From db098429f712e3cda729b937cd3f635482f96b52 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 22 Oct 2015 11:10:49 +0100 Subject: [PATCH] JAL-1932 TrimRegionCommand bug fix, tests and purge of unused code --- help/html/menus/alignmentMenu.html | 2 +- help/html/menus/alwedit.html | 2 +- src/jalview/appletgui/AlignFrame.java | 14 +- src/jalview/commands/TrimRegionCommand.java | 134 +++--------------- src/jalview/gui/AlignFrame.java | 17 +-- test/jalview/commands/TrimRegionCommandTest.java | 160 ++++++++++++++++++++++ 6 files changed, 197 insertions(+), 132 deletions(-) create mode 100644 test/jalview/commands/TrimRegionCommandTest.java diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index b006c89..ce339cc 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -196,7 +196,7 @@ "Deselect All" to deselect all columns.
  • Remove Right (Control R)
    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.
    • diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index a8390c2..846a1bd 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -75,7 +75,7 @@ deselect all columns.
  • Remove Right (Control R)
    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.
    • diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 80ab5d5..50ec7e0 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -2294,18 +2294,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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( @@ -2609,6 +2605,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } + @Override public void changeColour(ColourSchemeI cs) { @@ -3759,6 +3756,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.add(statusBar, BorderLayout.SOUTH); } + @Override public void setStatus(String string) { statusBar.setText(string); diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java index b4d92a0..dc6c424 100644 --- a/src/jalview/commands/TrimRegionCommand.java +++ b/src/jalview/commands/TrimRegionCommand.java @@ -21,39 +21,30 @@ 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 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) { @@ -64,109 +55,24 @@ public class TrimRegionCommand extends EditCommand 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; diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 5c29b9b..d20d62e 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -845,6 +845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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); @@ -1401,6 +1402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.makeEPS(f); } + @Override public void createSVG(File f) { alignPanel.makeSVG(f); @@ -1574,6 +1576,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -2569,18 +2572,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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( @@ -3497,6 +3496,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param cs * DOCUMENT ME! */ + @Override public void changeColour(ColourSchemeI cs) { // TODO: pull up to controller method @@ -5755,6 +5755,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.firePropertyChange("alignment", null, al); } + @Override public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(b); diff --git a/test/jalview/commands/TrimRegionCommandTest.java b/test/jalview/commands/TrimRegionCommandTest.java new file mode 100644 index 0000000..d593d41 --- /dev/null +++ b/test/jalview/commands/TrimRegionCommandTest.java @@ -0,0 +1,160 @@ +/* + * 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 . + * 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()); + } +} -- 1.7.10.2