--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="bin/main" path="src">
+ <attributes>
+ <attribute name="gradle_scope" value="main"/>
+ <attribute name="gradle_used_by_scope" value=""/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="bin/test" path="test">
+ <attributes>
+ <attribute name="test" value="true"/>
+ <attribute name="gradle_scope" value="test"/>
+ <attribute name="gradle_used_by_scope" value=""/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+ <attributes>
+ <attribute name="module" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
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- <classpathentry kind="lib" path="resources"/>
- <classpathentry kind="lib" path="j11lib/apache-mime4j-0.6.jar"/>
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- <classpathentry kind="lib" path="utils/ant-contrib-1.0b3.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/axis-ant.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/classgraph-4.1.6.jar">
- <attributes>
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- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/hamcrest-core-1.3.jar">
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- </classpathentry>
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- </classpathentry>
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- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/testnglibs/bsh-2.0b4.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/testnglibs/guava-collections-r03.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/testnglibs/jcommander.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/testnglibs/junit-4.12.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/testnglibs/snakeyaml.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/testnglibs/testng-sources.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/testnglibs/testng.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="utils/wsdl4j.jar">
- <attributes>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
+ <classpathentry kind="output" path="bin/main"/>
+</classpath>
*/
package jalview.analysis;
--import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
--
+ import jalview.commands.RemoveGapColCommand;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
--import jalview.io.gff.Gff3Helper;
import jalview.io.gff.SequenceOntologyI;
import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.util.IntRangeComparator;
import jalview.util.MapList;
import jalview.util.MappingUtils;
--import jalview.util.StringUtils;
--import java.io.UnsupportedEncodingException;
--import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
return false;
}
String name = seq2.getName();
- final DBRefEntry[] xrefs = seq1.getDBRefs();
+ final List<DBRefEntry> xrefs = seq1.getDBRefs();
if (xrefs != null)
{
- for (DBRefEntry xref : xrefs)
+ for (int ix = 0, nx = xrefs.size(); ix < nx; ix++)
{
- DBRefEntry xref = xrefs.get(ix);
++ DBRefEntry xref = xrefs.get(ix);
String xrefName = xref.getSource() + "|" + xref.getAccessionId();
// case-insensitive test, consistent with DBRefEntry.equalRef()
if (xrefName.equalsIgnoreCase(name))
List<DBRefEntry> direct = new ArrayList<>();
HashSet<String> directSources = new HashSet<>();
- if (contig.getDBRefs() != null)
+ List<DBRefEntry> refs = contig.getDBRefs();
+ if (refs != null)
{
- for (DBRefEntry dbr : contig.getDBRefs())
+ for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
- DBRefEntry dbr = refs.get(ib);
- MapList map;
- if (dbr.hasMap() && dbr.getMap().getMap().isTripletMap())
++ DBRefEntry dbr = refs.get(ib);
++ MapList map;
+ if (dbr.hasMap() && (map = dbr.getMap().getMap()).isTripletMap())
{
- MapList map = dbr.getMap().getMap();
// check if map is the CDS mapping
if (mapping.getMap().equals(map))
{
List<DBRefEntry> propagated = new ArrayList<>();
// and generate appropriate mappings
- for (DBRefEntry cdsref : direct)
+ for (int ic = 0, nc = direct.size(); ic < nc; ic++)
{
- DBRefEntry cdsref = direct.get(ic);
- Mapping m = cdsref.getMap();
++ DBRefEntry cdsref = direct.get(ic);
++ Mapping m = cdsref.getMap();
// clone maplist and mapping
MapList cdsposmap = new MapList(
Arrays.asList(new int[][]
{ new int[] { cdsSeq.getStart(), cdsSeq.getEnd() } }),
- cdsref.getMap().getMap().getToRanges(), 3, 1);
- Mapping cdsmap = new Mapping(cdsref.getMap().getTo(),
- cdsref.getMap().getMap());
+ m.getMap().getToRanges(), 3, 1);
- Mapping cdsmap = new Mapping(m.getTo(),m.getMap());
++ Mapping cdsmap = new Mapping(m.getTo(), m.getMap());
// create dbref
DBRefEntry newref = new DBRefEntry(cdsref.getSource(),
int phase = 0;
try
{
- phase = Integer.parseInt(sf.getPhase());
+ String s = sf.getPhase();
+ if (s != null)
+ {
+ phase = Integer.parseInt(s);
+ }
} catch (NumberFormatException e)
{
- // SwingJS -- need to avoid these.
- // ignore
++ // leave as zero
}
/*
* phase > 0 on first codon means 5' incomplete - skip to the start
}
/**
- * Maps exon features from dna to protein, and computes variants in peptide
- * product generated by variants in dna, and adds them as sequence_variant
- * features on the protein sequence. Returns the number of variant features
- * added.
- *
- * @param dnaSeq
- * @param peptide
- * @param dnaToProtein
- */
- public static int computeProteinFeatures(SequenceI dnaSeq,
- SequenceI peptide, MapList dnaToProtein)
- {
- while (dnaSeq.getDatasetSequence() != null)
- {
- dnaSeq = dnaSeq.getDatasetSequence();
- }
- while (peptide.getDatasetSequence() != null)
- {
- peptide = peptide.getDatasetSequence();
- }
-
- transferFeatures(dnaSeq, peptide, dnaToProtein, SequenceOntologyI.EXON);
-
- /*
- * compute protein variants from dna variants and codon mappings;
- * NB - alternatively we could retrieve this using the REST service e.g.
- * http://rest.ensembl.org/overlap/translation
- * /ENSP00000288602?feature=transcript_variation;content-type=text/xml
- * which would be a bit slower but possibly more reliable
- */
-
- /*
- * build a map with codon variations for each potentially varying peptide
- */
- LinkedHashMap<Integer, List<DnaVariant>[]> variants = buildDnaVariantsMap(
- dnaSeq, dnaToProtein);
-
- /*
- * scan codon variations, compute peptide variants and add to peptide sequence
- */
- int count = 0;
- for (Entry<Integer, List<DnaVariant>[]> variant : variants.entrySet())
- {
- int peptidePos = variant.getKey();
- List<DnaVariant>[] codonVariants = variant.getValue();
- count += computePeptideVariants(peptide, peptidePos, codonVariants);
- }
-
- return count;
- }
-
- /**
- * Computes non-synonymous peptide variants from codon variants and adds them
- * as sequence_variant features on the protein sequence (one feature per
- * allele variant). Selected attributes (variant id, clinical significance)
- * are copied over to the new features.
- *
- * @param peptide
- * the protein sequence
- * @param peptidePos
- * the position to compute peptide variants for
- * @param codonVariants
- * a list of dna variants per codon position
- * @return the number of features added
- */
- static int computePeptideVariants(SequenceI peptide, int peptidePos,
- List<DnaVariant>[] codonVariants)
- {
- String residue = String.valueOf(peptide.getCharAt(peptidePos - 1));
- int count = 0;
- String base1 = codonVariants[0].get(0).base;
- String base2 = codonVariants[1].get(0).base;
- String base3 = codonVariants[2].get(0).base;
-
- /*
- * variants in first codon base
- */
- for (DnaVariant dnavar : codonVariants[0])
- {
- if (dnavar.variant != null)
- {
- String alleles = (String) dnavar.variant.getValue(Gff3Helper.ALLELES);
- if (alleles != null)
- {
- for (String base : alleles.split(","))
- {
- if (!base1.equalsIgnoreCase(base))
- {
- String codon = base.toUpperCase() + base2.toLowerCase()
- + base3.toLowerCase();
- String canonical = base1.toUpperCase() + base2.toLowerCase()
- + base3.toLowerCase();
- if (addPeptideVariant(peptide, peptidePos, residue, dnavar,
- codon, canonical))
- {
- count++;
- }
- }
- }
- }
- }
- }
-
- /*
- * variants in second codon base
- */
- for (DnaVariant var : codonVariants[1])
- {
- if (var.variant != null)
- {
- String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
- if (alleles != null)
- {
- for (String base : alleles.split(","))
- {
- if (!base2.equalsIgnoreCase(base))
- {
- String codon = base1.toLowerCase() + base.toUpperCase()
- + base3.toLowerCase();
- String canonical = base1.toLowerCase() + base2.toUpperCase()
- + base3.toLowerCase();
- if (addPeptideVariant(peptide, peptidePos, residue, var,
- codon, canonical))
- {
- count++;
- }
- }
- }
- }
- }
- }
-
- /*
- * variants in third codon base
- */
- for (DnaVariant var : codonVariants[2])
- {
- if (var.variant != null)
- {
- String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
- if (alleles != null)
- {
- for (String base : alleles.split(","))
- {
- if (!base3.equalsIgnoreCase(base))
- {
- String codon = base1.toLowerCase() + base2.toLowerCase()
- + base.toUpperCase();
- String canonical = base1.toLowerCase() + base2.toLowerCase()
- + base3.toUpperCase();
- if (addPeptideVariant(peptide, peptidePos, residue, var,
- codon, canonical))
- {
- count++;
- }
- }
- }
- }
- }
- }
-
- return count;
- }
-
- /**
-- * Helper method that adds a peptide variant feature. ID and
-- * clinical_significance attributes of the dna variant (if present) are copied
-- * to the new feature.
-- *
-- * @param peptide
-- * @param peptidePos
-- * @param residue
-- * @param var
-- * @param codon
-- * the variant codon e.g. aCg
-- * @param canonical
-- * the 'normal' codon e.g. aTg
-- * @return true if a feature was added, else false
-- */
-- static boolean addPeptideVariant(SequenceI peptide, int peptidePos,
-- String residue, DnaVariant var, String codon, String canonical)
-- {
-- /*
-- * get peptide translation of codon e.g. GAT -> D
-- * note that variants which are not single alleles,
-- * e.g. multibase variants or HGMD_MUTATION etc
-- * are currently ignored here
-- */
-- String trans = codon.contains("-") ? null
-- : (codon.length() > CODON_LENGTH ? null
-- : ResidueProperties.codonTranslate(codon));
-- if (trans == null)
-- {
-- return false;
-- }
-- String desc = canonical + "/" + codon;
-- String featureType = "";
-- if (trans.equals(residue))
-- {
-- featureType = SequenceOntologyI.SYNONYMOUS_VARIANT;
-- }
-- else if (ResidueProperties.STOP.equals(trans))
-- {
-- featureType = SequenceOntologyI.STOP_GAINED;
-- }
-- else
-- {
-- String residue3Char = StringUtils
-- .toSentenceCase(ResidueProperties.aa2Triplet.get(residue));
-- String trans3Char = StringUtils
-- .toSentenceCase(ResidueProperties.aa2Triplet.get(trans));
-- desc = "p." + residue3Char + peptidePos + trans3Char;
-- featureType = SequenceOntologyI.NONSYNONYMOUS_VARIANT;
-- }
-- SequenceFeature sf = new SequenceFeature(featureType, desc, peptidePos,
-- peptidePos, var.getSource());
--
-- StringBuilder attributes = new StringBuilder(32);
-- String id = (String) var.variant.getValue(VARIANT_ID);
-- if (id != null)
-- {
-- if (id.startsWith(SEQUENCE_VARIANT))
-- {
-- id = id.substring(SEQUENCE_VARIANT.length());
-- }
-- sf.setValue(VARIANT_ID, id);
-- attributes.append(VARIANT_ID).append("=").append(id);
-- // TODO handle other species variants JAL-2064
-- StringBuilder link = new StringBuilder(32);
-- try
-- {
-- link.append(desc).append(" ").append(id).append(
-- "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
-- .append(URLEncoder.encode(id, "UTF-8"));
-- sf.addLink(link.toString());
-- } catch (UnsupportedEncodingException e)
-- {
-- // as if
-- }
-- }
-- String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE);
-- if (clinSig != null)
-- {
-- sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
-- attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=")
-- .append(clinSig);
-- }
-- peptide.addSequenceFeature(sf);
-- if (attributes.length() > 0)
-- {
-- sf.setAttributes(attributes.toString());
-- }
-- return true;
-- }
--
-- /**
- * Builds a map whose key is position in the protein sequence, and value is a
- * list of the base and all variants for each corresponding codon position.
- * <p>
- * This depends on dna variants being held as a comma-separated list as
- * property "alleles" on variant features.
- *
- * @param dnaSeq
- * @param dnaToProtein
- * @return
- */
- @SuppressWarnings("unchecked")
- static LinkedHashMap<Integer, List<DnaVariant>[]> buildDnaVariantsMap(
- SequenceI dnaSeq, MapList dnaToProtein)
- {
- /*
- * map from peptide position to all variants of the codon which codes for it
- * LinkedHashMap ensures we keep the peptide features in sequence order
- */
- LinkedHashMap<Integer, List<DnaVariant>[]> variants = new LinkedHashMap<>();
-
- List<SequenceFeature> dnaFeatures = dnaSeq.getFeatures()
- .getFeaturesByOntology(SequenceOntologyI.SEQUENCE_VARIANT);
- if (dnaFeatures.isEmpty())
- {
- return variants;
- }
-
- int dnaStart = dnaSeq.getStart();
- int[] lastCodon = null;
- int lastPeptidePostion = 0;
-
- /*
- * build a map of codon variations for peptides
- */
- for (SequenceFeature sf : dnaFeatures)
- {
- int dnaCol = sf.getBegin();
- if (dnaCol != sf.getEnd())
- {
- // not handling multi-locus variant features
- continue;
- }
-
- /*
- * ignore variant if not a SNP
- */
- String alls = (String) sf.getValue(Gff3Helper.ALLELES);
- if (alls == null)
- {
- continue; // non-SNP VCF variant perhaps - can't process this
- }
-
- String[] alleles = alls.toUpperCase().split(",");
- boolean isSnp = true;
- for (String allele : alleles)
- {
- if (allele.trim().length() > 1)
- {
- isSnp = false;
- }
- }
- if (!isSnp)
- {
- continue;
- }
-
- int[] mapsTo = dnaToProtein.locateInTo(dnaCol, dnaCol);
- if (mapsTo == null)
- {
- // feature doesn't lie within coding region
- continue;
- }
- int peptidePosition = mapsTo[0];
- List<DnaVariant>[] codonVariants = variants.get(peptidePosition);
- if (codonVariants == null)
- {
- codonVariants = new ArrayList[CODON_LENGTH];
- codonVariants[0] = new ArrayList<>();
- codonVariants[1] = new ArrayList<>();
- codonVariants[2] = new ArrayList<>();
- variants.put(peptidePosition, codonVariants);
- }
-
- /*
- * get this peptide's codon positions e.g. [3, 4, 5] or [4, 7, 10]
- */
- int[] codon = peptidePosition == lastPeptidePostion ? lastCodon
- : MappingUtils.flattenRanges(dnaToProtein.locateInFrom(
- peptidePosition, peptidePosition));
- lastPeptidePostion = peptidePosition;
- lastCodon = codon;
-
- /*
- * save nucleotide (and any variant) for each codon position
- */
- for (int codonPos = 0; codonPos < CODON_LENGTH; codonPos++)
- {
- String nucleotide = String.valueOf(
- dnaSeq.getCharAt(codon[codonPos] - dnaStart)).toUpperCase();
- List<DnaVariant> codonVariant = codonVariants[codonPos];
- if (codon[codonPos] == dnaCol)
- {
- if (!codonVariant.isEmpty()
- && codonVariant.get(0).variant == null)
- {
- /*
- * already recorded base value, add this variant
- */
- codonVariant.get(0).variant = sf;
- }
- else
- {
- /*
- * add variant with base value
- */
- codonVariant.add(new DnaVariant(nucleotide, sf));
- }
- }
- else if (codonVariant.isEmpty())
- {
- /*
- * record (possibly non-varying) base value
- */
- codonVariant.add(new DnaVariant(nucleotide));
- }
- }
- }
- return variants;
- }
-
- /**
* Makes an alignment with a copy of the given sequences, adding in any
* non-redundant sequences which are mapped to by the cross-referenced
* sequences.
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
if (xrefs != null)
{
- // BH 2019.01.25 streamlined this triply nested loop to remove all iterators
- for (SequenceI xref : xrefs)
++ // BH 2019.01.25 recoded to remove iterators
+
+ for (int ix = 0, nx = xrefs.length; ix < nx; ix++)
{
- DBRefEntry[] dbrefs = xref.getDBRefs();
+ SequenceI xref = xrefs[ix];
+ List<DBRefEntry> dbrefs = xref.getDBRefs();
if (dbrefs != null)
{
- for (DBRefEntry dbref : dbrefs)
+ for (int ir = 0, nir = dbrefs.size(); ir < nir; ir++)
{
- DBRefEntry dbref = dbrefs.get(ir);
- Mapping map = dbref.getMap();
- SequenceI mto;
- if (dbref.getMap() == null || dbref.getMap().getTo() == null
- || dbref.getMap().getTo().isProtein() != isProtein)
++ DBRefEntry dbref = dbrefs.get(ir);
++ Mapping map = dbref.getMap();
++ SequenceI mto;
+ if (map == null || (mto = map.getTo()) == null
+ || mto.isProtein() != isProtein)
{
continue;
}
private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
boolean fromDna)
{
- List<DBRefEntry> dbrSourceSet = new ArrayList<DBRefEntry>(sourceRefs);
- DBRefEntry[] dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
- for (SequenceI sq : dataset.getSequences())
++ List<DBRefEntry> dbrSourceSet = new ArrayList<>(sourceRefs);
+ List<SequenceI> dsSeqs = dataset.getSequences();
+ for (int ids = 0, nds = dsSeqs.size(); ids < nds; ids++)
{
+ SequenceI sq = dsSeqs.get(ids);
boolean dupeFound = false;
// !fromDna means we are looking only for nucleotide sequences, not
// protein
*/
Object[][] originalData;
- private float originalTransparency;
+ float originalTransparency;
- Map<String, FeatureMatcherSetI> originalFilters;
+ private ViewStyleI originalViewStyle;
+
+ private Map<String, FeatureMatcherSetI> originalFilters;
final JInternalFrame frame;
if (evt.isPopupTrigger())
{
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
+ showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
- else if (evt.getClickCount() == 2)
+ else if (evt.getClickCount() == 2
+ && table.columnAtPoint(pt) == TYPE_COLUMN)
{
boolean invertSelection = evt.isAltDown();
boolean toggleSelection = Platform.isControlDown(evt);
javax.swing.event.InternalFrameEvent evt)
{
fr.removePropertyChangeListener(change);
-- };
++ }
});
frame.setLayer(JLayeredPane.PALETTE_LAYER);
inConstruction = false;
* save the colour, and repaint stuff
*/
fr.setColour(featureType, acg);
- ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
+ refreshDisplay(updateStructsAndOverview);
- updateColoursTab();
+ updateColoursPanel();
}
/**
* (note this might now be an empty filter with no conditions)
*/
fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
- ap.paintAlignment(true, true);
+ refreshDisplay(true);
- updateFiltersTab();
+ updateFiltersPanel();
}
+
+ /**
+ * Repaints alignment, structure and overview (if shown). If there is a
+ * complementary view which is showing this view's features, then also
+ * repaints that.
+ *
+ * @param updateStructsAndOverview
+ */
+ void refreshDisplay(boolean updateStructsAndOverview)
+ {
+ ap.paintAlignment(true, updateStructsAndOverview);
+ AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
+ if (complement != null && complement.isShowComplementFeatures())
+ {
+ AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+ af2.alignPanel.paintAlignment(true, updateStructsAndOverview);
+ }
+ }
}
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.util.UrlLink;
+ import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
/**
* Opens a panel showing a text report of feature dteails
*
+ * @param seqName
+ *
* @param sf
*/
- protected void showFeatureDetails(SequenceFeature sf)
+ protected void showFeatureDetails(String seqName, SequenceFeature sf)
{
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
- // it appears Java's CSS does not support border-collapse :-(
- cap.addStylesheetRule("table { border-collapse: collapse;}");
- cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
- cap.setText(sf.getDetailsReport(seqName));
-
- Desktop.addInternalFrame(cap,
+ JInternalFrame details;
+ if (Platform.isJS())
+ {
+ details = new JInternalFrame();
+ JPanel panel = new JPanel(new BorderLayout());
+ panel.setOpaque(true);
+ panel.setBackground(Color.white);
+ // TODO JAL-3026 set style of table correctly for feature details
+ JLabel reprt = new JLabel(MessageManager
+ .formatMessage("label.html_content", new Object[]
- { sf.getDetailsReport() }));
++ { sf.getDetailsReport(seqName) }));
+ reprt.setBackground(Color.WHITE);
+ reprt.setOpaque(true);
+ panel.add(reprt, BorderLayout.CENTER);
+ details.setContentPane(panel);
+ details.pack();
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ // it appears Java's CSS does not support border-collaps :-(
+ cap.addStylesheetRule("table { border-collapse: collapse;}");
+ cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
- cap.setText(sf.getDetailsReport());
++ cap.setText(sf.getDetailsReport(seqName));
+ details = cap;
+ }
+ Desktop.addInternalFrame(details,
MessageManager.getString("label.feature_details"), 500, 500);
}
Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
continue;
}
-- ;
if (!urlLink.isValid())
{
Cache.log.error(urlLink.getInvalidMessage());
createSequenceDetailsReport(ap.av.getSequenceSelection());
}
- protected void sequenceDetails_actionPerformed()
- {
- createSequenceDetailsReport(new SequenceI[] { sequence });
- }
-
public void createSequenceDetailsReport(SequenceI[] sequences)
{
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
StringBuilder contents = new StringBuilder(128);
+ contents.append("<html><body>");
for (SequenceI seq : sequences)
{
contents.append("<p><h2>" + MessageManager.formatMessage(
*/
protected void outline_actionPerformed()
{
- SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_outline_colour"),
- Color.BLUE);
-
- if (col != null)
+ String title = MessageManager
+ .getString("label.select_outline_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- sg.setOutlineColour(col);
- }
-
- refresh();
+ @Override
+ public void colourSelected(Color c)
+ {
+ getGroup().setOutlineColour(c);
+ refresh();
- };
++ }
+ };
+ JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
+ title, Color.BLUE, listener);
}
/**
}
}
- public void colourByStructure(String pdbid)
- {
- Annotation[] anots = ap.av.getStructureSelectionManager()
- .colourSequenceFromStructure(sequence, pdbid);
-
- AlignmentAnnotation an = new AlignmentAnnotation("Structure",
- "Coloured by " + pdbid, anots);
-
- ap.av.getAlignment().addAnnotation(an);
- an.createSequenceMapping(sequence, 0, true);
- // an.adjustForAlignment();
- ap.av.getAlignment().setAnnotationIndex(an, 0);
-
- ap.adjustAnnotationHeight();
-
- sequence.addAlignmentAnnotation(an);
-
- }
-
- public void editSequence_actionPerformed(ActionEvent actionEvent)
+ /**
+ * Shows a dialog where sequence characters may be edited. Any changes are
+ * applied, and added as an available 'Undo' item in the edit commands
+ * history.
+ */
+ public void editSequence_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
}
EditNameDialog dialog = new EditNameDialog(
- sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1),
- seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1),
- null, MessageManager.getString("label.edit_sequence"), null,
++ seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
+ null, MessageManager.getString("label.edit_sequence"), null);
+ dialog.showDialog(ap.alignFrame,
MessageManager.getString("label.edit_sequence"),
- ap.alignFrame);
-
- if (dialog.accept)
- {
- EditCommand editCommand = new EditCommand(
- MessageManager.getString("label.edit_sequences"),
- Action.REPLACE,
- dialog.getName().replace(' ', ap.av.getGapCharacter()),
- sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
-
- ap.alignFrame.addHistoryItem(editCommand);
-
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
- }
+ new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE,
+ dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(
+ ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
+ ap.alignFrame.addHistoryItem(editCommand);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ }
+ });
}
}
* Wrapped mode, but not the scale above in Unwrapped mode.
*
*/
-public class SeqCanvas extends JComponent implements ViewportListenerI
+@SuppressWarnings("serial")
+public class SeqCanvas extends JPanel implements ViewportListenerI
{
- /*
- * pixels gap between sequences and annotations when in wrapped mode
+ /**
+ * vertical gap in pixels between sequences and annotations when in wrapped mode
*/
static final int SEQS_ANNOTATION_GAP = 3;
return filter == null ? true : filter.matches(sf);
}
+ /**
+ * Answers true unless the specified group is set to hidden. Defaults to true
+ * if group visibility is not set.
+ *
+ * @param group
+ * @return
+ */
+ public boolean isGroupVisible(String group)
+ {
+ if (!featureGroups.containsKey(group))
+ {
+ return true;
+ }
+ return featureGroups.get(group);
+ }
+
+ /**
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
+ */
+ public void orderFeatures(Comparator<String> order)
+ {
+ Arrays.sort(renderOrder, order);
+ }
+
@Override
+ public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
+ int pos)
+ {
+ SequenceI ds = sequence.getDatasetSequence();
+ if (ds == null)
+ {
+ ds = sequence;
+ }
+ final char residue = ds.getCharAt(pos - ds.getStart());
+
+ List<SequenceFeature> found = new ArrayList<>();
+ List<AlignedCodonFrame> mappings = this.av.getAlignment()
+ .getCodonFrame(sequence);
+
+ /*
+ * fudge: if no mapping found, check the complementary alignment
+ * todo: only store in one place? StructureSelectionManager?
+ */
+ if (mappings.isEmpty())
+ {
+ mappings = this.av.getCodingComplement().getAlignment()
+ .getCodonFrame(sequence);
+ }
+
+ /*
+ * todo: direct lookup of CDS for peptide and vice-versa; for now,
+ * have to search through an unordered list of mappings for a candidate
+ */
+ Mapping mapping = null;
+ SequenceI mapFrom = null;
+
+ for (AlignedCodonFrame acf : mappings)
+ {
+ mapping = acf.getMappingForSequence(sequence);
+ if (mapping == null || !mapping.getMap().isTripletMap())
+ {
+ continue; // we are only looking for 3:1 or 1:3 mappings
+ }
+ SearchResultsI sr = new SearchResults();
+ acf.markMappedRegion(ds, pos, sr);
+ for (SearchResultMatchI match : sr.getResults())
+ {
+ int fromRes = match.getStart();
+ int toRes = match.getEnd();
+ mapFrom = match.getSequence();
+ List<SequenceFeature> fs = findFeaturesAtResidue(
+ match.getSequence(), fromRes, toRes);
+ for (SequenceFeature sf : fs)
+ {
+ if (!found.contains(sf))
+ {
+ found.add(sf);
+ }
+ }
+ }
+
+ /*
+ * just take the first mapped features we find
+ */
+ if (!found.isEmpty())
+ {
+ break;
+ }
+ }
+ if (found.isEmpty())
+ {
+ return null;
+ }
+
+ /*
+ * sort by renderorder, inefficiently
+ */
+ List<SequenceFeature> result = new ArrayList<>();
+ for (String type : renderOrder)
+ {
+ for (SequenceFeature sf : found)
+ {
+ if (type.equals(sf.getType()))
+ {
+ result.add(sf);
+ if (result.size() == found.size())
+ {
+ return new MappedFeatures(mapping, mapFrom, pos, residue,
+ result);
+ }
+ }
+ }
+ }
+
+ return new MappedFeatures(mapping, mapFrom, pos, residue, result);
+ }
+
+ @Override
public boolean isVisible(SequenceFeature feature)
{
if (feature == null)
git://source.jalview.org / jalview.git / commitdiff