*/
package jalview.gui;
+import jalview.analysis.Conservation;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.ext.varna.RnaModel;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.FeatureColour;
-import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.util.StringUtils;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import jalview.ws.jws2.Jws2Discoverer;
import java.util.jar.JarOutputStream;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
import org.exolab.castor.xml.Marshaller;
* 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<>();
}
}
}
return sq;
}
+
/**
* @return true if the forward reference was fully resolved
*/
public jalview.datamodel.Mapping mp = _jmap;
@Override
+ public boolean isResolvable()
+ {
+ return super.isResolvable() && mp.getTo() != null;
+ };
+
+ @Override
boolean resolve()
{
SequenceI seq = getSrefDatasetSeq();
public void resolveFrefedSequences()
{
- Iterator<SeqFref> nextFref=frefedSequence.iterator();
- int toresolve=frefedSequence.size();
- int unresolved=0,failedtoresolve=0;
- while (nextFref.hasNext()) {
+ Iterator<SeqFref> nextFref = frefedSequence.iterator();
+ int toresolve = frefedSequence.size();
+ int unresolved = 0, failedtoresolve = 0;
+ while (nextFref.hasNext())
+ {
SeqFref ref = nextFref.next();
if (ref.isResolvable())
{
- try {
+ try
+ {
if (ref.resolve())
{
nextFref.remove();
- } else {
+ }
+ else
+ {
failedtoresolve++;
}
- } catch (Exception x) {
- System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref());
+ } catch (Exception x)
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ + ref.getSref());
x.printStackTrace();
failedtoresolve++;
- }
- } else {
+ }
+ }
+ else
+ {
unresolved++;
}
}
- if (unresolved>0)
+ if (unresolved > 0)
{
System.err.println("Jalview Project Import: There were " + unresolved
+ " forward references left unresolved on the stack.");
}
- if (failedtoresolve>0)
+ if (failedtoresolve > 0)
{
System.err.println("SERIOUS! " + failedtoresolve
+ " resolvable forward references failed to resolve.");
* 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();
JalviewModel object = new JalviewModel();
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
}
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<>();
// SAVE SEQUENCES
for (final SequenceI jds : rjal.getSequences())
{
final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
: jds.getDatasetSequence();
String id = seqHash(jds);
-
- if (seqRefIds.get(id) != null)
- {
- // This happens for two reasons: 1. multiple views are being serialised.
- // 2. the hashCode has collided with another sequence's code. This DOES
- // HAPPEN! (PF00072.15.stk does this)
- // JBPNote: Uncomment to debug writing out of files that do not read
- // back in due to ArrayOutOfBoundExceptions.
- // System.err.println("vamsasSeq backref: "+id+"");
- // System.err.println(jds.getName()+"
- // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(jds));
- // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
- // System.err.println(rsq.getName()+"
- // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(rsq));
- }
- else
- {
- vamsasSeq = createVamsasSequence(id, jds);
- vamsasSet.addSequence(vamsasSeq);
- seqRefIds.put(id, jds);
+ if (vamsasSetIds.get(id) == null)
+ {
+ if (seqRefIds.get(id) != null && !storeDS)
+ {
+ // This happens for two reasons: 1. multiple views are being
+ // serialised.
+ // 2. the hashCode has collided with another sequence's code. This
+ // DOES
+ // HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read
+ // back in due to ArrayOutOfBoundExceptions.
+ // System.err.println("vamsasSeq backref: "+id+"");
+ // System.err.println(jds.getName()+"
+ // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(jds));
+ // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ // System.err.println(rsq.getName()+"
+ // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(rsq));
+ }
+ else
+ {
+ vamsasSeq = createVamsasSequence(id, jds);
+ vamsasSet.addSequence(vamsasSeq);
+ vamsasSetIds.put(id, vamsasSeq);
+ seqRefIds.put(id, jds);
+ }
}
-
jseq = new JSeq();
jseq.setStart(jds.getStart());
jseq.setEnd(jds.getEnd());
if (av.isHiddenRepSequence(jds))
{
jalview.datamodel.SequenceI[] reps = av
- .getRepresentedSequences(jds)
- .getSequencesInOrder(rjal);
+ .getRepresentedSequences(jds).getSequencesInOrder(rjal);
for (int h = 0; h < reps.length; h++)
{
pdb.setFile(matchedFile); // entry.getFile());
if (pdbfiles == null)
{
- pdbfiles = new ArrayList<String>();
+ pdbfiles = new ArrayList<>();
}
if (!pdbfiles.contains(pdbId))
}
}
- if (entry.getProperty() != null && !entry.getProperty().isEmpty())
+ Enumeration<String> props = entry.getProperties();
+ if (props.hasMoreElements())
{
PdbentryItem item = new PdbentryItem();
- Hashtable properties = entry.getProperty();
- Enumeration en2 = properties.keys();
- while (en2.hasMoreElements())
+ while (props.hasMoreElements())
{
Property prop = new Property();
- String key = en2.nextElement().toString();
+ String key = props.nextElement();
prop.setName(key);
- prop.setValue(properties.get(key).toString());
+ prop.setValue(entry.getProperty(key).toString());
item.addProperty(prop);
}
pdb.addPdbentryItem(item);
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())
// group has references so set its ID field
jGroup.setId(groupRefs.get(sg));
}
- if (sg.cs != null)
+ ColourSchemeI colourScheme = sg.getColourScheme();
+ if (colourScheme != null)
{
- if (sg.cs.conservationApplied())
+ ResidueShaderI groupColourScheme = sg
+ .getGroupColourScheme();
+ if (groupColourScheme.conservationApplied())
{
- jGroup.setConsThreshold(sg.cs.getConservationInc());
+ jGroup.setConsThreshold(groupColourScheme.getConservationInc());
- if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, jms));
}
else
{
- jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(colourScheme.getSchemeName());
}
}
- else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
+ else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
{
jGroup.setColour("AnnotationColourGradient");
jGroup.setAnnotationColours(constructAnnotationColours(
- (jalview.schemes.AnnotationColourGradient) sg.cs,
+ (jalview.schemes.AnnotationColourGradient) colourScheme,
userColours, jms));
}
- else if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ else if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, jms));
}
else
{
- jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(colourScheme.getSchemeName());
}
- jGroup.setPidThreshold(sg.cs.getThreshold());
+ jGroup.setPidThreshold(groupColourScheme.getThreshold());
}
jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
view.setWidth(size.width);
view.setHeight(size.height);
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
+ view.setStartRes(vpRanges.getStartRes());
+ view.setStartSeq(vpRanges.getStartSeq());
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
.getGlobalColourScheme()));
}
+ ResidueShaderI vcs = av.getResidueShading();
ColourSchemeI cs = av.getGlobalColourScheme();
if (cs != null)
{
- if (cs.conservationApplied())
+ if (vcs.conservationApplied())
{
- view.setConsThreshold(cs.getConservationInc());
+ view.setConsThreshold(vcs.getConservationInc());
if (cs instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(setUserColourScheme(cs, userColours, jms));
}
}
-
- if (cs instanceof ResidueColourScheme)
- {
- view.setPidThreshold(cs.getThreshold());
- }
+ view.setPidThreshold(vcs.getThreshold());
}
view.setConservationSelected(av.getConservationSelected());
.getFeatureRenderer().getRenderOrder()
.toArray(new String[0]);
- Vector<String> settingsAdded = new Vector<String>();
+ Vector<String> settingsAdded = new Vector<>();
if (renderOrder != null)
{
for (String featureType : renderOrder)
{
FeatureColourI fcol = ap.getSeqPanel().seqCanvas
- .getFeatureRenderer()
- .getFeatureStyle(featureType);
+ .getFeatureRenderer().getFeatureStyle(featureType);
Setting setting = new Setting();
setting.setType(featureType);
if (!fcol.isSimpleColour())
setting.setAutoScale(fcol.isAutoScaled());
setting.setThreshold(fcol.getThreshold());
// -1 = No threshold, 0 = Below, 1 = Above
- setting.setThreshstate(fcol.isAboveThreshold() ? 1
- : (fcol.isBelowThreshold() ? 0 : -1));
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol
+ .isBelowThreshold() ? 0 : -1));
}
else
{
// is groups actually supposed to be a map here ?
Iterator<String> en = ap.getSeqPanel().seqCanvas
- .getFeatureRenderer()
- .getFeatureGroups().iterator();
- Vector<String> groupsAdded = new Vector<String>();
+ .getFeatureRenderer().getFeatureGroups().iterator();
+ 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]);
return matchedFile;
}
+ /**
+ * Populates the AnnotationColours xml for save. This captures the settings of
+ * the options in the 'Colour by Annotation' dialog.
+ *
+ * @param acg
+ * @param userColours
+ * @param jms
+ * @return
+ */
private AnnotationColours constructAnnotationColours(
AnnotationColourGradient acg, List<UserColourScheme> userColours,
JalviewModelSequence jms)
AnnotationColours ac = new AnnotationColours();
ac.setAboveThreshold(acg.getAboveThreshold());
ac.setThreshold(acg.getAnnotationThreshold());
- ac.setAnnotation(acg.getAnnotation());
- if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ // 2.10.2 save annotationId (unique) not annotation label
+ ac.setAnnotation(acg.getAnnotation().annotationId);
+ if (acg.getBaseColour() instanceof UserColourScheme)
{
ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
userColours, jms));
}
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
}
ac.setMaxColour(acg.getMaxColour().getRGB());
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
SplitFrame sf = createSplitFrame(dnaFrame, af);
addedToSplitFrames.add(dnaFrame);
addedToSplitFrames.add(af);
+ dnaFrame.setMenusForViewport();
+ af.setMenusForViewport();
if (af.viewport.isGatherViewsHere())
{
gatherTo.add(sf);
Viewport view = candidate.getKey();
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
view.getHeight());
+ af.setMenusForViewport();
System.err.println("Failed to restore view " + view.getTitle()
+ " to split frame");
}
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- finalErrorMessage, "Error "
- + (saving ? "saving" : "loading")
- + " Jalview file", JOptionPane.WARNING_MESSAGE);
+ JvOptionPane
+ .showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage, "Error "
+ + (saving ? "saving" : "loading")
+ + " Jalview file",
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
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
* @param pdbId
* @return
*/
- String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
+ String origFile)
{
if (alreadyLoadedPDB.containsKey(pdbId))
{
return alreadyLoadedPDB.get(pdbId).toString();
}
- String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
+ String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
+ origFile);
if (tempFile != null)
{
alreadyLoadedPDB.put(pdbId, tempFile);
* @param prefix
* a prefix for the temporary file name, must be at least three
* characters long
+ * @param origFile
+ * null or original file - so new file can be given the same suffix
+ * as the old one
* @return
*/
protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix)
+ String jarEntryName, String prefix, String origFile)
{
BufferedReader in = null;
PrintWriter out = null;
-
+ String suffix = ".tmp";
+ if (origFile == null)
+ {
+ origFile = jarEntryName;
+ }
+ int sfpos = origFile.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (origFile.length() - 3))
+ {
+ suffix = "." + origFile.substring(sfpos + 1);
+ }
try
{
JarInputStream jin = jprovider.getJarInputStream();
if (entry != null)
{
in = new BufferedReader(new InputStreamReader(jin, UTF_8));
- File outFile = File.createTempFile(prefix, ".tmp");
+ File outFile = File.createTempFile(prefix, suffix);
outFile.deleteOnExit();
out = new PrintWriter(new FileOutputStream(outFile));
String data;
List<SequenceI> hiddenSeqs = null;
-
- List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
+ List<SequenceI> tmpseqs = new ArrayList<>();
boolean multipleView = false;
SequenceI referenceseqForView = null;
if (!incompleteSeqs.containsKey(seqId))
{
// may not need this check, but keep it for at least 2.9,1 release
- if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
- {
+ if (tmpSeq.getStart() != jseqs[i].getStart()
+ || tmpSeq.getEnd() != jseqs[i].getEnd())
+ {
System.err
.println("Warning JAL-2154 regression: updating start/end for sequence "
- + tmpSeq.toString());
+ + tmpSeq.toString() + " to " + jseqs[i]);
}
- } else {
+ }
+ else
+ {
incompleteSeqs.remove(seqId);
}
+ if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
+ {
+ // most likely we are reading a dataset XML document so
+ // update from vamsasSeq section of XML for this sequence
+ tmpSeq.setName(vamsasSeq[vi].getName());
+ tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+ tmpSeq.setSequence(vamsasSeq[vi].getSequence());
+ vi++;
+ }
+ else
+ {
+ // reading multiple views, so vamsasSeq set is a subset of JSeq
+ multipleView = true;
+ }
tmpSeq.setStart(jseqs[i].getStart());
tmpSeq.setEnd(jseqs[i].getEnd());
tmpseqs.add(tmpSeq);
- multipleView = true;
}
else
{
{
if (hiddenSeqs == null)
{
- hiddenSeqs = new ArrayList<SequenceI>();
+ hiddenSeqs = new ArrayList<>();
}
hiddenSeqs.add(tmpSeq);
{
// load sequence features, database references and any associated PDB
// structures for the alignment
+ //
+ // prior to 2.10, this part would only be executed the first time a
+ // sequence was encountered, but not afterwards.
+ // now, for 2.10 projects, this is also done if the xml doc includes
+ // dataset sequences not actually present in any particular view.
+ //
for (int i = 0; i < vamsasSeq.length; i++)
{
if (jseqs[i].getFeaturesCount() > 0)
}
}
-
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ // adds feature to datasequence's feature set (since Jalview 2.10)
+ al.getSequenceAt(i).addSequenceFeature(sf);
}
}
if (vamsasSeq[i].getDBRefCount() > 0)
{
- addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
+ // adds dbrefs to datasequence's set (since Jalview 2.10)
+ addDBRefs(
+ al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i)
+ : al.getSequenceAt(i).getDatasetSequence(),
+ vamsasSeq[i]);
}
if (jseqs[i].getPdbidsCount() > 0)
{
entry.setId(ids[p].getId());
if (ids[p].getType() != null)
{
- if (ids[p].getType().equalsIgnoreCase("PDB"))
+ if (PDBEntry.Type.getType(ids[p].getType()) != null)
{
- entry.setType(PDBEntry.Type.PDB);
+ entry.setType(PDBEntry.Type.getType(ids[p].getType()));
}
else
{
entry.setType(PDBEntry.Type.FILE);
}
}
- if (ids[p].getFile() != null)
+ // jprovider is null when executing 'New View'
+ if (ids[p].getFile() != null && jprovider != null)
{
if (!pdbloaded.containsKey(ids[p].getFile()))
{
- entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
}
else
{
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
+ if (ids[p].getPdbentryItem() != null)
+ {
+ for (PdbentryItem item : ids[p].getPdbentryItem())
+ {
+ for (Property pr : item.getProperty())
+ {
+ entry.setProperty(pr.getName(), pr.getValue());
+ }
+ }
+ }
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(entry);
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ // adds PDBEntry to datasequence's set (since Jalview 2.10)
+ if (al.getSequenceAt(i).getDatasetSequence() != null)
+ {
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ else
+ {
+ al.getSequenceAt(i).addPDBId(entry);
+ }
}
}
}
if (maps[m].getMapping() != null)
{
mapping = addMapping(maps[m].getMapping());
- }
- if (dnaseq != null && mapping.getTo() != null)
- {
- cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
- }
- else
- {
- // defer to later
- frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
- mapping));
+ if (dnaseq != null && mapping.getTo() != null)
+ {
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
+ mapping));
+ }
}
}
al.addCodonFrame(cf);
// ////////////////////////////////
// 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);
&& jGroup.getAnnotationColours() != null)
{
addAnnotSchemeGroup = true;
- cs = null;
}
else
{
- cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(jGroup.getPidThreshold(), true);
+ cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
}
}
+ int pidThreshold = jGroup.getPidThreshold();
- Vector<SequenceI> seqs = new Vector<SequenceI>();
+ Vector<SequenceI> seqs = new Vector<>();
for (int s = 0; s < jGroup.getSeqCount(); s++)
{
SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
-
+ sg.getGroupColourScheme().setThreshold(pidThreshold, true);
+ sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold());
sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
sg.textColour = new java.awt.Color(jGroup.getTextCol1());
}
if (jGroup.getConsThreshold() != 0)
{
- jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3,
- sg.getSequences(null), 0, sg.getWidth() - 1);
+ Conservation c = new Conservation("All", sg.getSequences(null),
+ 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.cs.setConservation(c);
if (addAnnotSchemeGroup)
{
// reconstruct the annotation colourscheme
- sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
- null, al, jms, false);
+ sg.setColourScheme(constructAnnotationColour(
+ jGroup.getAnnotationColours(), null, al, jms, false));
}
}
}
String rnaTitle = ss.getTitle();
String sessionState = ss.getViewerState();
String tempStateFile = copyJarEntry(jprovider, sessionState,
- "varna");
+ "varna", null);
RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
appVarna.addModelSession(rna, rnaTitle, tempStateFile);
}
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++)
{
// Originally : ids[p].getFile()
// : TODO: verify external PDB file recovery still works in normal
// jalview project load
- jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
jpdb.setId(ids[p].getId());
int x = structureState.getXpos();
// Probably don't need to do this anymore...
// Desktop.desktop.getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile());
jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
.getId() + "");
if (sviewid == null)
*/
String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera");
+ "chimera", null);
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();
// filename
// translation differently.
StructureData filedat = oldFiles.get(new File(oldfilenam));
+ if (filedat == null)
+ {
+ String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
+ filedat = oldFiles.get(new File(reformatedOldFilename));
+ }
newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
StructureData filedat = oldFiles.get(id);
String pdbFile = filedat.getFilePath();
SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
- binding.getSsm().setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
+ binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
binding.addSequenceForStructFile(pdbFile, seq);
}
// and add the AlignmentPanel's reference to the view panel
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
uniqueSeqSetId, viewId);
- af.setFileName(file, "Jalview");
+ af.setFileName(file, FileFormat.Jalview);
for (int i = 0; i < JSEQ.length; i++)
{
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
+ af.viewport.setThreshold(view.getPidThreshold());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
+ af.viewport.setIncrement(view.getConsThreshold());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(
af.viewport.setThresholdTextColour(view.getTextColThreshold());
af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
.isShowUnconserved() : false);
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
+ af.viewport.getRanges().setStartRes(view.getStartRes());
+ // startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
// apply colourschemes
}
else
{
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.getSequenceConsensusHash());
+ cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
}
af.viewport.setGlobalColourScheme(cs);
+ af.viewport.getResidueShading().setThreshold(
+ view.getPidThreshold(), true);
+ af.viewport.getResidueShading().setConsensus(
+ af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
if (view.getConservationSelected() && cs != null)
{
- cs.setConservationInc(view.getConsThreshold());
+ af.viewport.getResidueShading().setConservationInc(
+ view.getConsThreshold());
}
af.changeColour(cs);
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);
return af;
}
+ /**
+ * Reads saved data to restore Colour by Annotation settings
+ *
+ * @param viewAnnColour
+ * @param af
+ * @param al
+ * @param jms
+ * @param checkGroupAnnColour
+ * @return
+ */
private ColourSchemeI constructAnnotationColour(
AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
JalviewModelSequence jms, boolean checkGroupAnnColour)
{
boolean propagateAnnColour = false;
- ColourSchemeI cs = null;
AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
if (checkGroupAnnColour && al.getGroups() != null
&& al.getGroups().size() > 0)
// pre 2.8.1 behaviour
// check to see if we should transfer annotation colours
propagateAnnColour = true;
- for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+ for (SequenceGroup sg : al.getGroups())
{
- if (sg.cs instanceof AnnotationColourGradient)
+ if (sg.getColourScheme() instanceof AnnotationColourGradient)
{
propagateAnnColour = false;
}
}
}
- // int find annotation
- if (annAlignment.getAlignmentAnnotation() != null)
+
+ /*
+ * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
+ */
+ String annotationId = viewAnnColour.getAnnotation();
+ AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
+
+ /*
+ * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
+ */
+ if (matchedAnnotation == null && annAlignment.getAlignmentAnnotation() != null)
{
for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
{
- if (annAlignment.getAlignmentAnnotation()[i].label
- .equals(viewAnnColour.getAnnotation()))
+ if (annotationId
+ .equals(annAlignment.getAlignmentAnnotation()[i].label))
{
- if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
- {
- annAlignment.getAlignmentAnnotation()[i]
- .setThreshold(new jalview.datamodel.GraphLine(
- viewAnnColour.getThreshold(), "Threshold",
- java.awt.Color.black)
-
- );
- }
-
- if (viewAnnColour.getColourScheme().equals("None"))
- {
- cs = new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i],
- new java.awt.Color(viewAnnColour.getMinColour()),
- new java.awt.Color(viewAnnColour.getMaxColour()),
- viewAnnColour.getAboveThreshold());
- }
- else if (viewAnnColour.getColourScheme().startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i],
- getUserColourScheme(jms,
- viewAnnColour.getColourScheme()),
- viewAnnColour.getAboveThreshold());
- }
- else
- {
- cs = new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al,
- viewAnnColour.getColourScheme()),
- viewAnnColour.getAboveThreshold());
- }
- if (viewAnnColour.hasPerSequence())
- {
- ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
- .isPerSequence());
- }
- if (viewAnnColour.hasPredefinedColours())
- {
- ((AnnotationColourGradient) cs)
- .setPredefinedColours(viewAnnColour
- .isPredefinedColours());
- }
- if (propagateAnnColour && al.getGroups() != null)
- {
- // Also use these settings for all the groups
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
-
- if (sg.cs == null)
- {
- continue;
- }
+ matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
+ break;
+ }
+ }
+ }
+ if (matchedAnnotation == null)
+ {
+ System.err.println("Failed to match annotation colour scheme for "
+ + annotationId);
+ return null;
+ }
+ if (matchedAnnotation.getThreshold() == null)
+ {
+ matchedAnnotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(),
+ "Threshold", Color.black));
+ }
- /*
- * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
- * new AnnotationColourGradient(
- * annAlignment.getAlignmentAnnotation()[i], new
- * java.awt.Color(viewAnnColour. getMinColour()), new
- * java.awt.Color(viewAnnColour. getMaxColour()),
- * viewAnnColour.getAboveThreshold()); } else
- */
- {
- sg.cs = new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i], sg.cs,
- viewAnnColour.getAboveThreshold());
- if (cs instanceof AnnotationColourGradient)
- {
- if (viewAnnColour.hasPerSequence())
- {
- ((AnnotationColourGradient) cs)
- .setSeqAssociated(viewAnnColour.isPerSequence());
- }
- if (viewAnnColour.hasPredefinedColours())
- {
- ((AnnotationColourGradient) cs)
- .setPredefinedColours(viewAnnColour
- .isPredefinedColours());
- }
- }
- }
+ AnnotationColourGradient cs = null;
+ if (viewAnnColour.getColourScheme().equals("None"))
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation, new Color(
+ viewAnnColour.getMinColour()), new Color(
+ viewAnnColour.getMaxColour()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme(
+ jms, viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(matchedAnnotation,
+ ColourSchemeProperty.getColourScheme(al,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
- }
- }
+ boolean perSequenceOnly = viewAnnColour.isPerSequence();
+ boolean useOriginalColours = viewAnnColour.isPredefinedColours();
+ cs.setSeqAssociated(perSequenceOnly);
+ cs.setPredefinedColours(useOriginalColours);
- break;
+ if (propagateAnnColour && al.getGroups() != null)
+ {
+ // Also use these settings for all the groups
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ SequenceGroup sg = al.getGroups().get(g);
+ if (sg.getGroupColourScheme() == null)
+ {
+ continue;
}
+ AnnotationColourGradient groupScheme = new AnnotationColourGradient(
+ matchedAnnotation, sg.getColourScheme(),
+ viewAnnColour.getAboveThreshold());
+ sg.setColourScheme(groupScheme);
+ groupScheme.setSeqAssociated(perSequenceOnly);
+ groupScheme.setPredefinedColours(useOriginalColours);
}
}
return cs;
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
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
}
// create a new dataset
if (ds == null)
* dataset alignment
* @param dseqs
* vector to add new dataset sequence to
+ * @param ignoreUnrefed
+ * - when true, don't create new sequences from vamsasSeq if it's id
+ * doesn't already have an asssociated Jalview sequence.
+ * @param vseqpos
+ * - used to reorder the sequence in the alignment according to the
+ * vamsasSeq array ordering, to preserve ordering of dataset
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+ boolean reorder = false;
SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
dsq = sq.getDatasetSequence();
}
+ else
+ {
+ reorder = true;
+ }
if (sq == null && ignoreUnrefed)
{
return;
// + (post ? "appended" : ""));
}
}
+ else
+ {
+ // sequence refs are identical. We may need to update the existing dataset
+ // alignment with this one, though.
+ if (ds != null && dseqs == null)
+ {
+ int opos = ds.findIndex(dsq);
+ SequenceI tseq = null;
+ if (opos != -1 && vseqpos != opos)
+ {
+ // remove from old position
+ ds.deleteSequence(dsq);
+ }
+ if (vseqpos < ds.getHeight())
+ {
+ if (vseqpos != opos)
+ {
+ // save sequence at destination position
+ tseq = ds.getSequenceAt(vseqpos);
+ ds.replaceSequenceAt(vseqpos, dsq);
+ ds.addSequence(tseq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
}
/*
{
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