X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;fp=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=d81a6b08a63d763b32fe7c85d29e163891421072;hb=daf64249356f9a156423bd56ab0336d9da2e5325;hp=1cab8ca897b315b96af5ef62922f0f01d60a1cfe;hpb=4f9c22055c3cdbfc9c4375dcb74755a89ec32b62;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 1cab8ca..d81a6b0 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -182,8 +182,8 @@ public class VamsasAppDatastore Vobject obj = getjv2vObj(seqsetidobj); if (obj != null && !(obj instanceof Alignment)) { - Cache.log - .warn("IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:" + Cache.log.warn( + "IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:" + seqsetidobj + " to object " + obj); } return obj; @@ -199,8 +199,8 @@ public class VamsasAppDatastore if (Cache.log.isDebugEnabled()) { - Cache.log.debug("Returning null VorbaID binding for jalview object " - + jvobj); + Cache.log.debug( + "Returning null VorbaID binding for jalview object " + jvobj); } return null; } @@ -216,8 +216,8 @@ public class VamsasAppDatastore if (id == null) { id = cdoc.registerObject(vobj); - Cache.log - .debug("Registering new object and returning null for getvObj2jv"); + Cache.log.debug( + "Registering new object and returning null for getvObj2jv"); return null; } if (vobj2jv.containsKey(vobj.getVorbaId())) @@ -238,27 +238,27 @@ public class VamsasAppDatastore { Cache.log.error("Failed to get id for " + (vobj.isRegisterable() ? "registerable" - : "unregisterable") + " object " + vobj); + : "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 " + Cache.log.debug( + "Warning? Overwriting existing vamsas id binding for " + vobj.getVorbaId(), - new Exception( - MessageManager - .getString("exception.overwriting_vamsas_id_binding"))); + new Exception(MessageManager.getString( + "exception.overwriting_vamsas_id_binding"))); } 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.")); + + jvobj, + new Exception("Overwriting jalview object binding.")); } /* * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " @@ -337,9 +337,8 @@ public class VamsasAppDatastore if (vbound.getV_parent() != null && dataset != vbound.getV_parent()) { - throw new Error( - MessageManager - .getString("error.implementation_error_cannot_map_alignment_sequences")); + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_map_alignment_sequences")); // This occurs because the dataset for the alignment we are // trying to } @@ -372,7 +371,8 @@ public class VamsasAppDatastore // flag. // this *will* break when alignment contains both nucleotide and amino // acid sequences. - String dict = jal.isNucleotide() ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA + String dict = jal.isNucleotide() + ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA; Vector dssmods = new Vector(); for (int i = 0; i < jal.getHeight(); i++) @@ -381,8 +381,8 @@ public class VamsasAppDatastore // referenced // sequences // to dataset. - Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence( - this, sq, dict, dataset); + Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this, + sq, dict, dataset); sequence = (Sequence) dssync.getVobj(); if (dssync.getModified()) { @@ -440,8 +440,8 @@ public class VamsasAppDatastore else { // always prepare to clone the alignment - boolean alismod = av.isUndoRedoHashModified((long[]) alignRDHash - .get(av.getSequenceSetId())); + boolean alismod = av.isUndoRedoHashModified( + (long[]) alignRDHash.get(av.getSequenceSetId())); // todo: verify and update mutable alignment props. // TODO: Use isLocked methods if (alignment.getModifiable() == null @@ -461,8 +461,8 @@ public class VamsasAppDatastore { // removeValignmentSequences(alignment, docseqs); docseqs.removeAllElements(); - System.out - .println("Sequence deletion from alignment is not implemented."); + System.out.println( + "Sequence deletion from alignment is not implemented."); } if (modified) @@ -501,17 +501,18 @@ public class VamsasAppDatastore // unbind alignment from view. // create new binding and new alignment. // mark trail on new alignment as being derived from old ? - System.out - .println("update edited alignment to new alignment in document."); + System.out.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)); + SequenceI alseq = (SequenceI) getvObj2jv( + valseq = alignment.getAlignmentSequence(i)); if (alseq != null && alseq.getSequenceFeatures() != null) { /* @@ -556,8 +557,8 @@ public class VamsasAppDatastore if (aa[i].groupRef != null) { // TODO: store any group associated annotation references - Cache.log - .warn("Group associated sequence annotation is not stored in VAMSAS document."); + Cache.log.warn( + "Group associated sequence annotation is not stored in VAMSAS document."); continue; } if (aa[i].sequenceRef != null) @@ -590,7 +591,8 @@ public class VamsasAppDatastore else { // add Alignment Annotation - uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]); + uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj( + aa[i]); if (an == null) { an = new uk.ac.vamsas.objects.core.AlignmentAnnotation(); @@ -639,8 +641,8 @@ public class VamsasAppDatastore ae = new AnnotationElement(); ae.setDescription(aa[i].annotations[a].description); ae.addGlyph(new Glyph()); - ae.getGlyph(0).setContent( - aa[i].annotations[a].displayCharacter); // assume + ae.getGlyph(0) + .setContent(aa[i].annotations[a].displayCharacter); // assume // jax-b // takes // care @@ -655,9 +657,10 @@ public class VamsasAppDatastore 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); @@ -678,12 +681,13 @@ public class VamsasAppDatastore if (aa[i].threshold != null && aa[i].threshold.displayed) { an.addProperty(Properties.newProperty(THRESHOLD, - Properties.FLOATTYPE, "" + aa[i].threshold.value)); + Properties.FLOATTYPE, + "" + aa[i].threshold.value)); if (aa[i].threshold.label != null) { - an.addProperty(Properties.newProperty(THRESHOLD - + "Name", Properties.STRINGTYPE, "" - + aa[i].threshold.label)); + an.addProperty(Properties.newProperty( + THRESHOLD + "Name", Properties.STRINGTYPE, + "" + aa[i].threshold.label)); } } } @@ -696,14 +700,14 @@ public class VamsasAppDatastore // LOCK METHODS) { // 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 { // verify annotation - update (perhaps) - Cache.log - .info("updated alignment sequence annotation added."); + Cache.log.info( + "updated alignment sequence annotation added."); } } } @@ -777,18 +781,19 @@ public class VamsasAppDatastore * @param alignment * @param docseqs */ - private void removeValignmentSequences(Alignment alignment, Vector docseqs) + private void removeValignmentSequences(Alignment alignment, + Vector docseqs) { // delete these from document. This really needs to be a generic document // API function derived by CASTOR. Enumeration en = docseqs.elements(); while (en.hasMoreElements()) { - alignment.removeAlignmentSequence((AlignmentSequence) en - .nextElement()); + alignment.removeAlignmentSequence( + (AlignmentSequence) en.nextElement()); } - Entry pe = addProvenance(alignment.getProvenance(), "Removed " - + docseqs.size() + " sequences"); + Entry pe = addProvenance(alignment.getProvenance(), + "Removed " + docseqs.size() + " sequences"); en = alignment.enumerateAlignmentAnnotation(); Vector toremove = new Vector(); while (en.hasMoreElements()) @@ -827,8 +832,8 @@ public class VamsasAppDatastore en = toremove.elements(); while (en.hasMoreElements()) { - alignment - .removeAlignmentAnnotation((uk.ac.vamsas.objects.core.AlignmentAnnotation) en + alignment.removeAlignmentAnnotation( + (uk.ac.vamsas.objects.core.AlignmentAnnotation) en .nextElement()); } // TODO: search through alignment annotations to remove any references to @@ -877,17 +882,16 @@ public class VamsasAppDatastore modal = true; alseq.setName(jvalsq.getName()); } - if (jvalsq.getDescription() != null - && (alseq.getDescription() == null || !jvalsq.getDescription() - .equals(alseq.getDescription()))) + if (jvalsq.getDescription() != null && (alseq.getDescription() == null + || !jvalsq.getDescription().equals(alseq.getDescription()))) { modal = true; alseq.setDescription(jvalsq.getDescription()); } if (getjv2vObj(jvalsq.getDatasetSequence()) == null) { - Cache.log - .warn("Serious Implementation error - Unbound dataset sequence in alignment: " + Cache.log.warn( + "Serious Implementation error - Unbound dataset sequence in alignment: " + jvalsq.getDatasetSequence()); } alseq.setRefid(getjv2vObj(jvalsq.getDatasetSequence())); @@ -927,8 +931,8 @@ public class VamsasAppDatastore || !valseq.getSequence().equals(alseq.getSequenceAsString())) { // this might go *horribly* wrong - alseq.setSequence(new String(valseq.getSequence()).replace( - valGapchar, gapChar)); + alseq.setSequence(new String(valseq.getSequence()) + .replace(valGapchar, gapChar)); alseq.setStart((int) valseq.getStart()); alseq.setEnd((int) valseq.getEnd()); modal = true; @@ -938,23 +942,22 @@ public class VamsasAppDatastore modal = true; alseq.setName(valseq.getName()); } - if (alseq.getDescription() == null - || (valseq.getDescription() != null && !alseq - .getDescription().equals(valseq.getDescription()))) + if (alseq.getDescription() == null || (valseq.getDescription() != null + && !alseq.getDescription().equals(valseq.getDescription()))) { alseq.setDescription(valseq.getDescription()); modal = true; } if (modal && Cache.log.isDebugEnabled()) { - Cache.log.debug("Updating apparently edited sequence " - + alseq.getName()); + Cache.log.debug( + "Updating apparently edited sequence " + alseq.getName()); } } else { - alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq - .getSequence().replace(valGapchar, gapChar), + alseq = new jalview.datamodel.Sequence(valseq.getName(), + valseq.getSequence().replace(valGapchar, gapChar), (int) valseq.getStart(), (int) valseq.getEnd()); Vobject datsetseq = (Vobject) valseq.getRefid(); @@ -970,8 +973,8 @@ public class VamsasAppDatastore // inherit description line from dataset. if (alseq.getDatasetSequence().getDescription() != null) { - alseq.setDescription(alseq.getDatasetSequence() - .getDescription()); + alseq.setDescription( + alseq.getDatasetSequence().getDescription()); } } // if @@ -984,8 +987,8 @@ public class VamsasAppDatastore } else { - Cache.log - .error("Invalid dataset sequence id (null) for alignment sequence " + Cache.log.error( + "Invalid dataset sequence id (null) for alignment sequence " + valseq.getVorbaId()); } bindjvvobj(alseq, valseq); @@ -1055,9 +1058,10 @@ public class VamsasAppDatastore { // 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.setContent(String - .valueOf(alan.annotations[a].secondaryStructure)); + ss.setDict( + uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE); + ss.setContent( + String.valueOf(alan.annotations[a].secondaryStructure)); ae.addGlyph(ss); } an.addAnnotationElement(ae); @@ -1072,7 +1076,8 @@ public class VamsasAppDatastore // uk.ac.vamsas. // objects.core.AlignmentSequence alsref = (uk.ac.vamsas. // objects.core.AlignmentSequence) sref; - uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(alan); + uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj( + alan); int[] gapMap = getGapMap(AlSeqMaps, alan); if (an == null) { @@ -1116,8 +1121,8 @@ public class VamsasAppDatastore else { // verify existing alignment sequence annotation is up to date - System.out - .println("make new alignment dataset sequence annotation if modification has happened."); + System.out.println( + "make new alignment dataset sequence annotation if modification has happened."); } } @@ -1150,7 +1155,8 @@ public class VamsasAppDatastore // uk.ac.vamsas. // objects.core.AlignmentSequence alsref = (uk.ac.vamsas. // objects.core.AlignmentSequence) sref; - uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(alan); + uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj( + alan); int[] gapMap = getGapMap(AlSeqMaps, alan); if (an == null) { @@ -1184,8 +1190,8 @@ public class VamsasAppDatastore else { // verify existing alignment sequence annotation is up to date - System.out - .println("make new alignment sequence annotation if modification has happened."); + System.out.println( + "make new alignment sequence annotation if modification has happened."); } } } @@ -1326,8 +1332,8 @@ public class VamsasAppDatastore @Override public JarInputStream getJarInputStream() throws IOException { - jalview.bin.Cache.log - .debug("Returning client input stream for Jalview from Vamsas Document."); + jalview.bin.Cache.log.debug( + "Returning client input stream for Jalview from Vamsas Document."); return new JarInputStream(cappdata.getClientInputStream()); } }; @@ -1374,8 +1380,8 @@ public class VamsasAppDatastore @Override public JarInputStream getJarInputStream() throws IOException { - jalview.bin.Cache.log - .debug("Returning user input stream for Jalview from Vamsas Document."); + jalview.bin.Cache.log.debug( + "Returning user input stream for Jalview from Vamsas Document."); return new JarInputStream(cappdata.getUserInputStream()); } }; @@ -1420,9 +1426,9 @@ public class VamsasAppDatastore // TODO implement this : af.getNumberOfViews String seqsetidobj = av.getSequenceSetId(); views = Desktop.getViewports(seqsetidobj); - Cache.log.debug("Found " - + (views == null ? " no " : "" + views.length) - + " views for '" + av.getSequenceSetId() + "'"); + Cache.log + .debug("Found " + (views == null ? " no " : "" + views.length) + + " views for '" + av.getSequenceSetId() + "'"); if (views.length > 1) { // we need to close the original document view. @@ -1505,7 +1511,8 @@ public class VamsasAppDatastore // from another client throw new Error(MessageManager.formatMessage( "error.implementation_error_old_jalview_object_not_bound", - new String[] { oldjvobject.toString() })); + new String[] + { oldjvobject.toString() })); } if (newjvobject != null) { @@ -1530,22 +1537,22 @@ public class VamsasAppDatastore jxml.setSkipList(skipList); if (dojvsync) { - jxml.saveState(new JarOutputStream(cappdata - .getClientOutputStream())); + jxml.saveState( + new JarOutputStream(cappdata.getClientOutputStream())); } } catch (Exception e) { // 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.", - e); + jalview.bin.Cache.log.error( + "Couldn't update jalview client application data. Giving up - local settings probably lost.", + e); } } else { - jalview.bin.Cache.log - .error("Couldn't access client application data for vamsas session. This is probably a vamsas client bug."); + jalview.bin.Cache.log.error( + "Couldn't access client application data for vamsas session. This is probably a vamsas client bug."); } } @@ -1605,7 +1612,8 @@ public class VamsasAppDatastore DataSet dataset = root.getDataSet(_ds); int i, iSize = dataset.getSequenceCount(); List dsseqs; - jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset); + jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv( + dataset); int jremain = 0; if (jdataset == null) { @@ -1662,22 +1670,25 @@ public class VamsasAppDatastore // add any new dataset sequence feature annotations if (dataset.getDataSetAnnotations() != null) { - for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++) + for (int dsa = 0; dsa < dataset + .getDataSetAnnotationsCount(); dsa++) { DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa); // TODO: deal with group annotation on datset sequences. if (dseta.getSeqRefCount() == 1) { - SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta - .getSeqRef(0)); // TODO: deal with group dataset + SequenceI dsSeq = (SequenceI) getvObj2jv( + (Vobject) dseta.getSeqRef(0)); // TODO: deal with group + // dataset // annotations if (dsSeq == null) { - jalview.bin.Cache.log - .warn("Couldn't resolve jalview sequenceI for dataset object reference " - + ((Vobject) dataset.getDataSetAnnotations( - dsa).getSeqRef(0)).getVorbaId() - .getId()); + jalview.bin.Cache.log.warn( + "Couldn't resolve jalview sequenceI for dataset object reference " + + ((Vobject) dataset + .getDataSetAnnotations(dsa) + .getSeqRef(0)).getVorbaId() + .getId()); } else { @@ -1693,15 +1704,15 @@ public class VamsasAppDatastore // JBPNote: we could just add them to all alignments but // that may complicate cross references in the jalview // datamodel - Cache.log - .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview."); + Cache.log.warn( + "Ignoring dataset annotation with annotationElements. Not yet supported in jalview."); } } } else { - Cache.log - .warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features."); + Cache.log.warn( + "Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features."); } } } @@ -1709,7 +1720,8 @@ public class VamsasAppDatastore { // LOAD ALIGNMENTS from DATASET - for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++) + for (int al = 0, nal = dataset + .getAlignmentCount(); al < nal; al++) { uk.ac.vamsas.objects.core.Alignment alignment = dataset .getAlignment(al); @@ -1722,8 +1734,8 @@ public class VamsasAppDatastore // TODO check that correct alignment object is retrieved when // hidden seqs exist. jal = (av.hasHiddenRows()) ? av.getAlignment() - .getHiddenSequences().getFullAlignment() : av - .getAlignment(); + .getHiddenSequences().getFullAlignment() + : av.getAlignment(); } iSize = alignment.getAlignmentSequenceCount(); boolean refreshal = false; @@ -1743,7 +1755,8 @@ public class VamsasAppDatastore for (i = 0; i < iSize; i++) { AlignmentSequence valseq = alignment.getAlignmentSequence(i); - jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq); + jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv( + valseq); if (syncFromAlignmentSequence(valseq, valGapchar, gapChar, dsseqs) && alseq != null) { @@ -1758,7 +1771,8 @@ public class VamsasAppDatastore .getAlignmentSequenceAnnotation(); for (int a = 0; a < vasannot.length; a++) { - jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO: + jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv( + vasannot[a]); // TODO: // 1:many // jalview // alignment @@ -1793,8 +1807,8 @@ public class VamsasAppDatastore // OBJECT LOCK // METHODS) { - Cache.log - .info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation"); + 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: @@ -1824,10 +1838,11 @@ public class VamsasAppDatastore 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++) + for (int an = 0, anSize = newasAnnots + .size(); an < anSize; an++) { - jal.addAnnotation((AlignmentAnnotation) newasAnnots - .elementAt(an)); + jal.addAnnotation( + (AlignmentAnnotation) newasAnnots.elementAt(an)); // TODO: check if anything has to be done - like calling // adjustForAlignment or something. newasAnnots.setElementAt(null, an); @@ -1844,7 +1859,8 @@ public class VamsasAppDatastore for (int j = 0; j < an.length; j++) { - jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]); + jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv( + an[j]); if (jan != null) { // update or stay the same. @@ -1854,16 +1870,16 @@ public class VamsasAppDatastore // 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."); + Cache.log.debug( + "update from vamsas alignment annotation to existing jalview alignment annotation."); if (an[j].getModifiable() == null) // TODO: USE VAMSAS // LIBRARY OBJECT LOCK // METHODS) { // 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. @@ -1887,18 +1903,18 @@ public class VamsasAppDatastore // /////////////////////////////// // construct alignment view alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT, alignment.getVorbaId() - .toString()); + AlignFrame.DEFAULT_HEIGHT, + alignment.getVorbaId().toString()); av = alignFrame.getViewport(); newAlignmentViews.addElement(av); - String title = alignment - .getProvenance() + String title = alignment.getProvenance() .getEntry( alignment.getProvenance().getEntryCount() - 1) .getAction(); if (alignment.getPropertyCount() > 0) { - for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++) + for (int p = 0, pe = alignment + .getPropertyCount(); p < pe; p++) { if (alignment.getProperty(p).getName().equals("title")) { @@ -1977,7 +1993,8 @@ public class VamsasAppDatastore DataSet dataset = root.getDataSet(_ds); if (dataset.getSequenceMappingCount() > 0) { - for (int sm = 0, smCount = dataset.getSequenceMappingCount(); sm < smCount; sm++) + for (int sm = 0, smCount = dataset + .getSequenceMappingCount(); sm < smCount; sm++) { Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this, dataset.getSequenceMapping(sm)); @@ -2034,10 +2051,11 @@ public class VamsasAppDatastore // 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], + 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. @@ -2082,16 +2100,14 @@ public class VamsasAppDatastore Glyph[] glyphs = ae[aa].getGlyph(); for (int g = 0; g < glyphs.length; g++) { - if (glyphs[g] - .getDict() - .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE)) + if (glyphs[g].getDict().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)) + else if (glyphs[g].getDict().equals( + uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO)) { Cache.log.debug("ignoring hydrophobicity glyph marker."); AeContent[HASHPHOB] = true; @@ -2109,8 +2125,8 @@ public class VamsasAppDatastore } else { - Cache.log - .debug("IMPLEMENTATION TODO: Ignoring unknown glyph type " + Cache.log.debug( + "IMPLEMENTATION TODO: Ignoring unknown glyph type " + glyphs[g].getDict()); } } @@ -2121,9 +2137,9 @@ public class VamsasAppDatastore AeContent[HASVALS] = true; if (ae[aa].getValueCount() > 1) { - Cache.log.warn("ignoring additional " - + (ae[aa].getValueCount() - 1) - + " values in annotation element."); + Cache.log.warn( + "ignoring additional " + (ae[aa].getValueCount() - 1) + + " values in annotation element."); } val = ae[aa].getValue(0); } @@ -2239,7 +2255,8 @@ public class VamsasAppDatastore { if (gl == null) { - gl = new GraphLine(val.floatValue(), "", java.awt.Color.black); + gl = new GraphLine(val.floatValue(), "", + java.awt.Color.black); } else { @@ -2272,8 +2289,8 @@ public class VamsasAppDatastore } if (parsedRangeAnnotation == null) { - Cache.log - .debug("Inserting empty annotation row elements for a whole-alignment annotation."); + Cache.log.debug( + "Inserting empty annotation row elements for a whole-alignment annotation."); } else { @@ -2367,7 +2384,8 @@ public class VamsasAppDatastore && arow[i].description.length() < 3) { // copy over the description as the display char. - arow[i].displayCharacter = new String(arow[i].description); + arow[i].displayCharacter = new String( + arow[i].description); } } else @@ -2423,8 +2441,8 @@ public class VamsasAppDatastore } } catch (Exception e) { - Cache.log - .info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly."); + Cache.log.info( + "UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly."); } return jan; @@ -2448,9 +2466,8 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - MessageManager - .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2507,9 +2524,8 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - MessageManager - .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2552,8 +2568,10 @@ public class VamsasAppDatastore * @param maprange * where the from range is the local mapped range, and the to range * is the 'mapped' range in the MapRangeType - * @param default unit for local - * @param default unit for mapped + * @param default + * unit for local + * @param default + * unit for mapped * @return MapList */ private jalview.util.MapList parsemapType(MapType maprange, int localu, @@ -2564,8 +2582,9 @@ public class VamsasAppDatastore int[] mappedRange = getMapping(maprange.getMapped()); long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu; - long mu = maprange.getMapped().hasUnit() ? maprange.getMapped() - .getUnit() : mappedu; + long mu = maprange.getMapped().hasUnit() + ? maprange.getMapped().getUnit() + : mappedu; ml = new jalview.util.MapList(localRange, mappedRange, (int) lu, (int) mu); return ml; @@ -2637,9 +2656,9 @@ public class VamsasAppDatastore 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(), prov.getEntry(i) - .getId()); + jprov.addEntry(prov.getEntry(i).getUser(), + prov.getEntry(i).getAction(), prov.getEntry(i).getDate(), + prov.getEntry(i).getId()); } return jprov; @@ -2706,8 +2725,8 @@ public class VamsasAppDatastore return vobj2jv; } - public void storeSequenceMappings(AlignmentViewport viewport, String title) - throws Exception + public void storeSequenceMappings(AlignmentViewport viewport, + String title) throws Exception { AlignmentViewport av = viewport; try @@ -2721,13 +2740,13 @@ public class VamsasAppDatastore Cache.log.warn("Creating new dataset for an alignment."); jal.setDataset(null); } - dataset = (DataSet) ((Alignment) getjv2vObj(viewport - .getSequenceSetId())).getV_parent(); // jal.getDataset()); + dataset = (DataSet) ((Alignment) getjv2vObj( + viewport.getSequenceSetId())).getV_parent(); // jal.getDataset()); if (dataset == null) { dataset = (DataSet) getjv2vObj(jal.getDataset()); - Cache.log - .error("Can't find the correct dataset for the alignment in this view. Creating new one."); + Cache.log.error( + "Can't find the correct dataset for the alignment in this view. Creating new one."); } // Store any sequence mappings. @@ -2742,18 +2761,18 @@ public class VamsasAppDatastore 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]); + uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj( + dmps[smp]); if (mfrom != null) { - new jalview.io.vamsas.Sequencemapping(this, mps[smp], - mfrom, dataset); + new jalview.io.vamsas.Sequencemapping(this, mps[smp], mfrom, + dataset); } else { - Cache.log - .warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR " - + dmps[smp].getDisplayId(true) - + " to " + Cache.log.warn( + "NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR " + + dmps[smp].getDisplayId(true) + " to " + mps[smp].getTo().getName()); } } @@ -2763,8 +2782,8 @@ public class VamsasAppDatastore } catch (Exception e) { throw new Exception(MessageManager.formatMessage( - "exception.couldnt_store_sequence_mappings", - new String[] { title }), e); + "exception.couldnt_store_sequence_mappings", new String[] + { title }), e); } }