static StringBuffer copiedSequences;
- static Vector copiedHiddenColumns;
+ static Vector<int[]> copiedHiddenColumns;
protected void copy_actionPerformed()
{
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector();
+ copiedHiddenColumns = viewport.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : viewport.getAlignment().getHiddenColumns())
+ for (int[] region : copiedHiddenColumns)
{
- copiedHiddenColumns.addElement(new int[] {
- region[0] - hiddenOffset, region[1] - hiddenOffset });
+ region[0] = region[0] - hiddenOffset;
+ region[1] = region[1] - hiddenOffset;
}
}
else
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
{
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+ int[] region = copiedHiddenColumns.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
import java.awt.event.MouseListener;
import java.awt.event.TextEvent;
import java.awt.event.TextListener;
-import java.util.Iterator;
+import java.util.ArrayList;
import java.util.Vector;
//import javax.swing.JPanel;
.getOldHiddenColumns();
if (oldHidden != null)
{
- for (Iterator<int[]> itr = oldHidden.iterator(); itr.hasNext();)
+ ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopyAsList();
+ for (int[] positions : regions)
{
- int positions[] = itr.next();
av.hideColumns(positions[0], positions[1]);
}
}
+ // TODO not clear why we need to hide all the columns (above) if we are
+ // going to copy the hidden columns over wholesale anyway
av.getAlignment().setHiddenColumns(oldHidden);
}
ap.paintAlignment(true);
int res = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
- res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
-
- reveal = null;
- for (int[] region : av.getAlignment().getHiddenColumns())
- {
- if (res + 1 == region[0] || res - 1 == region[1])
- {
- reveal = region;
- break;
- }
- }
+ reveal = av.getAlignment().getHiddenColumns()
+ .getRegionWithEdgeAtRes(res);
repaint();
}
{
LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
- for (int[] range : hiddenColumns)
+ if (hiddenColumns != null)
{
- regionBuilder.append(delimiter).append(range[0]).append(between)
- .append(range[1]);
- }
+ for (int[] range : hiddenColumns)
+ {
+ regionBuilder.append(delimiter).append(range[0]).append(between)
+ .append(range[1]);
+ }
- regionBuilder.deleteCharAt(0);
+ regionBuilder.deleteCharAt(0);
+ }
return regionBuilder.toString();
} finally
{
try
{
LOCK.readLock().lock();
- List<Integer> positions = new ArrayList<>(
- hiddenColumns.size());
+ List<Integer> positions = null;
- positions.add(hiddenColumns.elementAt(0)[0]);
- for (int i = 1; i < hiddenColumns.size(); ++i)
+ if (hiddenColumns != null)
{
+ positions = new ArrayList<>(hiddenColumns.size());
- int result = 0;
- if (hiddenColumns != null)
+ positions.add(hiddenColumns.elementAt(0)[0]);
+ for (int i = 1; i < hiddenColumns.size(); ++i)
{
- int index = 0;
- int gaps = 0;
- do
+
+ int result = 0;
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.elementAt(index);
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index <= i);
+ int index = 0;
+ int gaps = 0;
+ do
+ {
+ int[] region = hiddenColumns.elementAt(index);
+ gaps += region[1] + 1 - region[0];
+ result = region[1] + 1;
+ index++;
+ } while (index <= i);
- result -= gaps;
+ result -= gaps;
+ }
+ positions.add(result);
}
- positions.add(result);
+ }
+ else
+ {
+ positions = new ArrayList<>();
}
return positions;
return copy;
}
+ /**
+ * Returns a copy of the vector of hidden regions, as a vector. Before using
+ * this method please consider if you really need access to the hidden regions
+ * - a new (or existing!) method on HiddenColumns might be more appropriate.
+ *
+ * @return hidden regions as vector of [start,end] pairs
+ */
public Vector<int[]> getHiddenColumnsCopy()
{
try
}
}
+ /**
+ * Returns a copy of the vector of hidden regions, as an ArrayList. Before
+ * using this method please consider if you really need access to the hidden
+ * regions - a new (or existing!) method on HiddenColumns might be more
+ * appropriate.
+ *
+ * @return hidden regions as an ArrayList of [start,end] pairs
+ */
public ArrayList<int[]> getHiddenColumnsCopyAsList()
{
try
}
+ /**
+ * Finds the hidden region (if any) which starts or ends at res
+ *
+ * @param res
+ * visible residue position, unadjusted for hidden columns
+ * @return region as [start,end] or null if no matching region is found
+ */
+ public int[] getRegionWithEdgeAtRes(int res)
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ int adjres = adjustForHiddenColumns(res);
+
+ int[] reveal = null;
+ if (hiddenColumns != null)
+ {
+ for (int[] region : hiddenColumns)
+ {
+ if (adjres + 1 == region[0] || adjres - 1 == region[1])
+ {
+ reveal = region;
+ break;
+ }
+ }
+ }
+ return reveal;
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
+
}
hiddenColumns = new ArrayList<>();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
- for (int[] region : viewport.getAlignment().getHiddenColumns())
+ ArrayList<int[]> hiddenRegions = viewport.getAlignment()
+ .getHiddenColumns().getHiddenColumnsCopyAsList();
+ for (int[] region : hiddenRegions)
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyEvent;
-import java.util.Iterator;
+import java.util.ArrayList;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
.getOldHiddenColumns();
if (oldHidden != null)
{
- for (Iterator<int[]> itr = oldHidden.iterator(); itr.hasNext();)
+ ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopyAsList();
+ for (int[] positions : regions)
{
- int positions[] = itr.next();
av.hideColumns(positions[0], positions[1]);
}
}
+ // TODO not clear why we need to hide all the columns (above) if we are
+ // going to copy the hidden columns over wholesale anyway
av.getAlignment().setHiddenColumns(oldHidden);
}
ap.paintAlignment(true);
int res = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
+ reveal = av.getAlignment().getHiddenColumns()
+ .getRegionWithEdgeAtRes(res);
+
res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
- for (int[] region : av.getAlignment().getHiddenColumns())
- {
- if (res + 1 == region[0] || res - 1 == region[1])
- {
- reveal = region;
- ToolTipManager.sharedInstance().registerComponent(this);
- this.setToolTipText(
- MessageManager.getString("label.reveal_hidden_columns"));
- repaint();
- return;
- }
- }
+ ToolTipManager.sharedInstance().registerComponent(this);
+ this.setToolTipText(
+ MessageManager.getString("label.reveal_hidden_columns"));
+ repaint();
}
/**
*/
package jalview.datamodel;
+import static org.testng.Assert.assertNull;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertSame;
public void testFindHiddenRegionPositions()
{
HiddenColumns hc = new HiddenColumns();
+
+ List<Integer> positions = hc.findHiddenRegionPositions();
+ assertTrue(positions.isEmpty());
+
hc.hideColumns(3, 7);
hc.hideColumns(10, 10);
hc.hideColumns(14, 15);
- List<Integer> positions = hc.findHiddenRegionPositions();
+ positions = hc.findHiddenRegionPositions();
assertEquals(3, positions.size());
assertEquals(3, positions.get(0).intValue());
assertEquals(5, positions.get(1).intValue());
public void testRegionsToString()
{
HiddenColumns hc = new HiddenColumns();
+
+ String result = hc.regionsToString(",", "--");
+ assertEquals("", result);
+
hc.hideColumns(3, 7);
hc.hideColumns(10, 10);
hc.hideColumns(14, 15);
- String result = hc.regionsToString(",", "--");
+ result = hc.regionsToString(",", "--");
assertEquals("3--7,10--10,14--15", result);
}
assertEquals(23, startEnd[1]);
}
+ @Test(groups = "Functional")
+ public void testGetRegionWithEdgeAtRes()
+ {
+ HiddenColumns hc = new HiddenColumns();
+
+ int[] result = hc.getRegionWithEdgeAtRes(5);
+ assertNull(result);
+
+ hc.hideColumns(3, 7);
+ hc.hideColumns(10, 10);
+ hc.hideColumns(14, 15);
+
+ result = hc.getRegionWithEdgeAtRes(3);
+ assertEquals(3, result[0]);
+ assertEquals(7, result[1]);
+
+ result = hc.getRegionWithEdgeAtRes(5);
+ assertEquals(10, result[0]);
+ assertEquals(10, result[1]);
+
+ result = hc.getRegionWithEdgeAtRes(6);
+ assertNull(result);
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff