"Deselect All" to deselect all columns.</em></li>
<li><strong>Remove Right (Control R)<br>
</strong><em>If the alignment has marked columns, the alignment will
- be trimmed to the left of the leftmost marked column. To
+ be trimmed to the right of the rightmost marked column. To
mark a column, mouse click the scale bar above the
alignment. Click again to unmark a column, or select
"Deselect All" to deselect all columns.</em></li>
deselect all columns.</em></li>
<li><strong>Remove Right (Control R)<br>
</strong><em>If the alignment has marked columns, the alignment will be
- trimmed to the left of the leftmost marked column. To mark a
+ trimmed to the right of the rightmost marked column. To mark a
column, mouse click the scale bar above the alignment. Click
again to unmark a column, or select "Deselect All" to
deselect all columns.</em></li>
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, viewport.getAlignment());
viewport.setStartRes(0);
}
else
{
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+ column, viewport.getAlignment());
}
statusBar.setText(MessageManager.formatMessage(
}
+ @Override
public void changeColour(ColourSchemeI cs)
{
this.add(statusBar, BorderLayout.SOUTH);
}
+ @Override
public void setStatus(String string)
{
statusBar.setText(string);
package jalview.commands;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.util.ShiftList;
-
-import java.util.List;
public class TrimRegionCommand extends EditCommand
{
- public static String TRIM_LEFT = "TrimLeft";
-
- public static String TRIM_RIGHT = "TrimRight";
-
- public ColumnSelection colSel = null;
-
- int[] start;
-
- ShiftList shiftList;
-
- SequenceGroup selectionGroup;
-
- List<int[]> deletedHiddenColumns;
-
int columnsDeleted;
- public TrimRegionCommand(String description, String command,
- SequenceI[] seqs, int column, AlignmentI al,
- ColumnSelection colSel, SequenceGroup selectedRegion)
+ /**
+ * Constructs and performs a trim alignment command
+ *
+ * @param description
+ * (to show in Undo/Redo menu)
+ * @param trimLeft
+ * if true trim to left of column, else to right
+ * @param seqs
+ * the sequences to trim
+ * @param column
+ * the alignment column (base 0) from which to trim
+ * @param al
+ */
+ public TrimRegionCommand(String description, boolean trimLeft,
+ SequenceI[] seqs, int column, AlignmentI al)
{
this.description = description;
- this.selectionGroup = selectedRegion;
- this.colSel = colSel;
- if (command.equalsIgnoreCase(TRIM_LEFT))
+ if (trimLeft)
{
if (column == 0)
{
setEdit(new Edit(Action.CUT, seqs, 0, column, al));
}
- else if (command.equalsIgnoreCase(TRIM_RIGHT))
+ else
{
int width = al.getWidth() - column - 1;
- if (width < 2)
+ if (width < 1)
{
return;
}
- columnsDeleted = width - 1;
+ columnsDeleted = width;
setEdit(new Edit(Action.CUT, seqs, column + 1, width, al));
}
- // We need to keep a record of the sequence start
- // in order to restore the state after a redo
- int i, isize = getEdit(0).seqs.length;
- start = new int[isize];
- for (i = 0; i < isize; i++)
- {
- start[i] = getEdit(0).seqs[i].getStart();
- }
performEdit(0, null);
}
- void cut(Edit command)
- {
- int column, j, jSize = command.seqs.length;
- for (j = 0; j < jSize; j++)
- {
- if (command.position == 0)
- {
- // This is a TRIM_LEFT command
- column = command.seqs[j].findPosition(command.number);
- command.seqs[j].setStart(column);
- }
- else
- {
- // This is a TRIM_RIGHT command
- column = command.seqs[j].findPosition(command.position) - 1;
- command.seqs[j].setEnd(column);
- }
- }
-
- super.cut(command, null);
-
- if (command.position == 0)
- {
- deletedHiddenColumns = colSel.compensateForEdit(0, command.number);
- if (selectionGroup != null)
- {
- selectionGroup.adjustForRemoveLeft(command.number);
- }
- }
- else
- {
- deletedHiddenColumns = colSel.compensateForEdit(command.position,
- command.number);
- if (selectionGroup != null)
- {
- selectionGroup.adjustForRemoveRight(command.position);
- }
- }
- }
-
- void paste(Edit command)
- {
- super.paste(command, null);
- int column, j, jSize = command.seqs.length;
- for (j = 0; j < jSize; j++)
- {
- if (command.position == 0)
- {
- command.seqs[j].setStart(start[j]);
- }
- else
- {
- column = command.seqs[j].findPosition(command.number
- + command.position) - 1;
- command.seqs[j].setEnd(column);
- }
- }
-
- if (command.position == 0)
- {
- colSel.compensateForEdit(0, -command.number);
- if (selectionGroup != null)
- {
- selectionGroup.adjustForRemoveLeft(-command.number);
- }
- }
-
- if (deletedHiddenColumns != null)
- {
- int[] region;
- for (int i = 0; i < deletedHiddenColumns.size(); i++)
- {
- region = deletedHiddenColumns.get(i);
- colSel.hideColumns(region[0], region[1]);
- }
- }
- }
-
+ @Override
public int getSize()
{
return columnsDeleted;
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
+ @Override
public void setMenusForViewport()
{
setMenusFromViewport(viewport);
alignPanel.makeEPS(f);
}
+ @Override
public void createSVG(File f)
{
alignPanel.makeSVG(f);
}
}
+ @Override
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, viewport.getAlignment());
viewport.setStartRes(0);
}
else
{
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+ column, viewport.getAlignment());
}
statusBar.setText(MessageManager.formatMessage(
* @param cs
* DOCUMENT ME!
*/
+ @Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
viewport.firePropertyChange("alignment", null, al);
}
+ @Override
public void setShowSeqFeatures(boolean b)
{
showSeqFeatures.setSelected(b);
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.commands;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ * Unit tests for TrimRegionCommand
+ *
+ * @author gmcarstairs
+ *
+ */
+public class TrimRegionCommandTest
+{
+ private AlignmentI al;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ SequenceI[] seqs = new SequenceI[2];
+ seqs[0] = new Sequence("seq0", "abcde-");
+ seqs[1] = new Sequence("seq1", "-ghjkl");
+ al = new Alignment(seqs);
+ al.setDataset(null);
+ }
+
+ /**
+ * Test performing, undoing and redoing a 'trim left'
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimLeft_withUndoAndRedo()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
+ al.getSequencesArray(), 2, al);
+ assertEquals(2, cmd.getSize());
+ assertEquals("cde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("hjkl", al.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * undo and verify
+ */
+ cmd.undoCommand(new AlignmentI[] { al });
+ assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * redo and verify
+ */
+ cmd.doCommand(new AlignmentI[] { al });
+ assertEquals("cde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("hjkl", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Trim left of no columns - should do nothing. This is the case where the
+ * first column is selected and 'Remove Left' is selected.
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimLeft_noColumns()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
+ al.getSequencesArray(), 0, al);
+ assertEquals(0, cmd.getSize());
+ assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Trim left of a single column
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimLeft_oneColumn()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Left", true,
+ al.getSequencesArray(), 1, al);
+ assertEquals(1, cmd.getSize());
+ assertEquals("bcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("ghjkl", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Trim right of no columns - should do nothing. This is the case where the
+ * last column is selected and 'Remove Right' is selected.
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimRight_noColumns()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
+ al.getSequencesArray(), 5, al);
+ assertEquals(0, cmd.getSize());
+ assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Trim right of a single column
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimRight_oneColumn()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
+ al.getSequencesArray(), 4, al);
+ assertEquals(1, cmd.getSize());
+ assertEquals("abcde", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjk", al.getSequenceAt(1).getSequenceAsString());
+ }
+
+ /**
+ * Test performing, undoing and redoing a 'trim right'
+ */
+ @Test(groups = { "Functional" })
+ public void testTrimRight_withUndoAndRedo()
+ {
+ TrimRegionCommand cmd = new TrimRegionCommand("Remove Right", false,
+ al.getSequencesArray(), 2, al);
+ assertEquals(3, cmd.getSize());
+ assertEquals("abc", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-gh", al.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * undo and verify
+ */
+ cmd.undoCommand(new AlignmentI[] { al });
+ assertEquals("abcde-", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-ghjkl", al.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * redo and verify
+ */
+ cmd.doCommand(new AlignmentI[] { al });
+ assertEquals("abc", al.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-gh", al.getSequenceAt(1).getSequenceAsString());
+ }
+}
git://source.jalview.org / jalview.git / commitdiff