import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
@Override
public void createPNG(File f)
{
- alignPanel.makeAlignmentImage(TYPE.PNG, f);
+ createPNG(f, null, 0.0f, 0, 0);
+ }
+
+ public void createPNG(File f, String renderer, float bitmapscale,
+ int bitmapwidth, int bitmapheight)
+ {
+ alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, bitmapscale,
+ bitmapwidth, bitmapheight);
}
/**
@Override
public void createEPS(File f)
{
- alignPanel.makeAlignmentImage(TYPE.EPS, f);
+ createEPS(f, null);
+ }
+
+ public void createEPS(File f, String renderer)
+ {
+ alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
}
/**
@Override
public void createSVG(File f)
{
- alignPanel.makeAlignmentImage(TYPE.SVG, f);
+ createSVG(f, null);
+ }
+
+ public void createSVG(File f, String renderer)
+ {
+ alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
}
@Override
.intValue();
}
}
- alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
- // was
- // duplicated
- // earlier
+ // annotation was duplicated earlier
+ alignment.addAnnotation(sequences[i].getAnnotation()[a]);
+ // take care of contact matrix too
+ ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]);
+ if (cm!=null)
+ {
+ alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+ }
+
alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
a);
}
}
public void showContactMapTree(AlignmentAnnotation aa,
- PAEContactMatrix cm)
+ ContactMatrixI cm)
{
int x = 4, y = 5;
int w = 400, h = 500;
{
NewickFile fin = new NewickFile(
new FileParse(cm.getNewick(), DataSourceType.PASTE));
- String title = "PAE Matrix Tree for "
- + cm.getReferenceSeq().getDisplayId(false);
+ String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree"
+ + aa.sequenceRef != null
+ ? (" for " + aa.sequenceRef.getDisplayId(false))
+ : "";
showColumnWiseTree(fin, aa, title, w, h, x, y);
} catch (Throwable xx)
* update non-sequence-related annotations
*/
@Override
- protected void setAnnotationsVisibility(boolean visible,
+ public void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
AlignmentAnnotation[] anns = alignPanel.getAlignment()