbaId().getId());
dsseqs.add(dsseq);
}
- if (vdseq.getDbRefCount()>0) {
- DbRef [] dbref = vdseq.getDbRef();
- for(int db=0; db<dbref.length; db++)
+ if (vdseq.getDbRefCount() > 0)
+ {
+ DbRef[] dbref = vdseq.getDbRef();
+ for (int db = 0; db < dbref.length; db++)
{
- jalview.datamodel.DBRefEntry dbr=(jalview.datamodel.DBRefEntry) getvObj2jv(dbref[db]);
- if (dbr==null) {
+ jalview.datamodel.DBRefEntry dbr = (jalview.datamodel.DBRefEntry)
+ getvObj2jv(dbref[db]);
+ if (dbr == null)
+ {
// add new dbref
- dsseq.addDBRef(dbr= new jalview.datamodel.DBRefEntry
- (
- dbref[db].getSource().toString(),
- dbref[db].getVersion().toString(),
- dbref[db].getAccessionId().toString()));
+ dsseq.addDBRef(dbr = new jalview.datamodel.DBRefEntry
+ (
+ dbref[db].getSource().toString(),
+ dbref[db].getVersion().toString(),
+ dbref[db].getAccessionId().toString()));
bindjvvobj(dbr, dbref[db]);
}
}
}
}
- if (newds) {
+ if (newds)
+ {
SequenceI[] seqs = new SequenceI[dsseqs.size()];
- for (i=0,iSize=dsseqs.size(); i<iSize; i++) {
- seqs[i]=(SequenceI) dsseqs.elementAt(i);
+ for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
+ {
+ seqs[i] = (SequenceI) dsseqs.elementAt(i);
dsseqs.setElementAt(null, i);
}
jdataset = new jalview.datamodel.Alignment(seqs);
}
// ////////
// add any new dataset sequence feature annotations
- if (dataset.getDataSetAnnotations() != null) {
- for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++) {
- DataSetAnnotations dseta=dataset.getDataSetAnnotations(dsa);
- SequenceI dsSeq=(SequenceI) getvObj2jv((Vobject) dseta.getSeqRef());
- if (dsSeq==null) {
- jalview.bin.Cache.log.warn("Couldn't resolve jalview sequenceI for dataset object reference "+((Vobject)dataset.getDataSetAnnotations(dsa).getSeqRef()).getVorbaId().getId());
- } else {
- if (dseta.getAnnotationElementCount()==0) {
- jalview.datamodel.SequenceFeature sf=(jalview.datamodel.SequenceFeature) getvObj2jv(dseta);
- if (sf==null) {
- dsSeq.addSequenceFeature(sf=getJalviewSeqFeature(dseta));
+ if (dataset.getDataSetAnnotations() != null)
+ {
+ for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
+ {
+ DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
+ SequenceI dsSeq = (SequenceI) getvObj2jv( (Vobject) dseta.getSeqRef());
+ if (dsSeq == null)
+ {
+ jalview.bin.Cache.log.warn(
+ "Couldn't resolve jalview sequenceI for dataset object reference " +
+ ( (Vobject) dataset.getDataSetAnnotations(dsa).getSeqRef()).
+ getVorbaId().getId());
+ }
+ else
+ {
+ if (dseta.getAnnotationElementCount() == 0)
+ {
+ jalview.datamodel.SequenceFeature sf = (jalview.datamodel.
+ SequenceFeature) getvObj2jv(dseta);
+ if (sf == null)
+ {
+ dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dseta));
bindjvvobj(sf, dseta);
}
- } else {
+ }
+ else
+ {
// TODO: deal with alignmentAnnotation style annotation
// appearing on dataset sequences.
// JBPNote: we could just add them to all alignments but
}
}
- if (dataset.getAlignmentCount()>0) {
+ if (dataset.getAlignmentCount() > 0)
+ {
// LOAD ALIGNMENTS from DATASET
- for (int al=0,nal=dataset.getAlignmentCount(); al<nal; al++) {
- org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(al);
+ for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
+ {
+ org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(
+ al);
AlignViewport av = (AlignViewport) getvObj2jv(alignment);
- jalview.datamodel.AlignmentI jal=null;
- if (av!=null)
+ jalview.datamodel.AlignmentI jal = null;
+ if (av != null)
+ {
jal = av.getAlignment();
+ }
iSize = alignment.getAlignmentSequenceCount();
- boolean newal=(jal==null) ? true : false;
- Vector newasAnnots=new Vector();
- char gapChar=' '; // default for new alignments read in from the document
- if (jal!=null) {
- dsseqs=jal.getSequences(); // for merge/update
- gapChar=jal.getGapCharacter();
- } else {
- dsseqs=new Vector();
+ boolean newal = (jal == null) ? true : false;
+ Vector newasAnnots = new Vector();
+ char gapChar = ' '; // default for new alignments read in from the document
+ if (jal != null)
+ {
+ dsseqs = jal.getSequences(); // for merge/update
+ gapChar = jal.getGapCharacter();
}
- char valGapchar=alignment.getGapChar().charAt(0);
+ else
+ {
+ dsseqs = new Vector();
+ }
+ char valGapchar = alignment.getGapChar().charAt(0);
for (i = 0; i < iSize; i++)
{
AlignmentSequence valseq = alignment.getAlignmentSequence(i);
jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
- if (alseq!=null) {
+ if (alseq != null)
+ {
//TODO: upperCase/LowerCase situation here ? do we allow it ?
//if (!alseq.getSequence().equals(valseq.getSequence())) {
// throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
if (Cache.log.isDebugEnabled())
- Cache.log.debug("Updating apparently edited sequence "+alseq.getName());
+ {
+ Cache.log.debug("Updating apparently edited sequence " +
+ alseq.getName());
+ }
// this might go *horribly* wrong
- alseq.setSequence(new String(valseq.getSequence()).replace(valGapchar, gapChar));
+ alseq.setSequence(new String(valseq.getSequence()).replace(
+ valGapchar, gapChar));
jremain--;
- } else {
+ }
+ else
+ {
alseq = new jalview.datamodel.Sequence(
valseq.getName(),
valseq.getSequence().replace(valGapchar, gapChar),
valseq.getStart(),
- valseq.getEnd() );
+ valseq.getEnd());
- Vobject datsetseq = (Vobject)valseq.getRefid();
- if (datsetseq!=null) {
- alseq.setDatasetSequence((SequenceI)getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
- } else {
- Cache.log.error("Invalid dataset sequence id (null) for alignment sequence "+valseq.getVorbaId());
+ Vobject datsetseq = (Vobject) valseq.getRefid();
+ if (datsetseq != null)
+ {
+ alseq.setDatasetSequence( (SequenceI) getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
+ }
+ else
+ {
+ Cache.log.error(
+ "Invalid dataset sequence id (null) for alignment sequence " +
+ valseq.getVorbaId());
}
bindjvvobj(alseq, valseq);
alseq.setVamsasId(valseq.getVorbaId().getId());
dsseqs.add(alseq);
}
- if (valseq.getAlignmentSequenceAnnotationCount()>0) {
- AlignmentSequenceAnnotation[] vasannot=valseq.getAlignmentSequenceAnnotation();
- for (int a=0; a<vasannot.length; a++) {
- jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations
- if (asa==null) {
+ if (valseq.getAlignmentSequenceAnnotationCount() > 0)
+ {
+ AlignmentSequenceAnnotation[] vasannot = valseq.
+ getAlignmentSequenceAnnotation();
+ for (int a = 0; a < vasannot.length; a++)
+ {
+ jalview.datamodel.AlignmentAnnotation asa = (jalview.
+ datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: 1:many jalview alignment sequence annotations
+ if (asa == null)
+ {
int se[] = getBounds(vasannot[a]);
asa = getjAlignmentAnnotation(jal, vasannot[a]);
- asa.sequenceRef=alseq;
- asa.createSequenceMapping(alseq, alseq.getStart()+se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.
+ asa.sequenceRef = alseq;
+ asa.createSequenceMapping(alseq, alseq.getStart() + se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.
bindjvvobj(asa, vasannot[a]);
newasAnnots.add(asa);
- } else {
+ }
+ else
+ {
// update existing annotation - can do this in place
- if (vasannot[a].getModifiable()) {
- Cache.log.info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
+ if (vasannot[a].getModifiable())
+ {
+ Cache.log.info(
+ "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
// TODO: should at least replace with new one - otherwise things will break
// basically do this:
// int se[] = getBounds(vasannot[a]);
}
}
}
- if (jal==null) {
+ if (jal == null)
+ {
SequenceI[] seqs = new SequenceI[dsseqs.size()];
- for (i=0,iSize=dsseqs.size(); i<iSize; i++) {
- seqs[i]=(SequenceI) dsseqs.elementAt(i);
+ for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
+ {
+ seqs[i] = (SequenceI) dsseqs.elementAt(i);
dsseqs.setElementAt(null, i);
}
jal = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas alignment imported into jalview "+alignment.getVorbaId().getId());
+ Cache.log.debug("New vamsas alignment imported into jalview " +
+ alignment.getVorbaId().getId());
jal.setDataset(jdataset);
}
- if (newasAnnots!=null && newasAnnots.size()>0) {
+ if (newasAnnots != null && newasAnnots.size() > 0)
+ {
// Add the new sequence annotations in to the alignment.
- for (int an=0,anSize=newasAnnots.size(); an<anSize; an++) {
- jal.addAnnotation((AlignmentAnnotation) newasAnnots.elementAt(an));
+ for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++)
+ {
+ jal.addAnnotation( (AlignmentAnnotation) newasAnnots.elementAt(
+ an));
// TODO: check if anything has to be done - like calling adjustForAlignment or something.
newasAnnots.setElementAt(null, an);
}
- newasAnnots=null;
+ newasAnnots = null;
}
// //////////////////////////////////////////
// //LOAD ANNOTATIONS FOR THE ALIGNMENT
// ////////////////////////////////////
- if (alignment.getAlignmentAnnotationCount()>0)
+ if (alignment.getAlignmentAnnotationCount() > 0)
{
- org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.getAlignmentAnnotation();
+ org.vamsas.objects.core.AlignmentAnnotation[] an = alignment.
+ getAlignmentAnnotation();
for (int j = 0; j < an.length; j++)
{
- jalview.datamodel.AlignmentAnnotation jan=(jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
- if (jan!=null) {
+ jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.
+ AlignmentAnnotation) getvObj2jv(an[j]);
+ if (jan != null)
+ {
// update or stay the same.
// TODO: should at least replace with a new one - otherwise things will break
// basically do this:
// jan.update(getjAlignmentAnnotation(jal, an[a])); // update from another annotation object in place.
Cache.log.debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
- if (an[j].getModifiable()) {
+ if (an[j].getModifiable())
+ {
// TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited.
- Cache.log.info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
+ Cache.log.info(
+ "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
}
// TODO: compare annotation element rows
// TODO: compare props.
- } else {
+ }
+ else
+ {
jan = getjAlignmentAnnotation(jal, an[j]);
jal.addAnnotation(jan);
bindjvvobj(jan, an[j]);
}
}
AlignFrame alignFrame;
- if (av==null) {
- Cache.log.debug("New alignframe for alignment "+alignment.getVorbaId());
+ if (av == null)
+ {
+ Cache.log.debug("New alignframe for alignment " +
+ alignment.getVorbaId());
// ///////////////////////////////
// construct alignment view
- alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- av=alignFrame.getViewport();
- String title = alignment.getProvenance().getEntry(alignment.getProvenance().getEntryCount()-1).getAction();
- if (alignment.getPropertyCount()>0) {
- for (int p=0,pe=alignment.getPropertyCount(); p<pe; p++) {
- if (alignment.getProperty(p).getName().equals("jalview:AlTitle")) {
+ alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ av = alignFrame.getViewport();
+ String title = alignment.getProvenance().getEntry(alignment.
+ getProvenance().getEntryCount() - 1).getAction();
+ if (alignment.getPropertyCount() > 0)
+ {
+ for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++)
+ {
+ if (alignment.getProperty(p).getName().equals(
+ "jalview:AlTitle"))
+ {
title = alignment.getProperty(p).getContent();
}
}
}
// TODO: automatically create meaningful title for a vamsas alignment using its provenance.
- jalview.gui.Desktop.addInternalFrame(alignFrame, title + "("+alignment.getVorbaId()+")",
+ jalview.gui.Desktop.addInternalFrame(alignFrame,
+ title + "(" + alignment.getVorbaId() + ")",
AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
bindjvvobj(av, alignment);
- } else {
+ }
+ else
+ {
// find the alignFrame for jal.
// TODO: fix this so we retrieve the alignFrame handing av *directly*
- alignFrame=getAlignFrameFor(av);
+ alignFrame = getAlignFrameFor(av);
}
// LOAD TREES
// /////////////////////////////////////
for (int t = 0; t < alignment.getTreeCount(); t++)
{
Tree tree = alignment.getTree(t);
- TreePanel tp=(TreePanel) getvObj2jv(tree);
- if (tp!=null) {
- Cache.log.info("Update from vamsas document to alignment associated tree not implemented yet.");
- } else {
+ TreePanel tp = (TreePanel) getvObj2jv(tree);
+ if (tp != null)
+ {
+ Cache.log.info(
+ "Update from vamsas document to alignment associated tree not implemented yet.");
+ }
+ else
+ {
// make a new tree
Object[] idata = this.recoverInputData(tree.getProvenance());
- try {
- AlignmentView inputData=null;
- if (idata!=null && idata[0]!=null)
+ try
+ {
+ AlignmentView inputData = null;
+ if (idata != null && idata[0] != null)
+ {
inputData = (AlignmentView) idata[0];
+ }
tp = alignFrame.ShowNewickTree(
new jalview.io.NewickFile(tree.getNewick(0).getContent()),
- tree.getNewick(0).getTitle()+" ("+tree.getVorbaId()+")",inputData,
+ tree.getNewick(0).getTitle() + " (" + tree.getVorbaId() +
+ ")", inputData,
600, 500,
t * 20 + 50, t * 20 + 50);
bindjvvobj(tp, tree);
- } catch (Exception e) {
- Cache.log.warn("Problems parsing treefile '"+tree.getNewick(0).getContent()+"'",e);
+ }
+ catch (Exception e)
+ {
+ Cache.log.warn("Problems parsing treefile '" +
+ tree.getNewick(0).getContent() + "'", e);
}
}
}
}
}
}
+
// bitfields - should be a template in j1.5
- private static int HASSECSTR=0;
- private static int HASVALS=1;
- private static int HASHPHOB=2;
- private static int HASDC=3;
- private static int HASDESCSTR=4;
- private static int HASTWOSTATE=5; // not used yet.
+ private static int HASSECSTR = 0;
+ private static int HASVALS = 1;
+ private static int HASHPHOB = 2;
+ private static int HASDC = 3;
+ private static int HASDESCSTR = 4;
+ private static int HASTWOSTATE = 5; // not used yet.
/**
* parses the AnnotationElements - if they exist - into jalview.datamodel.Annotation[] rows
* Two annotation rows are made if there are distinct annotation for both at 'pos' and 'after pos' at any particular site.
* @param annotation
* @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)}
*/
- private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation annotation) {
+ private Object[] parseRangeAnnotation(org.vamsas.objects.core.RangeAnnotation
+ annotation)
+ {
// set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made
// TODO: potentially we might make several annotation rows from one vamsas alignment annotation. the jv2Vobj binding mechanism
// 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[][] {
+ jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
+ {
new jalview.datamodel.Annotation[rangeMap.length],
new jalview.datamodel.Annotation[rangeMap.length]
};
- boolean mergeable=true; //false if 'after positions cant be placed on same annotation row as positions.
+ boolean mergeable = true; //false if 'after positions cant be placed on same annotation row as positions.
- if (annotation.getAnnotationElementCount()>0) {
+ if (annotation.getAnnotationElementCount() > 0)
+ {
AnnotationElement ae[] = annotation.getAnnotationElement();
for (int aa = 0; aa < ae.length; aa++)
{
- int pos = ae[aa].getPosition()-1;// pos counts from 1 to (|seg.start-seg.end|+1)
- if (pos>=0 && pos<rangeMap.length) {
- int row=ae[aa].getAfter()?1:0;
- if (anot[row][pos]!=null) {
+ int pos = ae[aa].getPosition() - 1; // pos counts from 1 to (|seg.start-seg.end|+1)
+ if (pos >= 0 && pos < rangeMap.length)
+ {
+ int row = ae[aa].getAfter() ? 1 : 0;
+ if (anot[row][pos] != null)
+ {
// only time this should happen is if the After flag is set.
- Cache.log.debug("Ignoring duplicate annotation site at "+pos);
+ Cache.log.debug("Ignoring duplicate annotation site at " + pos);
continue;
}
- if (anot[1-row][pos]!=null)
- mergeable=false;
+ if (anot[1 - row][pos] != null)
+ {
+ mergeable = false;
+ }
String desc = "";
- if (ae[aa].getDescription()!=null) {
+ if (ae[aa].getDescription() != null)
+ {
desc = ae[aa].getDescription();
- if (desc.length()>0) {
+ if (desc.length() > 0)
+ {
// have imported valid description string
- AeContent[HASDESCSTR]=true;
+ AeContent[HASDESCSTR] = true;
}
}
- String dc = null;//ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
- String ss = null;//ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
+ String dc = null; //ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
+ String ss = null; //ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
java.awt.Color colour = null;
- if (ae[aa].getGlyphCount()>0) {
+ if (ae[aa].getGlyphCount() > 0)
+ {
Glyph[] glyphs = ae[aa].getGlyph();
- for (int g=0; g<glyphs.length; g++) {
- if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) {
- ss=glyphs[g].getContent();
- AeContent[HASSECSTR]=true;
- } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) {
+ for (int g = 0; g < glyphs.length; g++)
+ {
+ if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+ GlyphDictionary.PROTEIN_SS_3STATE))
+ {
+ ss = glyphs[g].getContent();
+ AeContent[HASSECSTR] = true;
+ }
+ else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+ GlyphDictionary.
+ PROTEIN_HD_HYDRO))
+ {
Cache.log.debug("ignoring hydrophobicity glyph marker.");
- AeContent[HASHPHOB]=true;
- char c=(dc=glyphs[g].getContent()).charAt(0);
+ AeContent[HASHPHOB] = true;
+ char c = (dc = glyphs[g].getContent()).charAt(0);
// dc may get overwritten - but we still set the colour.
- colour = new java.awt.Color(c=='+'?255:0,c=='.'?255:0,c=='-'?255:0);
+ colour = new java.awt.Color(c == '+' ? 255 : 0,
+ c == '.' ? 255 : 0,
+ c == '-' ? 255 : 0);
- } else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.GlyphDictionary.DEFAULT)) {
+ }
+ else if (glyphs[g].getDict().equals(org.vamsas.objects.utils.
+ GlyphDictionary.DEFAULT))
+ {
dc = glyphs[g].getContent();
- AeContent[HASDC]=true;
- } else {
- Cache.log.debug("Ignoring unknown glyph type "+glyphs[g].getDict());
+ AeContent[HASDC] = true;
+ }
+ else
+ {
+ Cache.log.debug("Ignoring unknown glyph type " +
+ glyphs[g].getDict());
}
}
}
- float val=0;
- if (ae[aa].getValueCount()>0) {
- AeContent[HASVALS]=true;
- if (ae[aa].getValueCount()>1) {
- Cache.log.warn("ignoring additional "+(ae[aa].getValueCount()-1)+"values in annotation element.");
+ float val = 0;
+ if (ae[aa].getValueCount() > 0)
+ {
+ AeContent[HASVALS] = true;
+ if (ae[aa].getValueCount() > 1)
+ {
+ Cache.log.warn("ignoring additional " +
+ (ae[aa].getValueCount() - 1) +
+ "values in annotation element.");
}
val = ae[aa].getValue(0);
}
- if (colour==null) {
- anot[row][pos]=new jalview.datamodel.Annotation((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);
+ if (colour == null)
+ {
+ anot[row][pos] = new jalview.datamodel.Annotation( (dc != null) ?
+ dc : "", desc, (ss != null) ? ss.charAt(0) : ' ', val);
}
- } else {
- Cache.log.warn("Ignoring out of bound annotation element "+aa+" in "+annotation.getVorbaId().getId());
+ else
+ {
+ anot[row][pos] = new jalview.datamodel.Annotation( (dc != null) ?
+ dc : "", desc, (ss != null) ? ss.charAt(0) : ' ', val, colour);
+ }
+ }
+ else
+ {
+ Cache.log.warn("Ignoring out of bound annotation element " + aa +
+ " in " + annotation.getVorbaId().getId());
}
}
// decide on how many annotation rows are needed.
- if (mergeable) {
- for (int i=0; i<anot[0].length;i++) {
- if (anot[1][i]!=null) {
+ if (mergeable)
+ {
+ for (int i = 0; i < anot[0].length; i++)
+ {
+ if (anot[1][i] != null)
+ {
anot[0][i] = anot[1][i];
- anot[0][i].description = anot[0][i].description+" (after)";
- AeContent[HASDESCSTR]=true; // we have valid description string data
+ anot[0][i].description = anot[0][i].description + " (after)";
+ AeContent[HASDESCSTR] = true; // we have valid description string data
anot[1][i] = null;
}
}
anot[1] = null;
- } else {
- for (int i=0; i<anot[0].length;i++) {
- anot[1][i].description = anot[1][i].description+" (after)";
+ }
+ else
+ {
+ for (int i = 0; i < anot[0].length; i++)
+ {
+ anot[1][i].description = anot[1][i].description + " (after)";
}
}
- return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
- } else {
+ 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;
}
+
/**
* @param jal the jalview alignment to which the annotation will be attached (ideally - freshly updated from corresponding vamsas alignment)
* @param annotation
* @return unbound jalview alignment annotation object.
*/
- private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.datamodel.AlignmentI jal, org.vamsas.objects.core.RangeAnnotation annotation) {
- jalview.datamodel.AlignmentAnnotation jan =null;
- if (annotation==null)
+ private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.
+ datamodel.AlignmentI jal,
+ org.vamsas.objects.core.RangeAnnotation annotation)
+ {
+ jalview.datamodel.AlignmentAnnotation jan = null;
+ if (annotation == null)
+ {
return null;
+ }
// boolean hasSequenceRef=annotation.getClass().equals(org.vamsas.objects.core.AlignmentSequenceAnnotation.class);
//boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class));
/*int se[] = getBounds(annotation);
- if (se==null)
+ if (se==null)
se=new int[] {0,jal.getWidth()-1};
*/
Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
- String a_label=annotation.getLabel();
- String a_descr=annotation.getDescription();
- if (a_label==null || a_label.length()==0) {
+ String a_label = annotation.getLabel();
+ String a_descr = annotation.getDescription();
+ if (a_label == null || a_label.length() == 0)
+ {
a_label = annotation.getType();
- if (a_label.length()==0)
+ if (a_label.length() == 0)
+ {
a_label = "Unamed annotation";
+ }
}
- if (a_descr==null || a_descr.length()==0) {
- a_descr = "Annotation of type '"+annotation.getType()+"'";
+ if (a_descr == null || a_descr.length() == 0)
+ {
+ a_descr = "Annotation of type '" + annotation.getType() + "'";
}
- if (parsedRangeAnnotation==null) {
- Cache.log.debug("Inserting empty annotation row elements for a whole-alignment annotation.");
-
+ if (parsedRangeAnnotation == null)
+ {
+ Cache.log.debug(
+ "Inserting empty annotation row elements for a whole-alignment annotation.");
- } else {
- if (parsedRangeAnnotation[3]!=null) {
- Cache.log.warn("Ignoring 'After' annotation row in "+annotation.getVorbaId());
+ }
+ else
+ {
+ if (parsedRangeAnnotation[3] != null)
+ {
+ Cache.log.warn("Ignoring 'After' annotation row in " +
+ annotation.getVorbaId());
}
- jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
- boolean[] has=(boolean[])parsedRangeAnnotation[0];
+ jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[])
+ parsedRangeAnnotation[2];
+ boolean[] has = (boolean[]) parsedRangeAnnotation[0];
// VAMSAS: getGraph is only on derived annotation for alignments - in this way its 'odd' - there is already an existing TODO about removing this flag as being redundant
/*if ((annotation.getClass().equals(org.vamsas.objects.core.AlignmentAnnotation.class) && ((org.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
|| (hasSequenceRef=true && ((org.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
- */
- if (has[HASVALS]) {
+ */
+ if (has[HASVALS])
+ {
// make bounds and automatic description strings for jalview user's benefit (these shouldn't be written back to vamsas document)
- boolean first=true;
- float min=0,max=1;
- int lastval=0;
- for (int i=0;i<arow.length; i++) {
- if (arow[i]!=null) {
- if (i-lastval>1) {
+ boolean first = true;
+ float min = 0, max = 1;
+ int lastval = 0;
+ for (int i = 0; i < arow.length; i++)
+ {
+ if (arow[i] != null)
+ {
+ if (i - lastval > 1)
+ {
// do some interpolation *between* points
- if (arow[lastval]!=null) {
- float interval = arow[i].value-arow[lastval].value;
- interval/=i-lastval;
+ if (arow[lastval] != null)
+ {
+ float interval = arow[i].value - arow[lastval].value;
+ interval /= i - lastval;
float base = arow[lastval].value;
- for (int ip=lastval+1,np=0; ip<i; np++,ip++) {
- arow[ip] = new jalview.datamodel.Annotation("","",' ', interval*np+base);
+ for (int ip = lastval + 1, np = 0; ip < i; np++, ip++)
+ {
+ arow[ip] = new jalview.datamodel.Annotation("", "", ' ',
+ interval * np + base);
// NB - Interpolated points don't get a tooltip and description.
}
}
}
- lastval=i;
+ lastval = i;
// check range - shouldn't we have a min and max property in the annotation object ?
- if (first) { min=max=arow[i].value; first=false;}
- else { if (arow[i].value<min) { min=arow[i].value; }
- else if (arow[i].value>max) { max=arow[i].value; }
+ if (first)
+ {
+ min = max = arow[i].value;
+ first = false;
+ }
+ else
+ {
+ if (arow[i].value < min)
+ {
+ min = arow[i].value;
+ }
+ else if (arow[i].value > max)
+ {
+ max = arow[i].value;
+ }
}
// make tooltip and display char value
- if (!has[HASDESCSTR]) arow[i].description = arow[i].value + "";
- if (!has[HASDC]) arow[i].displayCharacter=arow[i].value+"";
+ if (!has[HASDESCSTR])
+ {
+ arow[i].description = arow[i].value + "";
+ }
+ if (!has[HASDC])
+ {
+ arow[i].displayCharacter = arow[i].value + "";
+ }
}
}
- int type=jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
- if (has[HASHPHOB]) {
+ int type = jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
+ if (has[HASHPHOB])
+ {
type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
}
- jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type);
- } else {
+ jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow,
+ min, max, type);
+ }
+ else
+ {
jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow);
jan.setThreshold(null);
}
- if (annotation.getLinkCount()>0) {
- Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation.");
+ if (annotation.getLinkCount() > 0)
+ {
+ Cache.log.warn("Ignoring " + annotation.getLinkCount() +
+ "links added to AlignmentAnnotation.");
}
- if (annotation.getModifiable()) {
- jan.editable=true;
+ if (annotation.getModifiable())
+ {
+ jan.editable = true;
}
- if (annotation.getPropertyCount()>0) {
+ if (annotation.getPropertyCount() > 0)
+ {
// look for special jalview properties
- org.vamsas.objects.core.Property[] props=annotation.getProperty();
- for (int p=0;p<props.length; p++) {
- if (props[p].getName().equalsIgnoreCase("jalview:graphType")) {
- try {
+ org.vamsas.objects.core.Property[] props = annotation.getProperty();
+ for (int p = 0; p < props.length; p++)
+ {
+ if (props[p].getName().equalsIgnoreCase("jalview:graphType"))
+ {
+ try
+ {
// probably a jalview annotation graph so recover the visualization hints.
- jan.graph = jalview.datamodel.AlignmentAnnotation.getGraphValueFromString(props[p].getContent());
- } catch (Exception e) {
- Cache.log.debug("Invalid graph type value in jalview:graphType property.");
+ jan.graph = jalview.datamodel.AlignmentAnnotation.
+ getGraphValueFromString(props[p].getContent());
}
- try {
- if (annotation.getGroup()!=null && annotation.getGroup().length()>0)
+ catch (Exception e)
+ {
+ Cache.log.debug(
+ "Invalid graph type value in jalview:graphType property.");
+ }
+ try
+ {
+ if (annotation.getGroup() != null &&
+ annotation.getGroup().length() > 0)
+ {
jan.graphGroup = Integer.parseInt(annotation.getGroup());
- } catch (Exception e) {
+ }
+ }
+ catch (Exception e)
+ {
Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
}
}
return null;
}
- private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta) {
+ private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
+ {
int[] se = getBounds(dseta);
SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta.getType(),
dseta.getDescription(), dseta.getStatus(), se[0], se[1], dseta
* @param dseta
* @return int[] { start, end}
*/
- private int[] getBounds(RangeType dseta) {
+ private int[] getBounds(RangeType dseta)
+ {
if (dseta != null)
{
int[] se = null;
- if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
+ if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
+ {
throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ }
if (dseta.getSegCount() > 0)
{
- se = getSegRange(dseta.getSeg(0),true);
+ se = getSegRange(dseta.getSeg(0), true);
for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
{
int nse[] = getSegRange(dseta.getSeg(s), true);
if (se[0] > nse[0])
+ {
se[0] = nse[0];
+ }
if (se[1] < nse[1])
+ {
se[1] = nse[1];
+ }
}
}
if (dseta.getPosCount() > 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 (se[0] > pos)
+ {
se[0] = pos;
+ }
if (se[1] < pos)
+ {
se[1] = pos;
+ }
}
}
return se;
}
return null;
}
+
/**
* map from a rangeType's internal frame to the referenced object's coordinate frame.
* @param dseta
* @return int [] { ref(pos)...} for all pos in rangeType's frame.
*/
- private int[] getMapping(RangeType dseta) {
- Vector posList=new Vector();
+ private int[] getMapping(RangeType dseta)
+ {
+ Vector posList = new Vector();
if (dseta != null)
{
int[] se = null;
- if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
+ if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
+ {
throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ }
if (dseta.getSegCount() > 0)
{
for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
{
se = getSegRange(dseta.getSeg(s), false);
- int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);
- for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {
+ int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
+ for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
+ {
posList.add(new Integer(p));
}
}
}
}
}
- if (posList!=null && posList.size()>0) {
- int[] range=new int[posList.size()];
- for (int i=0; i<range.length; i++)
- range[i] = ((Integer)posList.elementAt(i)).intValue();
+ if (posList != null && posList.size() > 0)
+ {
+ int[] range = new int[posList.size()];
+ for (int i = 0; i < range.length; i++)
+ {
+ range[i] = ( (Integer) posList.elementAt(i)).intValue();
+ }
posList.clear();
return range;
}
return null;
}
+
/* not needed now.
* Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov) {
jalview.datamodel.ProvenanceEntry[] entries = null;
}
return prov;
- }
+ }
*/
- jalview.datamodel.Provenance getJalviewProvenance(Provenance prov) {
+ jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
+ {
// TODO: fix App and Action entries and check use of provenance in jalview.
jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
for (int i = 0; i < prov.getEntryCount(); i++)
{
jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i).getAction(),
- prov.getEntry(i).getDate().toDate(), prov.getEntry(i).getId());
+ prov.getEntry(i).getDate().toDate(),
+ prov.getEntry(i).getId());
}
return jprov;
* @return default initial provenance list for a Jalview created vamsas
* object.
*/
- Provenance dummyProvenance() {
+ Provenance dummyProvenance()
+ {
return dummyProvenance(null);
}
- Entry dummyPEntry(String action) {
+ Entry dummyPEntry(String action)
+ {
Entry entry = new Entry();
entry.setApp(this.provEntry.getApp());
if (action != null)
+ {
entry.setAction(action);
+ }
else
+ {
entry.setAction("created.");
+ }
entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
entry.setUser(this.provEntry.getUser());
return entry;
}
- Provenance dummyProvenance(String action) {
+ Provenance dummyProvenance(String action)
+ {
Provenance prov = new Provenance();
prov.addEntry(dummyPEntry(action));
return prov;
}
- void addProvenance(Provenance p, String action) {
+ void addProvenance(Provenance p, String action)
+ {
p.addEntry(dummyPEntry(action));
}
git://source.jalview.org / jalview.git / blobdiff