import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
- public Hashtable hiddenRepSeqs;
-
- public ViewDef(String viewname, HiddenSequences hidseqs,
- ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+ public ViewDef(String vname, HiddenSequences hseqs,
+ HiddenColumns hcols, Hashtable hRepSeqs)
- this.viewname = viewname;
- this.hidseqs = hidseqs;
- this.hiddencols = hiddencols;
- this.hiddenRepSeqs = hiddenRepSeqs;
+ this.viewname = vname;
+ this.hidseqs = hseqs;
+ this.hiddencols = hcols;
+ this.hiddenRepSeqs = hRepSeqs;
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
List<SequenceGroup> list, Hashtable properties,
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
List<SequenceGroup> list, Hashtable properties,
String file, DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
String file, DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
- boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+ if (hidden == null)
+ {
+ hidden = new HiddenColumns();
+ }
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden,
return readAnnotationFile(al, null, file, sourceType);
}
return readAnnotationFile(al, null, file, sourceType);
}
String file, DataSourceType sourceType)
{
BufferedReader in = null;
String file, DataSourceType sourceType)
{
BufferedReader in = null;
{
StringTokenizer inval = new StringTokenizer(nextToken, ",");
while (inval.hasMoreTokens())
{
StringTokenizer inval = new StringTokenizer(nextToken, ",");
while (inval.hasMoreTokens())
+ "' invalid, setting to zero");
}
String label = st.hasMoreTokens() ? st.nextToken() : null;
+ "' invalid, setting to zero");
}
String label = st.hasMoreTokens() ? st.nextToken() : null;
- // consider warning if colour doesn't resolve to a real colour
- def = new UserColourScheme(value);
- sg.setIdColour(def.findColour());
+ Color idColour = ColorUtils.parseColourString(value);
+ sg.setIdColour(idColour == null ? Color.black : idColour);
return printAnnotations(viewport.isShowAnnotation() ? viewport
.getAlignment().getAlignmentAnnotation() : null, viewport
.getAlignment().getGroups(), viewport.getAlignment()
return printAnnotations(viewport.isShowAnnotation() ? viewport
.getAlignment().getAlignmentAnnotation() : null, viewport
.getAlignment().getGroups(), viewport.getAlignment()