/**
*
- * @param dna
- * @param seqs
- * @return
- */
- public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
- String source)
- {
- return findXrefSequences(seqs, dna, source, null);
- }
-
- /**
- *
* @param seqs
* sequences whose xrefs are being retrieved
* @param dna
* true if sequences are nucleotide
* @param source
- * @param dataset
- * alignment to search for product sequences.
+ * @param al
+ * alignment to search for cross-referenced sequences (and possibly
+ * add to)
+ * @param addedPeers
+ * a list of sequences to add to if 'peers' to the original sequences
+ * are found e.g. alternative protein products for a protein's gene
* @return products (as dataset sequences)
*/
public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
- String source, AlignmentI dataset)
+ String source, AlignmentI al, List<SequenceI> addedPeers)
{
+ AlignmentI dataset = al.getDataset() == null ? al : al.getDataset();
List<SequenceI> rseqs = new ArrayList<SequenceI>();
AlignedCodonFrame cf = new AlignedCodonFrame();
for (SequenceI seq : seqs)
int sf = map.getMap().getToLowest();
int st = map.getMap().getToHighest();
SequenceI mappedrg = ms.getSubSequence(sf, st);
- SequenceI loc = dss.getSubSequence(sf, st);
+ // SequenceI loc = dss.getSubSequence(sf, st);
if (mappedrg.getLength() > 0
- && mappedrg.getSequenceAsString().equals(
- loc.getSequenceAsString()))
+ && ms.getSequenceAsString().equals(
+ dss.getSequenceAsString()))
+ // && mappedrg.getSequenceAsString().equals(
+ // loc.getSequenceAsString()))
{
String msg = "Mapping updated from "
+ ms.getName()
for (SequenceFeature feat : sfs)
{
/*
- * we override the equality test here (but not
- * elsewhere) to ignore Parent attribute
+ * we override SequenceFeature.equals here (but
+ * not elsewhere) to ignore Parent attribute
* TODO not quite working yet!
*/
if (!copiedFeatures
cf.addMap(retrieved[rs].getDatasetSequence(),
dss, map.getMap());
}
+ else
+ {
+ addedPeers.add(map.getTo());
+ cf.addMap(retrieved[rs].getDatasetSequence(),
+ map.getTo(), map.getMap());
+ }
} catch (Exception e)
{
System.err
Alignment ral = null;
if (rseqs.size() > 0)
{
- SequenceI[] rsqs = new SequenceI[rseqs.size()];
- rseqs.toArray(rsqs);
- ral = new Alignment(rsqs);
+ ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
if (cf != null && !cf.isEmpty())
{
ral.addCodonFrame(cf);
rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
rnahelicesColour
.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
- setShowProductsEnabled();
+
+ showProducts.setEnabled(canShowProducts());
+
updateEditMenuBar();
}
}
}
- /*
- * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
- * chooser = new JalviewFileChooser(jalview.bin.Cache.
- * getProperty("LAST_DIRECTORY"));
- *
- * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
- * to Vamsas file"); chooser.setToolTipText("Export");
- *
- * int value = chooser.showSaveDialog(this);
- *
- * if (value == JalviewFileChooser.APPROVE_OPTION) {
- * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
- * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
- * chooser.getSelectedFile().getAbsolutePath(), this); } }
- */
/**
- * prototype of an automatically enabled/disabled analysis function
+ * Searches selected sequences for xRef products and builds the Show
+ * Cross-References menu (formerly called Show Products)
*
+ * @return true if Show Cross-references menu should be enabled.
*/
- protected void setShowProductsEnabled()
+ public boolean canShowProducts()
{
SequenceI[] selection = viewport.getSequenceSelection();
- if (canShowProducts(selection, viewport.getSelectionGroup() != null,
- viewport.getAlignment().getDataset()))
- {
- showProducts.setEnabled(true);
-
- }
- else
- {
- showProducts.setEnabled(false);
- }
- }
-
- /**
- * search selection for sequence xRef products and build the show products
- * menu.
- *
- * @param selection
- * @param dataset
- * @return true if showProducts menu should be enabled.
- */
- public boolean canShowProducts(SequenceI[] selection,
- boolean isRegionSelection, Alignment dataset)
- {
+ AlignmentI dataset = viewport.getAlignment().getDataset();
boolean showp = false;
try
{
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
- final Alignment ds = dataset;
String[] ptypes = (selection == null || selection.length == 0) ? null
: CrossRef.findSequenceXrefTypes(dna, selection, dataset);
- // Object[] prods =
- // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
- // selection, dataset, true);
- final SequenceI[] sel = selection;
+
for (int t = 0; ptypes != null && t < ptypes.length; t++)
{
showp = true;
- final boolean isRegSel = isRegionSelection;
final AlignFrame af = this;
final String source = ptypes[t];
JMenuItem xtype = new JMenuItem(ptypes[t]);
@Override
public void actionPerformed(ActionEvent e)
{
- // TODO: new thread for this call with vis-delay
- af.showProductsFor(af.viewport.getSequenceSelection(),
- isRegSel, dna, source);
+ showProductsFor(af.viewport.getSequenceSelection(), dna, source);
}
});
} catch (Exception e)
{
jalview.bin.Cache.log
- .warn("canTranslate threw an exception - please report to help@jalview.org",
+ .warn("canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
}
return showp;
}
- protected void showProductsFor(final SequenceI[] sel,
- final boolean isRegSel, final boolean dna, final String source)
+ protected void showProductsFor(final SequenceI[] sel, final boolean dna,
+ final String source)
{
Runnable foo = new Runnable()
{
new Object[] { source }), sttime);
try
{
- // update our local dataset reference
- Alignment ds = AlignFrame.this.getViewport().getAlignment()
- .getDataset();
- Alignment prods = CrossRef
- .findXrefSequences(sel, dna, source, ds);
- if (prods != null)
+ /*
+ * 'peer' sequences are any to add to this alignment, for example
+ * alternative protein products for my protein's gene
+ */
+ List<SequenceI> addedPeers = new ArrayList<SequenceI>();
+ AlignmentI alignment = AlignFrame.this.getViewport().getAlignment();
+ Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source,
+ alignment, addedPeers);
+ if (xrefs != null)
{
- SequenceI[] sprods = new SequenceI[prods.getHeight()];
- for (int s = 0; s < sprods.length; s++)
- {
- sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
- if (ds.getSequences() == null
- || !ds.getSequences().contains(
- sprods[s].getDatasetSequence()))
- {
- ds.addSequence(sprods[s].getDatasetSequence());
- }
- sprods[s].updatePDBIds();
- }
- Alignment al = new Alignment(sprods);
- al.setDataset(ds);
+ Alignment al = makeCrossReferencesAlignment(
+ alignment.getDataset(), xrefs);
/*
* Copy dna-to-protein mappings to new alignment
// TODO 1: no mappings are set up for EMBL product
// TODO 2: if they were, should add them to protein alignment, not
// dna
- List<AlignedCodonFrame> cf = prods.getCodonFrames();
- for (AlignedCodonFrame acf : cf)
- {
- al.addCodonFrame(acf);
- }
+ // List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
+ // for (AlignedCodonFrame acf : cf)
+ // {
+ // al.addCodonFrame(acf);
+ // }
AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
- String newtitle = "" + (dna ? "Proteins" : "Nucleotides")
- + " for " + (isRegSel ? "selected region of " : "")
- + getTitle();
+ String newtitle = String.format("%s %s %s",
+ MessageManager.getString(dna ? "label.proteins"
+ : "label.nucleotides"), MessageManager
+ .getString("label.for"), getTitle());
newFrame.setTitle(newtitle);
boolean asSplitFrame = Cache.getDefault(
AlignmentI copyAlignment = null;
final SequenceI[] sequenceSelection = AlignFrame.this.viewport
.getSequenceSelection();
+ List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
if (dna)
{
copyAlignment = AlignmentUtils.makeCdsAlignment(
sequenceSelection, cf);
al.getCodonFrames().clear();
al.getCodonFrames().addAll(cf);
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.registerMappings(cf);
}
else
{
copyAlignment = new Alignment(new Alignment(
sequenceSelection));
+ copyAlignment.getCodonFrames().addAll(cf);
}
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(cf);
+
+ /*
+ * add in any extra 'peer' sequences discovered
+ * (e.g. alternative protein products)
+ */
+ for (SequenceI peer : addedPeers)
+ {
+ copyAlignment.addSequence(peer);
+ }
+
+ /*
+ * align protein to dna
+ */
+ // TODO needs debugging
+ // if (dna)
+ // {
+ // al.alignAs(copyAlignment);
+ // }
+ // else
+ // {
+ // copyAlignment.alignAs(al);
+ // }
+
AlignFrame copyThis = new AlignFrame(copyAlignment,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
copyThis.setTitle(AlignFrame.this.getTitle());
- // SplitFrame with dna above, protein below
+
boolean showSequenceFeatures = viewport
.isShowSequenceFeatures();
newFrame.setShowSeqFeatures(showSequenceFeatures);
String linkedTitle = MessageManager
.getString("label.linked_view_title");
Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+ sf.adjustDivider();
}
else
{
new Object[] { source }), sttime);
}
+ /**
+ * @param alignment
+ * @param prods
+ * @return
+ */
+ protected Alignment makeCrossReferencesAlignment(
+Alignment dataset,
+ Alignment prods)
+ {
+ SequenceI[] sprods = new SequenceI[prods.getHeight()];
+ for (int s = 0; s < sprods.length; s++)
+ {
+ sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+ if (dataset.getSequences() == null
+ || !dataset.getSequences().contains(
+ sprods[s].getDatasetSequence()))
+ {
+ dataset.addSequence(sprods[s].getDatasetSequence());
+ }
+ sprods[s].updatePDBIds();
+ }
+ Alignment al = new Alignment(sprods);
+ al.setDataset(dataset);
+ return al;
+ }
+
};
Thread frunner = new Thread(foo);
frunner.start();
*/
public class SplitFrame extends GSplitFrame implements SplitContainerI
{
+ private static final int WINDOWS_INSETS_WIDTH = 28; // tbc
+
+ private static final int MAC_INSETS_WIDTH = 28;
+
+ private static final int WINDOWS_INSETS_HEIGHT = 50; // tbc
+
+ private static final int MAC_INSETS_HEIGHT = 50;
+ private static final int DESKTOP_DECORATORS_HEIGHT = 65;
private static final long serialVersionUID = 1L;
public SplitFrame(GAlignFrame top, GAlignFrame bottom)
* estimate width and height of SplitFrame; this.getInsets() doesn't seem to
* give the full additional size (a few pixels short)
*/
- int widthFudge = Platform.isAMac() ? 28 : 28; // Windows tbc
- int heightFudge = Platform.isAMac() ? 50 : 50; // tbc
+ int widthFudge = Platform.isAMac() ? MAC_INSETS_WIDTH
+ : WINDOWS_INSETS_WIDTH;
+ int heightFudge = Platform.isAMac() ? MAC_INSETS_HEIGHT
+ : WINDOWS_INSETS_HEIGHT;
int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
int height = ((AlignFrame) getTopFrame()).getHeight()
+ ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE
{
// allow about 65 pixels for Desktop decorators on Windows
- int newHeight = Math.min(height, Desktop.instance.getHeight() - 65);
+ int newHeight = Math.min(height, Desktop.instance.getHeight()
+ - DESKTOP_DECORATORS_HEIGHT);
if (newHeight != height)
{
int oldDividerLocation = getDividerLocation();
}
/**
+ * Adjust the divider for a sensible split of the real estate (for example,
+ * when many transcripts are shown with a single protein). This should only be
+ * called after the split pane has been laid out (made visible) so it has a
+ * height.
+ */
+ protected void adjustDivider()
+ {
+ final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
+ final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
+ final AlignmentI topAlignment = topViewport.getAlignment();
+ final AlignmentI bottomAlignment = bottomViewport.getAlignment();
+ boolean topAnnotations = topViewport.isShowAnnotation();
+ boolean bottomAnnotations = bottomViewport.isShowAnnotation();
+ int topCount = topAlignment.getHeight();
+ int bottomCount = bottomAlignment.getHeight();
+ int topCharHeight = topViewport.getViewStyle().getCharHeight();
+ int bottomCharHeight = bottomViewport.getViewStyle().getCharHeight();
+
+ /*
+ * estimate ratio of (topFrameContent / bottomFrameContent)
+ */
+ int insets = Platform.isAMac() ? MAC_INSETS_HEIGHT
+ : WINDOWS_INSETS_HEIGHT;
+ // allow 3 'rows' for scale, scrollbar, status bar
+ int topHeight = insets + (3 + topCount) * topCharHeight
+ + (topAnnotations ? topViewport.calcPanelHeight() : 0);
+ int bottomHeight = insets + (3 + bottomCount) * bottomCharHeight
+ + (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0);
+ double ratio = ((double) topHeight) / (topHeight + bottomHeight);
+
+ setRelativeDividerLocation(ratio);
+ }
+
+ /**
* Add a listener to tidy up when the frame is closed.
*/
protected void addCloseFrameListener()
git://source.jalview.org / jalview.git / commitdiff