// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- int alw, alStart;
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
- .getAlignment() : viewport.getSelectionGroup());
- alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes() + 1;
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+ .getAlignment() : viewport.getSelectionGroup();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = selectMarkedColumns(cs, invert, extendCurrent,
+ toggle, bs, sqcol.getStartRes(), sqcol.getEndRes());
+ 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[] {
+ MessageManager.getString(toggle ? "label.toggled"
+ : "label.marked"),
+ String.valueOf(columnCount),
+ MessageManager
+ .getString(invert ? "label.not_containing"
+ : "label.containing"),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.no_feature_of_type_found",
+ new String[] { featureType }));
+ if (!extendCurrent && cs != null)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * 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.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ static int findColumnsWithFeature(String featureType,
+ SequenceCollectionI sqcol,
+ BitSet bs)
+ {
+ final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
+ final int endPosition = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
int nseq = 0;
for (SequenceI sq : seqs)
{
- int tfeat = 0;
+ boolean sequenceHasFeature = false;
if (sq != null)
{
- SequenceFeature[] sf = sq.getSequenceFeatures();
- if (sf != null)
+ SequenceFeature[] sfs = sq.getSequenceFeatures();
+ if (sfs != null)
{
int ist = sq.findIndex(sq.getStart());
int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist > alw)
+ if (iend < startPosition || ist > endPosition)
{
// sequence not in region
continue;
}
- for (SequenceFeature sfpos : sf)
+ for (SequenceFeature sf : sfs)
{
- // future functionalty - featureType == null means mark columns
+ // future functionality - featureType == null means mark columns
// containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
+ if (sf != null && (featureType.equals(sf.getType())))
{
- tfeat++;
// optimisation - could consider 'spos,apos' like cursor argument
// - findIndex wastes time by starting from first character and
// counting
- int i = sq.findIndex(sfpos.getBegin());
- int j = sq.findIndex(sfpos.getEnd());
- if (j < alStart || i > alw)
+ int i = sq.findIndex(sf.getBegin());
+ int j = sq.findIndex(sf.getEnd());
+ if (j < startPosition || i > endPosition)
{
// feature is outside selected region
continue;
}
- if (i < alStart)
+ sequenceHasFeature = true;
+ if (i < startPosition)
{
- i = alStart;
+ i = startPosition;
}
if (i < ist)
{
i = ist;
}
- if (j > alw)
+ if (j > endPosition)
{
- j = alw;
+ j = endPosition;
}
for (; i <= j; i++)
{
}
}
- if (tfeat > 0)
+ if (sequenceHasFeature)
{
nseq++;
}
}
}
- ColumnSelection cs = viewport.getColumnSelection();
- if (bs.cardinality() > 0 || invert)
- {
- boolean changed = false;
- if (cs == null)
- {
- cs = new ColumnSelection();
- }
- else
- {
- if (!extendCurrent)
- {
- changed = !cs.isEmpty();
- cs.clear();
- }
- }
- if (invert)
- {
- // invert only in the currently selected sequence region
- for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
- && i < (alw);)
- {
- if (ibs < 0 || i < ibs)
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i++);
- }
- else
- {
- cs.addElement(i++);
- }
- }
- else
- {
- i = bs.nextClearBit(ibs);
- ibs = bs.nextSetBit(i);
- }
- }
- }
- else
- {
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
- .nextSetBit(i + 1))
- {
- changed = true;
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i);
- }
- else
- {
- cs.addElement(i);
- }
- }
- }
- if (changed)
- {
- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- MessageManager.getString(toggle ? "label.toggled"
- : "label.marked"),
- String.valueOf(invert ? alw - alStart
- - bs.cardinality() : bs.cardinality()),
- MessageManager
- .getString(invert ? "label.not_containing"
- : "label.containing"),
- featureType, Integer.valueOf(nseq).toString() }));
- return true;
- }
- }
- else
- {
- avcg.setStatus(MessageManager.formatMessage(
- "label.no_feature_of_type_found",
- new String[] { featureType }));
- if (!extendCurrent && cs != null)
- {
- cs.clear();
- alignPanel.paintAlignment(true);
- }
- }
- return false;
+ return nseq;
}
@Override
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
- if (SwingUtilities.isRightMouseButton(evt))
+ boolean ctrlDown = Platform.isControlDown(evt);
+ if (SwingUtilities.isRightMouseButton(evt) && !ctrlDown)
{
popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
table.getValueAt(selectedRow, 1), fr.getMinMax(),
else if (evt.getClickCount() == 2)
{
boolean invertSelection = evt.isAltDown();
- boolean ctrlDown = Platform.isControlDown(evt);
boolean toggleSelection = ctrlDown;
- boolean extendSelection = evt.isShiftDown() || ctrlDown;
+ boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
invertSelection, extendSelection, toggleSelection,
(String) table.getValueAt(selectedRow, 0));
--- /dev/null
+package jalview.controller;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.BitSet;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class AlignViewControllerTest
+{
+ @Test(groups = "Functional")
+ public void testFindColumnsWithFeature()
+ {
+ SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
+ SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
+ SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
+ SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+
+ /*
+ * features start/end are base 1
+ */
+ seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
+ null));
+ seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
+ null));
+ seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
+ null));
+ seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
+ 0f, null));
+
+ /*
+ * select the first three columns --> seq1 2-3
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(0); // base 0
+ sg.setEndRes(2);
+ sg.addSequence(seq1, false);
+ sg.addSequence(seq2, false);
+ sg.addSequence(seq3, false);
+ sg.addSequence(seq4, false);
+
+ BitSet bs = new BitSet();
+ int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+ bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(1));
+ assertTrue(bs.get(2));
+
+ /*
+ * select the first four columns: seq1 2:4, seq2 4:4
+ */
+ sg.setEndRes(3);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+ bs);
+ assertEquals(2, seqCount);
+ assertEquals(3, bs.cardinality());
+ assertTrue(bs.get(1));
+ assertTrue(bs.get(2));
+ assertTrue(bs.get(3));
+
+ /*
+ * select column 11: seq3 only
+ */
+ sg.setStartRes(10);
+ sg.setEndRes(10);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(1, bs.cardinality());
+ assertTrue(bs.get(10));
+
+ /*
+ * select columns 16-20: no Metal feature
+ */
+ sg.setStartRes(15);
+ sg.setEndRes(19);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+
+ /*
+ * look for a feature that isn't there
+ */
+ sg.setStartRes(0);
+ sg.setEndRes(19);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+ }
+
+ @Test(groups = "Functional")
+ public void testSelectMarkedColumns_invert()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(5); // this will be cleared
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * inverted selection of {3, 6} should select {4, 5, 7, 8}
+ */
+ assertTrue(AlignViewController.selectMarkedColumns(cs, true, false,
+ false, toMark, 3, 8));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(4));
+ assertTrue(selected.contains(5));
+ assertTrue(selected.contains(7));
+ assertTrue(selected.contains(8));
+ }
+
+ @Test(groups = "Functional")
+ public void testSelectMarkedColumns()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(5); // this will be cleared
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ assertTrue(AlignViewController.selectMarkedColumns(cs, false, false,
+ false, toMark, 3, 8));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(2, selected.size());
+ assertTrue(selected.contains(3));
+ assertTrue(selected.contains(6));
+ }
+
+ @Test(groups = "Functional")
+ public void testSelectMarkedColumns_extend()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(1);
+ cs.addElement(5);
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
+ */
+ assertTrue(AlignViewController.selectMarkedColumns(cs, false, true,
+ false, toMark, 3, 8));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(1));
+ assertTrue(selected.contains(3));
+ assertTrue(selected.contains(5));
+ assertTrue(selected.contains(6));
+ }
+
+ @Test(groups = "Functional")
+ public void testSelectMarkedColumns_toggle()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(1); // outside change range
+ cs.addElement(3);
+ cs.addElement(4);
+ cs.addElement(10); // outside change range
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
+ */
+ assertTrue(AlignViewController.selectMarkedColumns(cs, false, false,
+ true, toMark, 3, 8));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(1));
+ assertTrue(selected.contains(4));
+ assertTrue(selected.contains(6));
+ assertTrue(selected.contains(10));
+ }
+ // TODO testSelectMarkedColumns with combinations of invert/extend/toggle set
+}
git://source.jalview.org / jalview.git / commitdiff