import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
public class AlignViewport extends AlignmentViewport implements
AlignViewportI, SelectionSource, VamsasSource, CommandListener
{
- int startRes;
-
- int endRes;
-
- int startSeq;
-
- int endSeq;
-
boolean cursorMode = false;
Font font = new Font("SansSerif", Font.PLAIN, 10);
+ widthScale + "). Ignoring.");
widthScale = 1;
}
- if (applet.debug)
+ if (JalviewLite.debug)
{
System.err
.println("Alignment character width scaling factor is now "
+ heightScale + "). Ignoring.");
heightScale = 1;
}
- if (applet.debug)
+ if (JalviewLite.debug)
{
System.err
.println("Alignment character height scaling factor is now "
}
sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
- followHighlight = applet.getDefaultParameter("automaticScrolling",
- followHighlight);
- followSelection = followHighlight;
+ setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
+ isFollowHighlight()));
+ followSelection = isFollowHighlight();
showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
showSequenceLogo);
return sq;
}
- public int getStartRes()
- {
- return startRes;
- }
-
- public int getEndRes()
- {
- return endRes;
- }
-
- public int getStartSeq()
- {
- return startSeq;
- }
-
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- 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;
- }
-
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;
- }
-
- public int getEndSeq()
- {
- return endSeq;
- }
-
java.awt.Frame nullFrame;
protected FeatureSettings featureSettings = null;
return centreColumnLabels;
}
- public boolean followHighlight = true;
-
- public boolean getFollowHighlight()
- {
- return followHighlight;
- }
-
public boolean followSelection = true;
/**
return this;
}
+ /**
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
+ */
+ public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
+ {
+ if (complementPanel == null)
+ {
+ return;
+ }
+
+ /*
+ * 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())
+ {
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, seqOffset);
+ }
+ }
+
}