import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
private boolean gatherViewsHere = false;
private AnnotationColumnChooser annotationColumnSelectionState;
+
/**
* Creates a new AlignViewport object.
*
viewStyle.getFontSize()), false);
}
+
/**
* DOCUMENT ME!
*
*/
public void setAlignment(AlignmentI align)
{
- if (alignment != null && alignment.getCodonFrames() != null)
+ replaceMappings(align);
+ this.alignment = align;
+ }
+
+ /**
+ * Replace any codon mappings for this viewport with those for the given
+ * viewport
+ *
+ * @param align
+ */
+ public void replaceMappings(AlignmentI align)
+ {
+
+ /*
+ * Deregister current mappings (if any)
+ */
+ deregisterMappings();
+
+ /*
+ * Register new mappings (if any)
+ */
+ if (align != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).removeMappings(alignment.getCodonFrames());
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(align.getCodonFrames());
}
- this.alignment = align;
- if (alignment != null && alignment.getCodonFrames() != null)
+
+ /*
+ * replace mappings on our alignment
+ */
+ if (alignment != null && align != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).addMappings(alignment.getCodonFrames());
+ alignment.setCodonFrames(align.getCodonFrames());
+ }
+ }
+
+ protected void deregisterMappings()
+ {
+ AlignmentI al = getAlignment();
+ if (al != null)
+ {
+ Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+ if (mappings != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (noReferencesTo(acf))
+ {
+ ssm.deregisterMapping(acf);
+ }
+ }
+ }
}
}
*
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return getAlignment().getGapCharacter();
*
* @return DOCUMENT ME!
*/
+ @Override
public ColumnSelection getColumnSelection()
{
return colSel;
// 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
List<SequenceI> seqs = new ArrayList<SequenceI>();
for (SequenceI sq : alignment.getSequences())
{
- Vector<PDBEntry> pdbs = sq
- .getDatasetSequence().getAllPDBEntries();
+ Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
if (pdbs == null)
{
continue;
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
+ */
+ realiseMappings(getAlignment(), toAdd);
+
+ /*
+ * 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++)
+ for (int i = 0; i < toAdd.getHeight(); i++)
{
- getAlignment().addSequence(al.getSequenceAt(i));
+ getAlignment().addSequence(toAdd.getSequenceAt(i));
}
setEndSeq(getAlignment().getHeight());
}
/**
+ * Check if any added sequence could be the object of a mapping or
+ * cross-reference; if so, make the mapping explicit. Returns the count of
+ * mappings updated.
+ *
+ * @param al
+ * @param toAdd
+ */
+ protected int realiseMappings(AlignmentI al, AlignmentI toAdd)
+ {
+ // TODO this is proof of concept
+ // we might want to give the user some choice here
+ int count = 0;
+ for (SequenceI seq : toAdd.getSequences())
+ {
+ count += realiseMappingsTo(al, seq);
+ }
+ return count;
+ }
+
+ /**
+ * If the alignment holds any mappings to a virtual (placeholder) sequence
+ * that matches all or part of the given sequence, then update the mapping to
+ * point to the sequence. Returns the number of mappings updated.
+ *
+ * @param al
+ * @param seq
+ * @return
+ */
+ protected int realiseMappingsTo(AlignmentI al, SequenceI seq)
+ {
+ int count = 0;
+ Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ /*
+ * TODO could just go straight to realiseWith() here unless we want
+ * to give the user some choice before going ahead
+ */
+ if (mapping.isRealisableWith(seq))
+ {
+ count += mapping.realiseWith(seq);
+ }
+ }
+ return count;
+ }
+
+ /**
* Show a dialog with the option to open and link (cDNA <-> protein) as a new
* alignment, either as a standalone alignment or in a split frame. Returns
* true if the new alignment was opened, false if not, because the user
*/
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. Note this will include the
- * cDNA consensus annotation if it is protein (because the alignment holds
- * mappings to nucleotide)
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
*/
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
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 (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)
{
}
if (openSplitPane)
{
al.alignAs(thisAlignment);
- protein = openSplitFrame(newAlignFrame, thisAlignment,
- protein.getCodonFrames());
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
}
- /*
- * Register the mappings (held on the protein alignment) with the
- * StructureSelectionManager (for mouseover linking).
- */
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.addMappings(protein.getCodonFrames());
-
return true;
}
* containing a new alignment to be shown
* @param complement
* cdna/protein complement alignment to show in the other split half
- * @param mappings
* @return the protein alignment in the split frame
*/
protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
- AlignmentI complement, Set<AlignedCodonFrame> mappings)
+ AlignmentI complement)
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
- * is protein, the new frame will have a cDNA consensus annotation row
- * added.
+ * 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;
- AlignmentI protein = proteinFrame.viewport.getAlignment();
- protein.setCodonFrames(mappings);
-
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
cdnaFrame.setVisible(true);
proteinFrame.setVisible(true);
String linkedTitle = MessageManager
JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
- return protein;
+ return proteinFrame.viewport.getAlignment();
}
public AnnotationColumnChooser getAnnotationColumnSelectionState()
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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff