+++ /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.
- */
-
-// Prototype Right/Left Justify Script
-boolean left=true;
-
-import jalview.datamodel.*;
-
-def msaf = jalview.bin.Jalview.getCurrentAlignFrame();
-if (msaf==null)
-{
- return;
-}
-
-def al = msaf.getViewport().getAlignment();
-al.padGaps();
-def reg = msaf.getViewport().getSelectionGroup();
-int from,to;
-SequenceI[] seqs;
-
-from=0;
-to=al.getWidth()-1;
-seqs = al.getSequences();
-if (reg!=null) {
- seqs = reg.getSequences();
- from=reg.getStartRes();
- to=reg.getEndRes();
-}
-
-if ((to-from)<1) {
- return;
-}
-
-jalview.commands.EditCommand[] edits=new jalview.commands.EditCommand[seqs.length];
-int s=0;
-for (SequenceI seq:seqs) {
- ContiguousI cont = seq.findPositions(from+1,to+1);
- if (cont==null) { continue; }
- int dsstart=seq.getDatasetSequence().getStart();
- char[] sqchar=seq.getDatasetSequence().getSequence(-dsstart+cont.getBegin(),-dsstart+cont.getEnd()+1);
- println sqchar;
- char[] alseq = new char[to-from+1];
- int sqstart = left ? 0 : alseq.length-sqchar.length;
- int gaps = alseq.length-sqchar.length;
- int gapstart=left ? sqchar.length : 0;
- char gc = al.getGapCharacter();
- for (int gp=0;gp<gaps;gp++) {
- alseq[gapstart+gp]=gc;
- }
-
- for (int sqp=0;sqp<sqchar.length;sqp++) {
- alseq[sqp+sqstart]=sqchar[sqp];
- }
- SequenceI[] sqa=new SequenceI[1];
- sqa[0]=seq;
- // cant do this because the edit command isn't visible.
- // edits[s++]=new jalview.commands.EditCommand.Edit(jalview.commands.EditCommand.Action.REPLACE,sqa,(from).intValue(),(int)alseq.length,al, new String(alseq));
- edits[s++]=new jalview.commands.EditCommand("justify",jalview.commands.EditCommand.Action.REPLACE, new String(alseq),sqa,(from).intValue(),(to).intValue()+1,al);
- println alseq;
-}
-jalview.commands.EditCommand finalEdit=new jalview.commands.EditCommand("Justify "+(left ? "Left" : "Right"));
-for (jalview.commands.EditCommand edit:edits) {
- if (edit!=null) {finalEdit.addEdit(edit.getEdits().get(0)); }
-}
-msaf.addHistoryItem(finalEdit);
-msaf.getViewport().firePropertyChange("alignment",null,seqs);
one of the sequences (the shorter) is discarded. Press the
"Apply" button to remove redundant sequences. The
"Undo" button will undo the last redundancy deletion.</em></li>
+ <li><strong>Left Justify</strong> and <strong>Right
+ Justify<br>
+ </strong> <em>Moves all gaps to either right or left of the sequences in
+ the alignment or the currently selected region.</em></li>
<li><strong>Pad Gaps<br>
</strong><em>When selected, the alignment will be kept at minimal width
(so there are no empty columns before or after the first or last
action.remove_right = Remove right
action.remove_empty_columns = Remove Empty Columns
action.remove_all_gaps = Remove All Gaps
-action.left_justify_alignment = Left Justify Alignment
-action.right_justify_alignment = Right Justify Alignment
+tooltip.left_justify = Left justify whole alignment or selected region
+tooltip.right_justify = Right justify whole alignment or selected region
+action.left_justify = Left Justify
+action.right_justify = Right Justify
action.boxes = Boxes
action.text = Text
action.by_pairwise_id = By Pairwise Identity
*/
package jalview.api;
-import jalview.io.DataSourceType;
-
import java.util.List;
+import jalview.io.DataSourceType;
+
/**
* prototype abstract controller for a Jalview alignment view
*
boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
boolean toggle);
+ boolean justify_Region(boolean left);
+
}
*/
package jalview.api;
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.schemes.ColourSchemeI;
import jalview.viewmodel.ViewportRanges;
-import java.awt.Color;
-import java.awt.Font;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
/**
* @author jimp
*
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+ /**
+ * notify all concerned that the alignment data has changed and derived data
+ * needs to be recalculated
+ */
+ public void notifyAlignmentChanged();
}
--- /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 java.util.List;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.SequenceI;
+
+public class JustifyLeftOrRightCommand extends EditCommand
+{
+ /**
+ * Constructs and performs a trim alignment command
+ *
+ * @param description
+ * (to show in Undo/Redo menu)
+ * @param justifyLeft
+ * if true left justify, otherwise right
+ * @param seqs
+ * the sequences to justify
+ * @param start
+ * - leftmost column (base 0) to justify
+ *
+ * @param end
+ * - rightmost column (base 0) to justify
+ *
+ * @param al
+ */
+ public JustifyLeftOrRightCommand(String description, boolean left,
+ List<SequenceI> seqs, int from, int to, AlignmentI al)
+ {
+ this.description = description;
+
+ for (SequenceI seq : seqs)
+ {
+ ContiguousI cont = seq.findPositions(from + 1, to + 1);
+ if (cont == null)
+ {
+ continue;
+ }
+ int dsstart = seq.getDatasetSequence().getStart();
+ char[] sqchar = seq.getDatasetSequence().getSequence(
+ -dsstart + cont.getBegin(), -dsstart + cont.getEnd() + 1);
+ // debug
+ // println sqchar;
+ char[] alseq = new char[to - from + 1];
+ int sqstart = left ? 0 : alseq.length - sqchar.length;
+ int gaps = alseq.length - sqchar.length;
+ int gapstart = left ? sqchar.length : 0;
+ char gc = al.getGapCharacter();
+ for (int gp = 0; gp < gaps; gp++)
+ {
+ alseq[gapstart + gp] = gc;
+ }
+
+ for (int sqp = 0; sqp < sqchar.length; sqp++)
+ {
+ alseq[sqp + sqstart] = sqchar[sqp];
+ }
+ SequenceI[] sqa = new SequenceI[1];
+ sqa[0] = seq;
+
+ addEdit(new jalview.commands.EditCommand.Edit(
+ jalview.commands.EditCommand.Action.REPLACE, sqa, from,
+ to + 1, al, new String(alseq)));
+ // addEdit(new jalview.commands.EditCommand("justify",
+ // jalview.commands.EditCommand.Action.REPLACE,
+ // new String(alseq), sqa, from, to + 1, al).getEdit(0));
+ }
+
+ performEdit(0, null);
+ }
+}
*/
package jalview.controller;
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.util.BitSet;
-import java.util.List;
-
public class AlignViewController implements AlignViewControllerI
{
AlignViewportI viewport = null;
return false;
}
+ @Override
+ public boolean justify_Region(boolean left)
+ {
+ AlignmentI al = viewport.getAlignment();
+ SequenceGroup reg = viewport.getSelectionGroup();
+ int from, to;
+ List<SequenceI> seqs;
+
+ from = 0;
+ to = al.getWidth() - 1;
+ seqs = al.getSequences();
+ if (reg != null)
+ {
+ seqs = reg.getSequences();
+ from = reg.getStartRes();
+ to = reg.getEndRes();
+ }
+
+ if ((to - from) < 1)
+ {
+ return false;
+ }
+
+ al.padGaps();
+ jalview.commands.JustifyLeftOrRightCommand finalEdit = new jalview.commands.JustifyLeftOrRightCommand(
+ "Justify " + (left ? "Left" : "Right"), left, seqs, from, to,
+ al);
+ avcg.addHistoryItem(finalEdit);
+ viewport.notifyAlignmentChanged();
+ return true;
+ }
}
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+import java.util.Locale;
import java.util.Vector;
import javax.swing.ButtonGroup;
@Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
- AlignmentI al = viewport.getAlignment();
- al.justify(false);
- viewport.firePropertyChange("alignment", null, al);
+ avc.justify_Region(true);
}
/**
@Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
- AlignmentI al = viewport.getAlignment();
- al.justify(true);
- viewport.firePropertyChange("alignment", null, al);
+ avc.justify_Region(false);
}
@Override
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.SortedMap;
cut_actionPerformed();
}
});
+ JMenuItem justifyLeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.left_justify"));
+ justifyLeftMenuItem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.avc.justify_Region(true);
+ }
+ });
+ JMenuItem justifyRightMenuItem = new JMenuItem(
+ MessageManager.getString("action.right_justify"));
+ justifyRightMenuItem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.avc.justify_Region(false);
+ }
+ });
+
upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
editMenu.add(copy);
editMenu.add(cut);
+ editMenu.add(justifyLeftMenuItem);
+ editMenu.add(justifyRightMenuItem);
editMenu.add(editSequence);
editMenu.add(upperCase);
editMenu.add(lowerCase);
*/
package jalview.jbgui;
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.GeneticCodeI;
-import jalview.analysis.GeneticCodes;
-import jalview.api.SplitContainerI;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.io.FileFormats;
-import jalview.schemes.ResidueColourScheme;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
JMenuItem justifyLeftMenuItem = new JMenuItem(
- MessageManager.getString("action.left_justify_alignment"));
+ MessageManager.getString("action.left_justify"));
+ justifyLeftMenuItem.setToolTipText(
+ MessageManager.getString("tooltip.left_justify"));
justifyLeftMenuItem.addActionListener(new ActionListener()
{
@Override
}
});
JMenuItem justifyRightMenuItem = new JMenuItem(
- MessageManager.getString("action.right_justify_alignment"));
+ MessageManager.getString("action.right_justify"));
+ justifyRightMenuItem.setToolTipText(
+ MessageManager.getString("action.left_justify"));
+
justifyRightMenuItem.addActionListener(new ActionListener()
{
@Override
editMenu.add(removeAllGapsMenuItem);
editMenu.add(removeRedundancyMenuItem);
editMenu.addSeparator();
- // dont add these yet in the CVS build - they cannot be undone!
- // Excluded from Jalview 2.5 release - undo needs to be implemented.
- // editMenu.add(justifyLeftMenuItem);
- // editMenu.add(justifyRightMenuItem);
- // editMenu.addSeparator();
+
+ editMenu.add(justifyLeftMenuItem);
+ editMenu.add(justifyRightMenuItem);
+
+ editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
showMenu.add(showAllColumns);
*/
package jalview.viewmodel;
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
changeSupport.firePropertyChange(prop, oldvalue, newvalue);
}
+ @Override
+ public void notifyAlignmentChanged()
+ {
+ firePropertyChange("alignment", null, alignment);
+ }
+
// common hide/show column stuff
public void hideSelectedColumns()
git://source.jalview.org / jalview.git / commitdiff