import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
public class AlignViewport extends AlignmentViewport implements
SelectionSource, AlignViewportI, CommandListener
{
- int startRes;
-
- int endRes;
-
- int startSeq;
-
- int endSeq;
-
Font font;
NJTree currentTree = null;
init();
}
+ /**
+ * Apply any settings saved in user preferences
+ */
private void applyViewProperties()
{
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
SequenceAnnotationOrder.NONE.name()));
showAutocalculatedAbove = Cache.getDefault(
Preferences.SHOW_AUTOCALC_ABOVE, false);
-
+ viewStyle.setScaleProteinAsCdna(Cache.getDefault(
+ Preferences.SCALE_PROTEIN_TO_CDNA, true));
}
void init()
return sq;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartRes()
- {
- return startRes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndRes()
- {
- return endRes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartSeq()
- {
- return startSeq;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param res
- * DOCUMENT ME!
- */
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param seq
- * DOCUMENT ME!
- */
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param res
- * DOCUMENT ME!
- */
- public void setEndRes(int res)
- {
- if (res > (alignment.getWidth() - 1))
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " +
- // (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
-
- if (res < 0)
- {
- res = 0;
- }
-
- this.endRes = res;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param seq
- * DOCUMENT ME!
- */
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
-
- if (seq < 0)
- {
- seq = 0;
- }
-
- this.endSeq = seq;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndSeq()
- {
- return endSeq;
- }
-
boolean validCharWidth;
/**
return false;
}
- /**
- * when set, view will scroll to show the highlighted position
- */
- public boolean followHighlight = true;
-
- /**
- * @return true if view should scroll to show the highlighted region of a
- * sequence
- * @return
- */
- public boolean getFollowHighlight()
- {
- return followHighlight;
- }
-
public boolean followSelection = true;
/**
// TODO: create undo object for this JAL-1101
/*
- * If one alignment is protein and one nucleotide, with at least one
- * sequence name in common, offer to open a linked alignment.
+ * If any cDNA/protein mappings can be made between the alignments, offer to
+ * open a linked alignment with split frame option.
*/
- if (AlignmentUtils.isMappable(al, getAlignment()))
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
{
- if (openLinkedAlignment(al, title))
+ if (AlignmentUtils.isMappable(al, getAlignment()))
{
- return;
+ if (openLinkedAlignment(al, title))
+ {
+ return;
+ }
}
}
+
+ /*
+ * No mappings, or offer declined - add sequences to this alignment
+ */
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
// provenance) should share the same dataset sequence
{
getAlignment().addSequence(al.getSequenceAt(i));
}
- // TODO this call was done by SequenceFetcher but not FileLoader or
- // CutAndPasteTransfer. Is it needed?
- // JBPComment: this repositions the view to show the new sequences
- // JBPComment: so it is needed for UX
+
setEndSeq(getAlignment().getHeight());
firePropertyChange("alignment", null, getAlignment().getSequences());
}
/**
* Show a dialog with the option to open and link (cDNA <-> protein) as a new
- * alignment. Returns true if the new alignment was opened, false if not,
- * because the user declined the offer.
+ * 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
+ * declined the offer.
*
+ * @param al
* @param title
*/
protected boolean openLinkedAlignment(AlignmentI al, String title)
{
this.gatherViewsHere = gatherViewsHere;
}
+
+ /**
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
+ */
+ public void scrollComplementaryAlignment()
+ {
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResults sr = new SearchResults();
+ int seqOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
+ {
+ // TODO would like next line without cast but needs more refactoring...
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, seqOffset);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff