import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
private boolean gatherViewsHere = false;
private AnnotationColumnChooser annotationColumnSelectionState;
+
/**
* Creates a new AlignViewport object.
*
viewStyle.getFontSize()), false);
}
+
/**
* DOCUMENT ME!
*
*/
public void replaceMappings(AlignmentI align)
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
/*
* Deregister current mappings (if any)
*/
- if (alignment != null)
- {
- ssm.deregisterMappings(alignment.getCodonFrames());
- }
+ deregisterMappings();
/*
* Register new mappings (if any)
*/
if (align != null)
{
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
ssm.registerMappings(align.getCodonFrames());
}
}
}
+ protected void deregisterMappings()
+ {
+ AlignmentI al = getAlignment();
+ if (al != null)
+ {
+ List<AlignedCodonFrame> mappings = al.getCodonFrames();
+ if (mappings != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (noReferencesTo(acf))
+ {
+ ssm.deregisterMapping(acf);
+ }
+ }
+ }
+ }
+ }
+
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return getAlignment().getGapCharacter();
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
- */
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param tree
* DOCUMENT ME!
*/
// TODO: JAL-1126
if (historyList == null || redoList == null)
{
- return new long[]
- { -1, -1 };
+ return new long[] { -1, -1 };
}
- return new long[]
- { historyList.hashCode(), this.redoList.hashCode() };
+ return new long[] { historyList.hashCode(), this.redoList.hashCode() };
}
/**
/**
* Send the current selection to be broadcast to any selection listeners.
*/
+ @Override
public void sendSelection()
{
jalview.structure.StructureSelectionManager
}
/**
- * synthesize a column selection if none exists so it covers the given
- * selection group. if wholewidth is false, no column selection is made if the
- * selection group covers the whole alignment width.
- *
- * @param sg
- * @param wholewidth
- */
- public void expandColSelection(SequenceGroup sg, boolean wholewidth)
- {
- int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
- && sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
- {
- if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
- {
- // do nothing
- return;
- }
- if (colSel == null)
- {
- colSel = new ColumnSelection();
- }
- for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
- {
- colSel.addElement(cspos);
- }
- }
- }
-
- /**
* Returns the (Desktop) instance of the StructureSelectionManager
*/
@Override
List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
for (PDBEntry pdb : pdbEntries)
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
for (SequenceI sq : alignment.getSequences())
{
- Vector<PDBEntry> pdbs = sq
- .getDatasetSequence().getAllPDBEntries();
- if (pdbs == null)
+ Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+ if (pdbRefEntries == null)
{
continue;
}
- for (PDBEntry p1 : pdbs)
+ for (PDBEntry pdbRefEntry : pdbRefEntries)
{
- if (p1.getId().equals(pdb.getId()))
+ if (pdbRefEntry.getId().equals(pdb.getId()))
{
- if (!seqs.contains(sq))
+ if (pdbRefEntry.getChainCode() != null
+ && pdb.getChainCode() != null)
+ {
+ if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+ pdb.getChainCode())
+ && !choosenSeqs.contains(sq))
+ {
+ choosenSeqs.add(sq);
+ continue;
+ }
+ }
+ else
{
- seqs.add(sq);
- continue;
+ if (!choosenSeqs.contains(sq))
+ {
+ choosenSeqs.add(sq);
+ continue;
+ }
}
+
}
}
}
- seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
+ @Override
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
*
* @return true if alignment characters should be displayed
*/
+ @Override
public boolean isValidCharWidth()
{
return validCharWidth;
* may give the user the option to open a new frame, or split panel, with cDNA
* and protein linked.
*
- * @param al
+ * @param toAdd
* @param title
*/
- public void addAlignment(AlignmentI al, String title)
+ public void addAlignment(AlignmentI toAdd, String title)
{
// TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
// TODO: create undo object for this JAL-1101
/*
- * If any cDNA/protein mappings can be made between the alignments, offer to
- * open a linked alignment with split frame option.
+ * Ensure datasets are created for the new alignment as
+ * mappings operate on dataset sequences
+ */
+ toAdd.setDataset(null);
+
+ /*
+ * Check if any added sequence could be the object of a mapping or
+ * cross-reference; if so, make the mapping explicit
+ */
+ getAlignment().realiseMappings(toAdd.getSequences());
+
+ /*
+ * If any cDNA/protein mappings exist or can be made between the alignments,
+ * offer to open a split frame with linked alignments
*/
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
- if (al.getDataset() == null)
- {
- // need to create ds seqs
- for (SequenceI sq : al.getSequences())
- {
- if (sq.getDatasetSequence() == null)
- {
- sq.createDatasetSequence();
- }
- }
- }
- if (AlignmentUtils.isMappable(al, getAlignment()))
+ if (AlignmentUtils.isMappable(toAdd, getAlignment()))
{
- if (openLinkedAlignment(al, title))
+ if (openLinkedAlignment(toAdd, title))
{
return;
}
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
// provenance) should share the same dataset sequence
- for (int i = 0; i < al.getHeight(); i++)
+ AlignmentI al = getAlignment();
+ String gap = String.valueOf(al.getGapCharacter());
+ for (int i = 0; i < toAdd.getHeight(); i++)
{
- getAlignment().addSequence(al.getSequenceAt(i));
+ SequenceI seq = toAdd.getSequenceAt(i);
+ /*
+ * experimental!
+ * - 'align' any mapped sequences as per existing
+ * e.g. cdna to genome, domain hit to protein sequence
+ * very experimental! (need a separate menu option for this)
+ * - only add mapped sequences ('select targets from a dataset')
+ */
+ if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
+ {
+ al.addSequence(seq);
+ }
}
setEndSeq(getAlignment().getHeight());
*/
protected boolean openLinkedAlignment(AlignmentI al, String title)
{
- String[] options = new String[]
- { MessageManager.getString("action.no"),
+ String[] options = new String[] {
+ MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
* is a pre-requisite for building mappings.
*/
al.setDataset(null);
- AlignmentUtils.mapProteinToCdna(protein, cdna);
+ AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
/*
* Create the AlignFrame for the added alignment. If it is protein, mappings
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new Object[]
- { title }));
+ "label.successfully_loaded_file", new Object[] { title }));
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
- // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // if (!protocol.equals(DataSourceType.PASTE))
// {
// alignFrame.setFileName(file, format);
// }
if (openInNewWindow)
{
Desktop.addInternalFrame(newAlignFrame, title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
try
{
newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN",
- false));
+ "SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
- * is protein, the mappings to cDNA will be registered with StructureSelectionManager as a side-effect.
+ * is protein, the mappings to cDNA will be registered with
+ * StructureSelectionManager as a side-effect.
*/
AlignFrame copyMe = new AlignFrame(complement,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
AlignmentI al = newAlignFrame.viewport.getAlignment();
final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
: newAlignFrame;
- final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
- : copyMe;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
cdnaFrame.setVisible(true);
proteinFrame.setVisible(true);
String linkedTitle = MessageManager
if (!sr.isEmpty())
{
// TODO would like next line without cast but needs more refactoring...
- final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
- complementPanel.setFollowingComplementScroll(true);
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
+ complementPanel.setDontScrollComplement(true);
complementPanel.scrollToCentre(sr, verticalOffset);
}
}
+ /**
+ * Answers true if no alignment holds a reference to the given mapping
+ *
+ * @param acf
+ * @return
+ */
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
+ {
+ return true;
+ }
+ for (AlignFrame af : frames)
+ {
+ if (!af.isClosed())
+ {
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ AlignmentI al = ap.getAlignment();
+ if (al != null && al.getCodonFrames().contains(acf))
+ {
+ return false;
+ }
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Applies the supplied feature settings descriptor to currently known
+ * features. This supports an 'initial configuration' of feature colouring
+ * based on a preset or user favourite. This may then be modified in the usual
+ * way using the Feature Settings dialogue.
+ *
+ * @param featureSettings
+ */
+ @Override
+ public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
+ {
+ if (featureSettings == null)
+ {
+ return;
+ }
+
+ FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ fr.findAllFeatures(true);
+ List<String> renderOrder = fr.getRenderOrder();
+ FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
+ displayed.clear();
+ // TODO this clears displayed.featuresRegistered - do we care?
+
+ /*
+ * set feature colour if specified by feature settings
+ * set visibility of all features
+ */
+ for (String type : renderOrder)
+ {
+ FeatureColourI preferredColour = featureSettings
+ .getFeatureColour(type);
+ if (preferredColour != null)
+ {
+ fr.setColour(type, preferredColour);
+ }
+ if (featureSettings.isFeatureDisplayed(type))
+ {
+ displayed.setVisible(type);
+ }
+ }
+
+ /*
+ * set visibility of feature groups
+ */
+ for (String group : fr.getFeatureGroups())
+ {
+ fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+ }
+
+ /*
+ * order the features
+ */
+ if (featureSettings.optimiseOrder())
+ {
+ // TODO not supported (yet?)
+ }
+ else
+ {
+ fr.orderFeatures(featureSettings);
+ }
+ fr.setTransparency(featureSettings.getTransparency());
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff