import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
public HiddenSequences hidseqs;
- public ColumnSelection hiddencols;
+ public HiddenColumns hiddencols;
public Vector visibleGroups;
public Hashtable hiddenRepSeqs;
public ViewDef(String viewname, HiddenSequences hidseqs,
- ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+ HiddenColumns hiddencols, Hashtable hiddenRepSeqs)
{
this.viewname = viewname;
this.hidseqs = hidseqs;
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
List<SequenceGroup> list, Hashtable properties,
- ColumnSelection cs, AlignmentI al, ViewDef view)
+ HiddenColumns cs,
+ AlignmentI al, ViewDef view)
{
if (view != null)
{
if (cs != null && cs.hasHiddenColumns())
{
text.append("VIEW_HIDECOLS\t");
- List<int[]> hc = cs.getHiddenColumns();
+ List<int[]> hc = cs.getListOfCols();
boolean comma = false;
for (int[] r : hc)
{
String file, DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
+ HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
if (colSel == null)
{
colSel = new ColumnSelection();
}
- boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+ if (hidden == null)
+ {
+ hidden = new HiddenColumns();
+ }
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden,
file, protocol);
- if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+ if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
{
viewport.setColumnSelection(colSel);
+ viewport.getAlignment().setHiddenColumns(hidden);
}
return rslt;
return readAnnotationFile(al, null, file, sourceType);
}
- public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+ public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
String file, DataSourceType sourceType)
{
BufferedReader in = null;
}
if (in != null)
{
- return parseAnnotationFrom(al, colSel, in);
+ return parseAnnotationFrom(al, hidden, in);
}
} catch (Exception ex)
private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
- public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+ public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
BufferedReader in) throws Exception
{
nlinesread = 0;
{
if (st.hasMoreTokens())
{
- if (colSel == null)
+ if (hidden == null)
{
- colSel = new ColumnSelection();
+ hidden = new HiddenColumns();
}
- parseHideCols(colSel, st.nextToken());
+ parseHideCols(hidden, st.nextToken());
}
modified = true;
continue;
}
if (sr != null)
{
- if (colSel == null)
+ if (hidden == null)
{
System.err
.println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
else
{
// consider deferring this till after the file has been parsed ?
- colSel.hideInsertionsFor(sr);
+ hidden.hideInsertionsFor(sr);
}
}
modified = true;
return modified;
}
- private void parseHideCols(ColumnSelection colSel, String nextToken)
+ private void parseHideCols(HiddenColumns hidden, String nextToken)
{
StringTokenizer inval = new StringTokenizer(nextToken, ",");
while (inval.hasMoreTokens())
from = to = Integer.parseInt(range);
if (from >= 0)
{
- colSel.hideColumns(from, to);
+ hidden.hideColumns(from, to);
}
}
else
}
if (from > 0 && to >= from)
{
- colSel.hideColumns(from, to);
+ hidden.hideColumns(from, to);
}
}
}
return printAnnotations(viewport.isShowAnnotation() ? viewport
.getAlignment().getAlignmentAnnotation() : null, viewport
.getAlignment().getGroups(), viewport.getAlignment()
- .getProperties(), viewport.getColumnSelection(),
+ .getProperties(), viewport.getAlignment().getHiddenColumns(),
viewport.getAlignment(), null);
}