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.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;
* 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();
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<String, Sequence>();
+ HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
// SAVE SEQUENCES
for (final SequenceI jds : rjal.getSequences())
{
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())
view.setWidth(size.width);
view.setHeight(size.height);
- view.setStartRes(av.getStartRes());
- view.setStartSeq(av.getStartSeq());
+ view.setStartRes(vpRanges.getStartRes());
+ view.setStartSeq(vpRanges.getStartSeq());
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
.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++)
+ for (int[] region : hidden)
{
- 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));
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
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- finalErrorMessage, "Error "
- + (saving ? "saving" : "loading")
- + " Jalview file", JvOptionPane.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
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);
// ////////////////////////////////
// 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();
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
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.getColourScheme() instanceof AnnotationColourGradient)
{
}
}
}
- // 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(
- ResidueColourScheme.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.getColourScheme(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(ResidueColourScheme.NONE)) { sg.cs =
- * new AnnotationColourGradient(
- * annAlignment.getAlignmentAnnotation()[i], new
- * java.awt.Color(viewAnnColour. getMinColour()), new
- * java.awt.Color(viewAnnColour. getMaxColour()),
- * viewAnnColour.getAboveThreshold()); } else
- */
- {
- sg.setColourScheme(new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i], sg
- .getColourScheme(), 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
{
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