import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
if (bs.cardinality() > 0 || invert)
{
- boolean changed = selectMarkedColumns(cs, invert, extendCurrent,
- toggle, bs, sqcol.getStartRes(), sqcol.getEndRes());
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
if (changed)
{
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
- - bs.cardinality() : bs.cardinality();
+ - bs.cardinality()
+ : bs.cardinality();
avcg.setStatus(MessageManager.formatMessage(
"label.view_controller_toggled_marked",
new String[] {
- MessageManager.getString(toggle ? "label.toggled"
- : "label.marked"),
+ toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
String.valueOf(columnCount),
- MessageManager
- .getString(invert ? "label.not_containing"
- : "label.containing"),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
featureType, Integer.valueOf(nseq).toString() }));
return true;
}
avcg.setStatus(MessageManager.formatMessage(
"label.no_feature_of_type_found",
new String[] { featureType }));
- if (!extendCurrent && cs != null)
+ if (!extendCurrent)
{
cs.clear();
alignPanel.paintAlignment(true);
}
/**
- * Updates the column selection depending on the parameters, and returns true
- * if any change was made to the selection.
- *
- * @param columnSelection
- * the current column selection
- * @param invert
- * if true, deselect marked columns and select unmarked
- * @param extendCurrent
- * if true, extend rather than replacing the current column selection
- * @param toggle
- * if true, toggle the selection state of marked columns
- * @param markedColumns
- * a set identify marked columns
- * @param startCol
- * the first column of the range to operate over
- * @param endCol
- * the last column of the range to operate over
- * @return
- */
- static boolean selectMarkedColumns(ColumnSelection columnSelection,
- boolean invert, boolean extendCurrent, boolean toggle,
- BitSet markedColumns, int startCol, int endCol)
- {
- boolean changed = false;
- if (!extendCurrent && !toggle)
- {
- changed = !columnSelection.isEmpty();
- columnSelection.clear();
- }
- if (invert)
- {
- // invert only in the currently selected sequence region
- int i = markedColumns.nextClearBit(startCol);
- int ibs = markedColumns.nextSetBit(startCol);
- while (i >= startCol && i <= endCol)
- {
- if (ibs < 0 || i < ibs)
- {
- changed = true;
- if (toggle && columnSelection.contains(i))
- {
- columnSelection.removeElement(i++);
- }
- else
- {
- columnSelection.addElement(i++);
- }
- }
- else
- {
- i = markedColumns.nextClearBit(ibs);
- ibs = markedColumns.nextSetBit(i);
- }
- }
- }
- else
- {
- int i = markedColumns.nextSetBit(startCol);
- while (i >= startCol && i <= endCol)
- {
- changed = true;
- if (toggle && columnSelection.contains(i))
- {
- columnSelection.removeElement(i);
- }
- else
- {
- columnSelection.addElement(i);
- }
- i = markedColumns.nextSetBit(i + 1);
- }
- }
- return changed;
- }
-
- /**
- * Sets a bit in the BitSet for each column in the sequence collection which
- * includes the specified feature type. Returns the number of sequences which
- * have the feature in the selected range.
+ * Sets a bit in the BitSet for each column (base 0) in the sequence
+ * collection which includes the specified feature type. Returns the number of
+ * sequences which have the feature in the selected range.
*
* @param featureType
* @param sqcol
* @return
*/
static int findColumnsWithFeature(String featureType,
- SequenceCollectionI sqcol,
- BitSet bs)
+ SequenceCollectionI sqcol, BitSet bs)
{
final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
final int endPosition = sqcol.getEndRes() + 1;
// - findIndex wastes time by starting from first character and
// counting
- int i = sq.findIndex(sf.getBegin());
- int j = sq.findIndex(sf.getEnd());
- if (j < startPosition || i > endPosition)
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd());
+
+ if (sf.isContactFeature())
+ {
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startPosition
+ && sfStartCol <= endPosition)
+ {
+ bs.set(sfStartCol - 1);
+ sequenceHasFeature = true;
+ }
+ if (sfEndCol >= startPosition && sfEndCol <= endPosition)
+ {
+ bs.set(sfEndCol - 1);
+ sequenceHasFeature = true;
+ }
+ continue;
+ }
+
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol > endPosition || sfEndCol < startPosition)
{
// feature is outside selected region
continue;
}
sequenceHasFeature = true;
- if (i < startPosition)
+ if (sfStartCol < startPosition)
{
- i = startPosition;
+ sfStartCol = startPosition;
}
- if (i < ist)
+ if (sfStartCol < ist)
{
- i = ist;
+ sfStartCol = ist;
}
- if (j > endPosition)
+ if (sfEndCol > endPosition)
{
- j = endPosition;
+ sfEndCol = endPosition;
}
- for (; i <= j; i++)
+ for (; sfStartCol <= sfEndCol; sfStartCol++)
{
- bs.set(i - 1);
+ bs.set(sfStartCol - 1); // convert to base 0
}
}
}
}
@Override
- public boolean parseFeaturesFile(String file, String protocol,
+ public boolean parseFeaturesFile(String file, DataSourceType protocol,
boolean relaxedIdMatching)
{
boolean featuresFile = false;
return featuresFile;
}
+
+ @Override
+ public boolean markHighlightedColumns(boolean invert,
+ boolean extendCurrent, boolean toggle)
+ {
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+ // JBPNote this routine could also mark rows, not just columns.
+ BitSet bs = new BitSet();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+ .getAlignment() : viewport.getSelectionGroup();
+
+ // this could be a lambda... - the remains of the method is boilerplate,
+ // except for the different messages for reporting selection.
+ int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ alignPanel.paintAlignment(true);
+ int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
+ : bs.cardinality();
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.view_controller_toggled_marked",
+ new String[] {
+ toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ "Highlight", Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager
+ .formatMessage("No highlighted regions marked"));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
+ }
+ return false;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff