import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
* Map of reconstructed AlignFrame objects that appear to have come from
* SplitFrame objects (have a dna/protein complement view).
*/
- private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
+ private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
/*
* Map from displayed rna structure models to their saved session state jar
* entry names
*/
- private Map<RnaModel, String> rnaSessions = new HashMap<RnaModel, String>();
+ private Map<RnaModel, String> rnaSessions = new HashMap<>();
/**
* create/return unique hash string for sq
{
if (seqsToIds == null)
{
- seqsToIds = new IdentityHashMap<SequenceI, String>();
+ seqsToIds = new IdentityHashMap<>();
}
if (seqRefIds == null)
{
- seqRefIds = new HashMap<String, SequenceI>();
+ seqRefIds = new HashMap<>();
}
if (incompleteSeqs == null)
{
- incompleteSeqs = new HashMap<String, SequenceI>();
+ incompleteSeqs = new HashMap<>();
}
if (frefedSequence == null)
{
- frefedSequence = new ArrayList<SeqFref>();
+ frefedSequence = new ArrayList<>();
}
}
* This maintains a map of viewports, the key being the seqSetId. Important to
* set historyItem and redoList for multiple views
*/
- Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
+ Map<String, AlignViewport> viewportsAdded = new HashMap<>();
- Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
+ Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
String uniqueSetSuffix = "";
*/
private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
{
- Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
+ Hashtable<String, AlignFrame> dsses = new Hashtable<>();
/*
* ensure cached data is clear before starting
// NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
// //////////////////////////////////////////////////
- List<String> shortNames = new ArrayList<String>();
- List<String> viewIds = new ArrayList<String>();
+ List<String> shortNames = new ArrayList<>();
+ List<String> viewIds = new ArrayList<>();
// REVERSE ORDER
for (int i = frames.size() - 1; i > -1; i--)
{
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
- List<AlignFrame> frames = new ArrayList<AlignFrame>();
+ List<AlignFrame> frames = new ArrayList<>();
// resolve splitframes
if (af.getViewport().getCodingComplement() != null)
{
if (viewIds == null)
{
- viewIds = new ArrayList<String>();
+ viewIds = new ArrayList<>();
}
initSeqRefs();
- List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
+ List<UserColourScheme> userColours = new ArrayList<>();
AlignViewport av = ap.av;
ViewportRanges vpRanges = av.getRanges();
}
JSeq jseq;
- Set<String> calcIdSet = new HashSet<String>();
+ Set<String> calcIdSet = new HashSet<>();
// record the set of vamsas sequence XML POJO we create.
- HashMap<String, Sequence> vamsasSetIds = new HashMap<String, Sequence>();
+ HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
// SAVE SEQUENCES
for (final SequenceI jds : rjal.getSequences())
{
// TODO: omit sequence features from each alignment view's XML dump if we
// are storing dataset
- if (jds.getSequenceFeatures() != null)
+ List<jalview.datamodel.SequenceFeature> sfs = jds
+ .getSequenceFeatures();
+ for (SequenceFeature sf : sfs)
{
- jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
- int index = 0;
- while (index < sf.length)
- {
- Features features = new Features();
+ Features features = new Features();
- features.setBegin(sf[index].getBegin());
- features.setEnd(sf[index].getEnd());
- features.setDescription(sf[index].getDescription());
- features.setType(sf[index].getType());
- features.setFeatureGroup(sf[index].getFeatureGroup());
- features.setScore(sf[index].getScore());
- if (sf[index].links != null)
+ features.setBegin(sf.getBegin());
+ features.setEnd(sf.getEnd());
+ features.setDescription(sf.getDescription());
+ features.setType(sf.getType());
+ features.setFeatureGroup(sf.getFeatureGroup());
+ features.setScore(sf.getScore());
+ if (sf.links != null)
+ {
+ for (int l = 0; l < sf.links.size(); l++)
{
- for (int l = 0; l < sf[index].links.size(); l++)
- {
- OtherData keyValue = new OtherData();
- keyValue.setKey("LINK_" + l);
- keyValue.setValue(sf[index].links.elementAt(l).toString());
- features.addOtherData(keyValue);
- }
+ OtherData keyValue = new OtherData();
+ keyValue.setKey("LINK_" + l);
+ keyValue.setValue(sf.links.elementAt(l).toString());
+ features.addOtherData(keyValue);
}
- if (sf[index].otherDetails != null)
+ }
+ if (sf.otherDetails != null)
+ {
+ String key;
+ Iterator<String> keys = sf.otherDetails.keySet().iterator();
+ while (keys.hasNext())
{
- String key;
- Iterator<String> keys = sf[index].otherDetails.keySet()
- .iterator();
- while (keys.hasNext())
- {
- key = keys.next();
- OtherData keyValue = new OtherData();
- keyValue.setKey(key);
- keyValue.setValue(sf[index].otherDetails.get(key).toString());
- features.addOtherData(keyValue);
- }
+ key = keys.next();
+ OtherData keyValue = new OtherData();
+ keyValue.setKey(key);
+ keyValue.setValue(sf.otherDetails.get(key).toString());
+ features.addOtherData(keyValue);
}
-
- jseq.addFeatures(features);
- index++;
}
+
+ jseq.addFeatures(features);
}
if (jdatasq.getAllPDBEntries() != null)
pdb.setFile(matchedFile); // entry.getFile());
if (pdbfiles == null)
{
- pdbfiles = new ArrayList<String>();
+ pdbfiles = new ArrayList<>();
}
if (!pdbfiles.contains(pdbId))
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
tree.setCurrentTree((av.currentTree == tp.getTree()));
- tree.setNewick(tp.getTree().toString());
+ tree.setNewick(tp.getTree().print());
tree.setThreshold(tp.treeCanvas.threshold);
tree.setFitToWindow(tp.fitToWindow.getState());
/**
* store forward refs from an annotationRow to any groups
*/
- IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<SequenceGroup, String>();
+ IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
if (storeDS)
{
for (SequenceI sq : jal.getSequences())
.getFeatureRenderer().getRenderOrder()
.toArray(new String[0]);
- Vector<String> settingsAdded = new Vector<String>();
+ Vector<String> settingsAdded = new Vector<>();
if (renderOrder != null)
{
for (String featureType : renderOrder)
// is groups actually supposed to be a map here ?
Iterator<String> en = ap.getSeqPanel().seqCanvas
.getFeatureRenderer().getFeatureGroups().iterator();
- Vector<String> groupsAdded = new Vector<String>();
+ Vector<String> groupsAdded = new Vector<>();
while (en.hasNext())
{
String grp = en.next();
if (av.hasHiddenColumns())
{
- if (av.getColumnSelection() == null
- || av.getColumnSelection().getHiddenColumns() == null)
+ jalview.datamodel.HiddenColumns hidden = av.getAlignment()
+ .getHiddenColumns();
+ if (hidden == null)
{
warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
else
{
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
- .size(); c++)
+ ArrayList<int[]> hiddenRegions = hidden
+ .getHiddenColumnsCopy();
+ for (int[] region : hiddenRegions)
{
- int[] region = av.getColumnSelection().getHiddenColumns()
- .get(c);
HiddenColumns hc = new HiddenColumns();
hc.setStart(region[0]);
hc.setEnd(region[1]);
try
{
// create list to store references for any new Jmol viewers created
- newStructureViewers = new Vector<JalviewStructureDisplayI>();
+ newStructureViewers = new Vector<>();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
initSeqRefs();
}
AlignFrame af = null, _af = null;
- IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
- Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
+ IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
+ Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
final String file = jprovider.getFilename();
try
{
*/
protected void restoreSplitFrames()
{
- List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
- List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
- Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
+ List<SplitFrame> gatherTo = new ArrayList<>();
+ List<AlignFrame> addedToSplitFrames = new ArrayList<>();
+ Map<String, AlignFrame> dna = new HashMap<>();
/*
* Identify the DNA alignments
errorMessage = null;
}
- Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
+ Map<String, String> alreadyLoadedPDB = new HashMap<>();
/**
* when set, local views will be updated from view stored in JalviewXML
List<SequenceI> hiddenSeqs = null;
- List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
+ List<SequenceI> tmpseqs = new ArrayList<>();
boolean multipleView = false;
SequenceI referenceseqForView = null;
{
if (hiddenSeqs == null)
{
- hiddenSeqs = new ArrayList<SequenceI>();
+ hiddenSeqs = new ArrayList<>();
}
hiddenSeqs.add(tmpSeq);
Features[] features = jseqs[i].getFeatures();
for (int f = 0; f < features.length; f++)
{
- jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
- features[f].getType(), features[f].getDescription(),
- features[f].getStatus(), features[f].getBegin(),
- features[f].getEnd(), features[f].getFeatureGroup());
-
- sf.setScore(features[f].getScore());
+ SequenceFeature sf = new SequenceFeature(features[f].getType(),
+ features[f].getDescription(), features[f].getBegin(),
+ features[f].getEnd(), features[f].getScore(),
+ features[f].getFeatureGroup());
+ sf.setStatus(features[f].getStatus());
for (int od = 0; od < features[f].getOtherDataCount(); od++)
{
OtherData keyValue = features[f].getOtherData(od);
// ////////////////////////////////
// LOAD ANNOTATIONS
- List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
+ List<JvAnnotRow> autoAlan = new ArrayList<>();
/*
* store any annotations which forward reference a group's ID
*/
- Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
+ Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
if (vamsasSet.getAnnotationCount() > 0)
{
.get(an[i].getGroupRef());
if (aal == null)
{
- aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+ aal = new ArrayList<>();
groupAnnotRefs.put(an[i].getGroupRef(), aal);
}
aal.add(jaa);
}
int pidThreshold = jGroup.getPidThreshold();
- Vector<SequenceI> seqs = new Vector<SequenceI>();
+ Vector<SequenceI> seqs = new Vector<>();
for (int s = 0; s < jGroup.getSeqCount(); s++)
{
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{
- tp = af.ShowNewickTree(
+ tp = af.showNewickTree(
new jalview.io.NewickFile(tree.getNewick()),
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());
* Run through all PDB ids on the alignment, and collect mappings between
* distinct view ids and all sequences referring to that view.
*/
- Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
+ Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
for (int i = 0; i < jseqs.length; i++)
{
Set<Entry<File, StructureData>> fileData = data.getFileData()
.entrySet();
- List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
- List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
+ List<PDBEntry> pdbs = new ArrayList<>();
+ List<SequenceI[]> allseqs = new ArrayList<>();
for (Entry<File, StructureData> pdb : fileData)
{
String filePath = pdb.getValue().getFilePath();
getViewerJarEntryName(svattrib.getViewId()));
}
- List<String> pdbfilenames = new ArrayList<String>();
- List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
- List<String> pdbids = new ArrayList<String>();
+ List<String> pdbfilenames = new ArrayList<>();
+ List<SequenceI[]> seqmaps = new ArrayList<>();
+ List<String> pdbids = new ArrayList<>();
StringBuilder newFileLoc = new StringBuilder(64);
int cp = 0, ncp, ecp;
Map<File, StructureData> oldFiles = svattrib.getFileData();
}
// recover view properties and display parameters
- if (view.getViewName() != null)
- {
- af.viewport.viewName = view.getViewName();
- af.setInitialTabVisible();
- }
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
- view.getHeight());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
.isShowUnconserved() : false);
af.viewport.getRanges().setStartRes(view.getStartRes());
+
+ if (view.getViewName() != null)
+ {
+ af.viewport.viewName = view.getViewName();
+ af.setInitialTabVisible();
+ }
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+ view.getHeight());
// startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
}
af.viewport.setGlobalColourScheme(cs);
- af.viewport.getResidueShading().setThreshold(
- view.getPidThreshold(), true);
+ af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
+ view.getIgnoreGapsinConsensus());
af.viewport.getResidueShading().setConsensus(
af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
- Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
- Map<String, Float> featureOrder = new Hashtable<String, Float>();
+ Map<String, FeatureColourI> featureColours = new Hashtable<>();
+ Map<String, Float> featureOrder = new Hashtable<>();
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
fdi.setVisible(setting.getType());
}
}
- Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
+ Map<String, Boolean> fgtable = new Hashtable<>();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
String[] magicNames = new String[] { "Consensus", "Quality",
"Conservation" };
JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
- Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
+ Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
for (String nm : magicNames)
{
visan.put(nm, nullAnnot);
+ auan.template.getCalcId()), auan);
}
int hSize = al.getAlignmentAnnotation().length;
- List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+ List<JvAnnotRow> reorder = new ArrayList<>();
// work through any autoCalculated annotation already on the view
// removing it if it should be placed in a different location on the
// annotation panel.
- List<String> remains = new ArrayList<String>(visan.keySet());
+ List<String> remains = new ArrayList<>(visan.keySet());
for (int h = 0; h < hSize; h++)
{
jalview.datamodel.AlignmentAnnotation jalan = al
{
if (datasetIds == null)
{
- datasetIds = new Hashtable<String, AlignmentI>();
+ datasetIds = new Hashtable<>();
return null;
}
if (datasetIds.containsKey(datasetId))
{
if (datasetIds == null)
{
- datasetIds = new Hashtable<String, AlignmentI>();
+ datasetIds = new Hashtable<>();
}
datasetIds.put(datasetId, dataset);
}
// make a new datasetId and record it
if (dataset2Ids == null)
{
- dataset2Ids = new IdentityHashMap<AlignmentI, String>();
+ dataset2Ids = new IdentityHashMap<>();
}
else
{
// register sequence object so the XML parser can recover it.
if (seqRefIds == null)
{
- seqRefIds = new HashMap<String, SequenceI>();
+ seqRefIds = new HashMap<>();
}
if (seqsToIds == null)
{
- seqsToIds = new IdentityHashMap<SequenceI, String>();
+ seqsToIds = new IdentityHashMap<>();
}
seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
seqsToIds.put((SequenceI) jvobj, id);
git://source.jalview.org / jalview.git / blobdiff