X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ab99e065edd79a2053a65ca1de46f243d9e88ccc;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=5b6a8a555d249bd057b20cb5e646c88741ae5e74;hpb=f7f5b32a9eaa5e975fdcd1695d0a4b3675db1656;p=jalview.git
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
old mode 100755
new mode 100644
index 5b6a8a5..ab99e06
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,54 +1,111 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.appletgui;
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-
-public class AlignFrame
- extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.Conservation;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.JalviewLite;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+public class AlignFrame extends EmbmenuFrame implements ActionListener,
+ ItemListener, KeyListener
{
public AlignmentPanel alignPanel;
+
public AlignViewport viewport;
+
int DEFAULT_WIDTH = 700;
+
int DEFAULT_HEIGHT = 500;
String jalviewServletURL;
- public AlignFrame(AlignmentI al,
- jalview.bin.JalviewLite applet,
- String title,
- boolean embedded)
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
+ String title, boolean embedded)
{
-
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -57,8 +114,7 @@ public class AlignFrame
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -70,6 +126,13 @@ public class AlignFrame
viewport.updateConsensus(alignPanel);
annotationPanelMenuItem.setState(viewport.showAnnotation);
+ displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
+ followMouseOverFlag.setState(viewport.getFollowHighlight());
+ showGroupConsensus.setState(viewport.isShowGroupConsensus());
+ showGroupConservation.setState(viewport.isShowGroupConservation());
+ showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
+ showSequenceLogo.setState(viewport.isShowSequenceLogo());
+ normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
seqLimits.setState(viewport.showJVSuffix);
@@ -86,6 +149,10 @@ public class AlignFrame
{
sortPairwiseMenuItem_actionPerformed();
}
+ else if (param.equalsIgnoreCase("Length"))
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
}
param = applet.getParameter("wrap");
@@ -97,7 +164,12 @@ public class AlignFrame
wrapMenuItem_actionPerformed();
}
}
-
+ param = applet.getParameter("centrecolumnlabels");
+ if (param != null)
+ {
+ centreColumnLabelFlag.setState(true);
+ centreColumnLabelFlag_stateChanged();
+ }
try
{
param = applet.getParameter("windowWidth");
@@ -112,21 +184,43 @@ public class AlignFrame
int height = Integer.parseInt(param);
DEFAULT_HEIGHT = height;
}
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
-
- //Some JVMS send keyevents to Top frame or lowest panel,
- //Havent worked out why yet. So add to both this frame and seqCanvas for now
+ if (viewport.getAlignment().isNucleotide())
+ {
+ viewport.updateStrucConsensus(alignPanel);
+ if (viewport.getAlignment().hasRNAStructure())
+ {
+ RNAHelixColour.setEnabled(true);
+ }
+ else
+ {
+ RNAHelixColour.setEnabled(false);
+ }
+ }
+ else
+ {
+ RNAHelixColour.setEnabled(false);
+ purinePyrimidineColour.setEnabled(false);
+ }
+ // Some JVMS send keyevents to Top frame or lowest panel,
+ // Havent worked out why yet. So add to both this frame and seqCanvas for
+ // now
this.addKeyListener(this);
alignPanel.seqPanel.seqCanvas.addKeyListener(this);
alignPanel.idPanel.idCanvas.addKeyListener(this);
alignPanel.scalePanel.addKeyListener(this);
alignPanel.annotationPanel.addKeyListener(this);
+ alignPanel.annotationPanelHolder.addKeyListener(this);
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
+ alignPanel.alabels.addKeyListener(this);
createAlignFrameWindow(embedded, title);
- alignPanel.validate();
+
+ validate();
+ alignPanel.adjustAnnotationHeight();
alignPanel.paintAlignment(true);
}
@@ -141,25 +235,47 @@ public class AlignFrame
}
/**
- * DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
+ * Load a features file onto the alignment
+ *
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
*/
- public void parseFeaturesFile(String file, String type)
+ public boolean parseFeaturesFile(String file, String type)
{
+ return parseFeaturesFile(file, type, true);
+ }
+
+ /**
+ * Load a features file onto the alignment
+ *
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
+ * @param autoenabledisplay
+ * when true, display features flag will be automatically enabled if
+ * features are loaded
+ * @return true if data parsed as a features file
+ */
+ public boolean parseFeaturesFile(String file, String type,
+ boolean autoenabledisplay)
+ {
+ // TODO: test if importing a features file onto an alignment which already
+ // has features with links overwrites the original links.
+
Hashtable featureLinks = new Hashtable();
boolean featuresFile = false;
try
{
- featuresFile = new jalview.io.FeaturesFile(file,
- type).parse(viewport.alignment,
- alignPanel.seqPanel.seqCanvas.
- getFeatureRenderer().featureColours,
- featureLinks,
- true);
- }
- catch (Exception ex)
+ featuresFile = new jalview.io.FeaturesFile(file, type)
+ .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().featureColours, featureLinks,
+ true, viewport.applet.getDefaultParameter(
+ "relaxedidmatch", false));
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -168,323 +284,370 @@ public class AlignFrame
{
if (featureLinks.size() > 0)
{
- alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureLinks = featureLinks;
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
+ }
+ if (autoenabledisplay)
+ {
+ viewport.showSequenceFeatures = true;
+ sequenceFeatures.setState(true);
+ }
+ if (viewport.featureSettings != null)
+ {
+ viewport.featureSettings.refreshTable();
}
- viewport.showSequenceFeatures = true;
- sequenceFeatures.setState(true);
alignPanel.paintAlignment(true);
+ statusBar.setText("Successfully added features to alignment.");
}
-
+ return featuresFile;
}
+ @Override
public void keyPressed(KeyEvent evt)
{
- if (viewport.cursorMode &&
- ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
- evt.getKeyCode() <= KeyEvent.VK_9)
- ||
- (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
- evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
- )
- && Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
+ if (viewport.cursorMode
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+ && Character.isDigit(evt.getKeyChar()))
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
switch (evt.getKeyCode())
{
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed();
- break;
- case KeyEvent.VK_X:
- if (evt.isControlDown() || evt.isMetaDown())
- {
- cut_actionPerformed();
- }
- break;
- case KeyEvent.VK_C:
- if (viewport.cursorMode && !evt.isControlDown())
- {
- alignPanel.seqPanel.setCursorColumn();
- }
- if (evt.isControlDown() || evt.isMetaDown())
- {
- copy_actionPerformed();
- }
- break;
- case KeyEvent.VK_V:
- if (evt.isControlDown())
- {
- paste(evt.isShiftDown());
- }
- break;
- case KeyEvent.VK_A:
- if (evt.isControlDown() || evt.isMetaDown())
- {
- selectAllSequenceMenuItem_actionPerformed();
- }
- break;
- case KeyEvent.VK_DOWN:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, 1);
- }
- else
- {
- moveSelectedSequences(false);
- }
- break;
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed();
- case KeyEvent.VK_UP:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, -1);
- }
- else
- {
- moveSelectedSequences(true);
- }
- break;
+ alignPanel.alabels.cancelDrag();
+ break;
+ case KeyEvent.VK_X:
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ cut_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ copy_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_V:
+ if (evt.isControlDown())
+ {
+ paste(evt.isShiftDown());
+ }
+ break;
+ case KeyEvent.VK_A:
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ selectAllSequenceMenuItem_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_DOWN:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, 1);
+ }
+ else
+ {
+ moveSelectedSequences(false);
+ }
+ break;
- case KeyEvent.VK_LEFT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor( -1, 0);
- break;
+ case KeyEvent.VK_UP:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, -1);
+ }
+ else
+ {
+ moveSelectedSequences(true);
+ }
+ break;
- case KeyEvent.VK_RIGHT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor( 1, 0);
- break;
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(-1, 0);
+ break;
- case KeyEvent.VK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown()
- );
- }
- break;
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(1, 0);
+ break;
- case KeyEvent.VK_DELETE:
- case KeyEvent.VK_BACK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown());
- }
- else
- {
- cut_actionPerformed();
- alignPanel.seqPanel.seqCanvas.repaint();
- }
- break;
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ break;
- case KeyEvent.VK_S:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRow();
- }
- break;
- case KeyEvent.VK_P:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorPosition();
- }
- break;
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ else
+ {
+ cut_actionPerformed();
+ alignPanel.seqPanel.seqCanvas.repaint();
+ }
+ break;
- case KeyEvent.VK_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorPosition();
+ }
+ break;
- case KeyEvent.VK_Q:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
- }
- break;
- case KeyEvent.VK_M:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
- }
- break;
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
- case KeyEvent.VK_F2:
- viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is " +
- (viewport.cursorMode ? "on" : "off"));
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
- }
- break;
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
- case KeyEvent.VK_F:
- if (evt.isControlDown())
- {
- findMenuItem_actionPerformed();
- }
- break;
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText("Keyboard editing mode is "
+ + (viewport.cursorMode ? "on" : "off"));
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ break;
- case KeyEvent.VK_H:
+ case KeyEvent.VK_F:
+ if (evt.isControlDown())
{
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
- boolean hide = false;
- SequenceGroup sg = viewport.getSelectionGroup();
+ findMenuItem_actionPerformed();
+ }
+ break;
- if (toggleSeqs)
- {
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
- {
- hide = true;
- viewport.hideAllSelectedSeqs();
- }
- else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
- {
- viewport.showAllHiddenSeqs();
- }
- }
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ break;
+ }
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- viewport.hideSelectedColumns();
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- viewport.showAllHiddenColumns();
- }
- }
- break;
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(true);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ }
+ break;
+
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(false);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
}
+ break;
- case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
+ case KeyEvent.VK_Z:
+ if (evt.isControlDown())
+ {
+ undoMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_Y:
+ if (evt.isControlDown())
+ {
+ redoMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_L:
+ if (evt.isControlDown())
+ {
+ trimAlignment(true);
+ }
+ break;
+
+ case KeyEvent.VK_R:
+ if (evt.isControlDown())
+ {
+ trimAlignment(false);
+ }
+ break;
+
+ case KeyEvent.VK_E:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
{
- alignPanel.scrollUp(true);
+ this.removeAllGapsMenuItem_actionPerformed();
}
else
{
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ removeGappedColumnMenuItem_actionPerformed();
}
- break;
-
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ }
+ break;
+ case KeyEvent.VK_I:
+ if (evt.isControlDown())
+ {
+ if (evt.isAltDown())
{
- alignPanel.scrollUp(false);
+ invertColSel_actionPerformed();
}
else
{
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ invertSequenceMenuItem_actionPerformed();
}
- break;
+ }
+ break;
- case KeyEvent.VK_Z:
- if (evt.isControlDown())
- {
- undoMenuItem_actionPerformed();
- }
- break;
+ case KeyEvent.VK_U:
+ if (evt.isControlDown())
+ {
+ this.deleteGroups_actionPerformed();
+ }
+ break;
- case KeyEvent.VK_Y:
- if (evt.isControlDown())
- {
- redoMenuItem_actionPerformed();
- }
- break;
+ case KeyEvent.VK_T:
+ if (evt.isControlDown())
+ {
+ newView(null);
+ }
+ break;
- case KeyEvent.VK_L:
- if (evt.isControlDown())
- {
- trimAlignment(true);
- }
- break;
+ }
+ alignPanel.paintAlignment(true);
+ }
- case KeyEvent.VK_R:
- if (evt.isControlDown())
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ {
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // Hide everything by the current selection - this is a hack - we do the
+ // invert and then hide
+ // first check that there will be visible columns after the invert.
+ if ((viewport.getColumnSelection() != null
+ && viewport.getColumnSelection().getSelected() != null && viewport
+ .getColumnSelection().getSelected().size() > 0)
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
{
- trimAlignment(false);
- }
- break;
+ invertSequenceMenuItem_actionPerformed();
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
- case KeyEvent.VK_E:
- if (evt.isControlDown())
- {
- if (evt.isShiftDown())
- {
- this.removeAllGapsMenuItem_actionPerformed();
- }
- else
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
- }
- break;
- case KeyEvent.VK_I:
- if (evt.isControlDown())
- {
- if (evt.isAltDown())
- {
- viewport.invertColumnSelection();
- }
- else
- {
- this.invertSequenceMenuItem_actionPerformed();
- }
}
- break;
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection and indicate it should be hidden.
+ invertColSel_actionPerformed();
+ toggleCols = true;
+ }
+ }
- case KeyEvent.VK_U:
- if (evt.isControlDown())
- {
- this.deleteGroups_actionPerformed();
- }
- break;
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
+ {
+ hide = true;
+ viewport.hideAllSelectedSeqs();
+ }
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
+ {
+ viewport.showAllHiddenSeqs();
+ }
+ }
- case KeyEvent.VK_T:
- if (evt.isControlDown())
+ if (toggleCols)
+ {
+ if (viewport.getColumnSelection().getSelected().size() > 0)
+ {
+ viewport.hideSelectedColumns();
+ if (!toggleSeqs)
{
- newView(null);
+ viewport.setSelectionGroup(sg);
}
- break;
-
+ }
+ else if (!hide)
+ {
+ viewport.showAllHiddenColumns();
+ }
}
- alignPanel.paintAlignment(true);
}
+ @Override
public void keyReleased(KeyEvent evt)
- {}
+ {
+ }
+ @Override
public void keyTyped(KeyEvent evt)
- {}
+ {
+ }
+ @Override
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == colourTextMenuItem)
+ if (evt.getSource() == displayNonconservedMenuItem)
+ {
+ displayNonconservedMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == colourTextMenuItem)
{
colourTextMenuItem_actionPerformed();
}
@@ -544,12 +707,61 @@ public class AlignFrame
}
else if (evt.getSource() == autoCalculate)
{
- viewport.autocalculateConsensus = autoCalculate.getState();
+ viewport.autoCalculateConsensus = autoCalculate.getState();
+ }
+ else if (evt.getSource() == sortByTree)
+ {
+ viewport.sortByTree = sortByTree.getState();
+ }
+ else if (evt.getSource() == this.centreColumnLabelFlag)
+ {
+ centreColumnLabelFlag_stateChanged();
+ }
+ else if (evt.getSource() == this.followMouseOverFlag)
+ {
+ mouseOverFlag_stateChanged();
+ }
+ else if (evt.getSource() == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (evt.getSource() == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (evt.getSource() == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (evt.getSource() == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
+ else if (evt.getSource() == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (evt.getSource() == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
}
-
alignPanel.paintAlignment(true);
}
+ private void mouseOverFlag_stateChanged()
+ {
+ viewport.followHighlight = followMouseOverFlag.getState();
+ // TODO: could kick the scrollTo mechanism to reset view for current
+ // searchresults.
+ }
+
+ private void centreColumnLabelFlag_stateChanged()
+ {
+ viewport.centreColumnLabels = centreColumnLabelFlag.getState();
+ this.alignPanel.annotationPanel.repaint();
+ }
+
+ @Override
public void actionPerformed(ActionEvent evt)
{
Object source = evt.getSource();
@@ -630,6 +842,10 @@ public class AlignFrame
{
delete_actionPerformed();
}
+ else if (source == grpsFromSelection)
+ {
+ makeGrpsFromSelection_actionPerformed();
+ }
else if (source == deleteGroups)
{
deleteGroups_actionPerformed();
@@ -687,61 +903,76 @@ public class AlignFrame
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
- else if (source == hideSequences && viewport.getSelectionGroup() != null)
+ else if (source == hideSequences
+ && viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideAllButSelection)
+ {
+ toggleHiddenRegions(false, false);
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideAllSelection)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showAllHidden)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (source == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (source == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (source == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
+ else if (source == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (source == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
}
else if (source == featureSettings)
{
new FeatureSettings(alignPanel);
}
- else if(source== alProperties)
+ else if (source == alProperties)
{
- StringBuffer contents = new StringBuffer();
-
- float avg = 0;
- int min=Integer.MAX_VALUE, max=0;
- for(int i=0; imax)
- max = size;
- if(size 0)
@@ -1083,13 +1380,15 @@ public class AlignFrame
viewport.historyList.push(command);
viewport.redoList.removeAllElements();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.updateHiddenColumns();
}
}
+
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * TODO: JAL-1104 DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed()
{
@@ -1103,17 +1402,25 @@ public class AlignFrame
command.undoCommand(null);
AlignViewport originalSource = getOriginatingSource(command);
-
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ // JBPNote Test
+ if (originalSource != viewport)
+ {
+ System.err
+ .println("Warning: Viewport object mismatch whilst undoing");
+ }
+ originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
+ // viewport.getColumnSelection().getHiddenColumns()
+ // != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * TODO: JAL-1104 DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed()
{
@@ -1127,33 +1434,41 @@ public class AlignFrame
command.doCommand(null);
AlignViewport originalSource = getOriginatingSource(command);
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ // JBPNote Test
+ if (originalSource != viewport)
+ {
+ System.err
+ .println("Warning: Viewport object mismatch whilst re-doing");
+ }
+ originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
+ // viewport.getColumnSelection().getHiddenColumns()
+ // != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
AlignViewport getOriginatingSource(CommandI command)
{
AlignViewport originalSource = null;
- //For sequence removal and addition, we need to fire
- //the property change event FROM the viewport where the
- //original alignment was altered
+ // For sequence removal and addition, we need to fire
+ // the property change event FROM the viewport where the
+ // original alignment was altered
AlignmentI al = null;
if (command instanceof EditCommand)
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components
- .get(viewport.getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
for (int i = 0; i < comps.size(); i++)
{
if (comps.elementAt(i) instanceof AlignmentPanel)
{
- if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
{
- originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
break;
}
}
@@ -1162,11 +1477,11 @@ public class AlignFrame
if (originalSource == null)
{
- //The original view is closed, we must validate
- //the current view against the closed view first
+ // The original view is closed, we must validate
+ // the current view against the closed view first
if (al != null)
{
- PaintRefresher.validateSequences(al, viewport.alignment);
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
}
originalSource = viewport;
@@ -1182,98 +1497,54 @@ public class AlignFrame
{
return;
}
-
- if (up)
- {
- for (int i = 1; i < viewport.alignment.getHeight(); i++)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i + 1);
- }
- }
-
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ up ? null : viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
}
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
- if(viewport.cursorMode)
+ List sg = new Vector();
+ if (viewport.cursorMode)
+ {
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
{
- sg.addElement(viewport.alignment.getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.getHiddenRepSequences());
}
- else if(viewport.getSelectionGroup()!=null
- && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
- {
- sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
- }
- if(sg.size()<1)
+ if (sg.size() < 1)
{
return;
}
- Vector invertGroup = new Vector();
+ Vector invertGroup = new Vector();
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
- if(!sg.contains(viewport.alignment.getSequenceAt(i)))
- invertGroup.addElement(viewport.alignment.getSequenceAt(i));
+ if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
}
- SequenceI[] seqs1 = new SequenceI[sg.size()];
- for (int i = 0; i < sg.size(); i++)
- seqs1[i] = (SequenceI) sg.elementAt(i);
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
- SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+ SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
+ .size()]);
for (int i = 0; i < invertGroup.size(); i++)
- seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+ seqs2[i] = invertGroup.elementAt(i);
SlideSequencesCommand ssc;
if (right)
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs2, seqs1, size,
- viewport.getGapCharacter()
- );
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+ size, viewport.getGapCharacter());
else
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs1, seqs2, size,
- viewport.getGapCharacter()
- );
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+ size, viewport.getGapCharacter());
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
@@ -1286,7 +1557,7 @@ public class AlignFrame
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor( -size, 0);
+ alignPanel.seqPanel.moveCursor(-size, 0);
else
groupAdjustment = -size;
}
@@ -1294,30 +1565,30 @@ public class AlignFrame
if (groupAdjustment != 0)
{
viewport.getSelectionGroup().setStartRes(
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
viewport.getSelectionGroup().setEndRes(
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
-
boolean appendHistoryItem = false;
- if(viewport.historyList!=null
- && viewport.historyList.size()>0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ if (viewport.historyList != null && viewport.historyList.size() > 0
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)
{
- appendHistoryItem = ssc.appendSlideCommand(
- (SlideSequencesCommand)viewport.historyList.peek())
- ;
+ appendHistoryItem = ssc
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .peek());
}
- if(!appendHistoryItem)
+ if (!appendHistoryItem)
addHistoryItem(ssc);
repaint();
}
static StringBuffer copiedSequences;
+
static Vector copiedHiddenColumns;
+
protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
@@ -1331,26 +1602,25 @@ public class AlignFrame
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
+ int index = viewport.getAlignment().findIndex(seq);
orderedSeqs.put(index + "", seq);
}
int index = 0, startRes, endRes;
char ch;
- if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
+ if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
- i++)
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
+ .size(); i++)
{
- int[] region = (int[])
- viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+ int[] region = (int[]) viewport.getColumnSelection()
+ .getHiddenColumns().elementAt(i);
copiedHiddenColumns.addElement(new int[]
- {region[0] - hiddenOffset,
- region[1] - hiddenOffset});
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
else
@@ -1377,18 +1647,18 @@ public class AlignFrame
}
}
- //FIND START RES
- //Returns residue following index if gap
+ // FIND START RES
+ // Returns residue following index if gap
startRes = seq.findPosition(sg.getStartRes());
- //FIND END RES
- //Need to find the residue preceeding index if gap
+ // FIND END RES
+ // Need to find the residue preceeding index if gap
endRes = 0;
for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
{
ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
+ if (!jalview.util.Comparison.isGap((ch)))
{
endRes++;
}
@@ -1399,11 +1669,14 @@ public class AlignFrame
endRes += seq.getStart() - 1;
}
- copiedSequences.append(seq.getName() + "\t" +
- startRes + "\t" +
- endRes + "\t" +
- seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1) + "\n");
+ copiedSequences.append(seq.getName()
+ + "\t"
+ + startRes
+ + "\t"
+ + endRes
+ + "\t"
+ + seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1) + "\n");
}
}
@@ -1455,9 +1728,7 @@ public class AlignFrame
newtitle = newtitle.concat("- from " + getTitle());
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
- viewport.applet,
- newtitle,
- false);
+ viewport.applet, newtitle, false);
if (copiedHiddenColumns != null)
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
@@ -1468,16 +1739,16 @@ public class AlignFrame
}
jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ DEFAULT_HEIGHT);
}
else
{
addSequences(newSeqs);
}
- }
- catch (Exception ex)
- {} // could be anything being pasted in here
+ } catch (Exception ex)
+ {
+ } // could be anything being pasted in here
}
@@ -1485,23 +1756,18 @@ public class AlignFrame
{
for (int i = 0; i < seqs.length; i++)
{
- viewport.alignment.addSequence(seqs[i]);
+ viewport.getAlignment().addSequence(seqs[i]);
}
- //!newAlignment
- addHistoryItem(new EditCommand(
- "Add sequences",
- EditCommand.PASTE,
- seqs,
- 0,
- viewport.alignment.getWidth(),
- viewport.alignment)
- );
+ // !newAlignment
+ addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ seqs, 0, viewport.getAlignment().getWidth(),
+ viewport.getAlignment()));
- viewport.setEndSeq(viewport.alignment.getHeight());
- viewport.alignment.getWidth();
- viewport.firePropertyChange("alignment", null,
- viewport.alignment.getSequences());
+ viewport.setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getAlignment().getWidth();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
@@ -1529,10 +1795,10 @@ public class AlignFrame
}
// If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.alignment.getHeight())
+ if (sg.getSize() == viewport.getAlignment().getHeight())
{
viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
+ sg.getEndRes() + 1);
}
SequenceI[] cut = new SequenceI[seqs.size()];
@@ -1542,30 +1808,117 @@ public class AlignFrame
}
/*
- //ADD HISTORY ITEM
+ * //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences",
- EditCommand.CUT,
- cut,
- sg.getStartRes(),
- sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
viewport.setSelectionGroup(null);
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
if (viewport.getAlignment().getHeight() < 1)
{
this.setVisible(false);
}
+ viewport.sendSelection();
+ }
+
+ /**
+ * group consensus toggled
+ *
+ */
+ protected void showGroupConsensus_actionPerformed()
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /**
+ * group conservation toggled.
+ */
+ protected void showGroupConservation_actionPerformed()
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed()
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showSequenceLogo_actionPerformed()
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void normSequenceLogo_actionPerformed()
+ {
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
+ viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed()
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed()
+ {
+ if (viewport.getSelectionGroup() != null)
+ {
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true).getSequenceStrings(
+ viewport.getGapCharacter()), viewport.getAlignment()
+ .getGroups());
+ viewport.getAlignment().deleteAllGroups();
+ viewport.sequenceColours = null;
+ viewport.setSelectionGroup(null);
+ // set view properties for each group
+ for (int g = 0; g < gps.length; g++)
+ {
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+ viewport.getAlignment().addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (SequenceI sq : gps[g].getSequences(null))
+ viewport.setSequenceColour(sq, col);
+ }
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
}
protected void deleteGroups_actionPerformed()
{
- viewport.alignment.deleteAllGroups();
+ viewport.getAlignment().deleteAllGroups();
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
@@ -1579,10 +1932,11 @@ public class AlignFrame
{
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
- sg.setEndRes(viewport.alignment.getWidth() - 1);
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void deselectAllSequenceMenuItem_actionPerformed()
@@ -1599,6 +1953,7 @@ public class AlignFrame
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertSequenceMenuItem_actionPerformed()
@@ -1610,6 +1965,15 @@ public class AlignFrame
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
+ }
+
+ public void invertColSel_actionPerformed()
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
void trimAlignment(boolean trimLeft)
@@ -1631,132 +1995,119 @@ public class AlignFrame
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
+ TrimRegionCommand.TRIM_LEFT, seqs, column,
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
viewport.setStartRes(0);
}
else
{
trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
}
statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
addHistoryItem(trimRegion);
- Vector groups = viewport.alignment.getGroups();
-
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if ( (trimLeft && !sg.adjustForRemoveLeft(column))
- || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.alignment.deleteGroup(sg);
+ viewport.getAlignment().deleteGroup(sg);
}
}
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
}
}
public void removeGappedColumnMenuItem_actionPerformed()
{
- int start = 0, end = viewport.alignment.getWidth() - 1;
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
- RemoveGapColCommand removeGapCols =
- new RemoveGapColCommand("Remove Gapped Columns",
- seqs,
- start, end,
- viewport.alignment);
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+ "Remove Gapped Columns", seqs, start, end,
+ viewport.getAlignment());
addHistoryItem(removeGapCols);
- statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");
+ statusBar.setText("Removed " + removeGapCols.getSize()
+ + " empty columns.");
- //This is to maintain viewport position on first residue
- //of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
- // viewport.getColumnSelection().compensateForEdits(shifts);
+ // viewport.getColumnSelection().compensateForEdits(shifts);
viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
public void removeAllGapsMenuItem_actionPerformed()
{
- int start = 0, end = viewport.alignment.getWidth() - 1;
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
{
- seqs = viewport.alignment.getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
- //This is to maintain viewport position on first residue
- //of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
- addHistoryItem(new RemoveGapsCommand("Remove Gaps",
- seqs,
- start, end,
- viewport.alignment));
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+ viewport.getAlignment()));
viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
@@ -1764,54 +2115,52 @@ public class AlignFrame
{
new Finder(alignPanel);
}
+
/**
* create a new view derived from the current view
+ *
* @param viewtitle
* @return frame for the new view
*/
public AlignFrame newView(String viewtitle)
{
AlignmentI newal;
- if (viewport.hasHiddenRows)
+ if (viewport.hasHiddenRows())
{
- newal = new Alignment(viewport.getAlignment().
- getHiddenSequences()
- .getFullAlignment().
- getSequencesArray());
+ newal = new Alignment(viewport.getAlignment().getHiddenSequences()
+ .getFullAlignment().getSequencesArray());
}
else
{
- newal = new Alignment(viewport.alignment.getSequencesArray());
+ newal = new Alignment(viewport.getAlignment().getSequencesArray());
}
- if (viewport.alignment.getAlignmentAnnotation() != null)
+ if (viewport.getAlignment().getAlignmentAnnotation() != null)
{
- for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
{
- if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+ if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
{
- newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+ newal.addAnnotation(viewport.getAlignment()
+ .getAlignmentAnnotation()[i]);
}
}
}
- AlignFrame newaf = new AlignFrame(newal,
- viewport.applet,
- "",
- false);
+ AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
- newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+ newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel,
- newaf.alignPanel.av.getSequenceSetId());
+ newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
- newaf.alignPanel.av.getSequenceSetId());
+ newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
- newaf.alignPanel.av.getSequenceSetId());
+ newaf.alignPanel.av.getSequenceSetId());
- Vector comps = (Vector) PaintRefresher.components.get(viewport.
- getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
int viewSize = -1;
for (int i = 0; i < comps.size(); i++)
{
@@ -1822,10 +2171,12 @@ public class AlignFrame
}
String title = new String(this.getTitle());
- if (viewtitle!=null)
+ if (viewtitle != null)
+ {
+ title = viewtitle + " ( " + title + ")";
+ }
+ else
{
- title = viewtitle+" ( "+title+")";
- } else {
if (title.indexOf("(View") > -1)
{
title = title.substring(0, title.indexOf("(View"));
@@ -1839,6 +2190,7 @@ public class AlignFrame
newaf.viewport.redoList = viewport.redoList;
return newaf;
}
+
/**
*
* @return list of feature groups on the view
@@ -1846,36 +2198,47 @@ public class AlignFrame
public String[] getFeatureGroups()
{
FeatureRenderer fr = null;
- if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
{
return fr.getGroups();
}
return null;
}
+
/**
* get sequence feature groups that are hidden or shown
- * @param visible true is visible
+ *
+ * @param visible
+ * true is visible
* @return list
*/
public String[] getFeatureGroupsOfState(boolean visible)
{
FeatureRenderer fr = null;
- if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
{
return fr.getGroups(visible);
}
return null;
}
+
/**
* Change the display state for the given feature groups
- * @param groups list of group strings
- * @param state visible or invisible
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
*/
- public void setFeatureGroupState(String[] groups, boolean state) {
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
FeatureRenderer fr = null;
this.sequenceFeatures.setState(true);
viewport.showSequenceFeatures(true);
- if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
{
fr.setGroupState(groups, state);
alignPanel.seqPanel.seqCanvas.repaint();
@@ -1885,6 +2248,7 @@ public class AlignFrame
}
}
}
+
public void seqLimits_itemStateChanged()
{
viewport.setShowJVSuffix(seqLimits.getState());
@@ -1898,6 +2262,12 @@ public class AlignFrame
alignPanel.paintAlignment(true);
}
+ protected void displayNonconservedMenuItem_actionPerformed()
+ {
+ viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
protected void wrapMenuItem_actionPerformed()
{
viewport.setWrapAlignment(wrapMenuItem.getState());
@@ -1920,15 +2290,20 @@ public class AlignFrame
frame.add(overview);
// +50 must allow for applet frame window
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
- overview.getPreferredSize().width,
- overview.getPreferredSize().height + 50);
+ overview.getPreferredSize().width,
+ overview.getPreferredSize().height + 50);
frame.pack();
+ final AlignmentPanel ap = alignPanel;
frame.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
- alignPanel.setOverviewPanel(null);
+ if (ap != null)
+ {
+ ap.setOverviewPanel(null);
+ }
};
});
@@ -1944,7 +2319,8 @@ public class AlignFrame
{
if (viewport.getAbovePIDThreshold())
{
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background");
cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
@@ -1958,19 +2334,18 @@ public class AlignFrame
if (viewport.getConservationSelected())
{
- Alignment al = (Alignment) viewport.alignment;
+ Alignment al = (Alignment) viewport.getAlignment();
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
+ c.verdict(false, viewport.getConsPercGaps());
cs.setConservation(c);
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
- "Background"));
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs, "Background"));
}
else
@@ -1978,102 +2353,41 @@ public class AlignFrame
cs.setConservation(null);
}
- cs.setConsensus(viewport.hconsensus);
+ cs.setConsensus(viewport.getSequenceConsensusHash());
}
viewport.setGlobalColourScheme(cs);
- if (viewport.getColourAppliesToAllGroups())
- {
- Vector groups = viewport.alignment.getGroups();
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if (cs == null)
- {
- sg.cs = null;
- continue;
- }
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(
- sg.getSequences(viewport.hiddenRepSequences),
- sg.getWidth());
- }
- else
- {
- try
- {
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- sg.cs = cs;
- }
- }
-
- if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
- }
- else
- {
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(viewport.
- hiddenRepSequences), 0,
- viewport.alignment.getWidth() - 1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
- sg.cs.setConservation(c);
- }
- else
- {
- sg.cs.setConservation(null);
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- }
- }
-
if (alignPanel.getOverviewPanel() != null)
{
alignPanel.getOverviewPanel().updateOverviewImage();
}
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()
- .sequenceColoursChanged(alignPanel);
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(viewport.applet)
+ .sequenceColoursChanged(alignPanel);
alignPanel.paintAlignment(true);
}
protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
+ if (viewport.getAbovePIDThreshold()
+ && viewport.getGlobalColourScheme() != null)
{
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
+ if (viewport.getConservationSelected()
+ && viewport.getGlobalColourScheme() != null)
{
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
- "Background");
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
@@ -2105,26 +2419,38 @@ public class AlignFrame
public void sortPairwiseMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(),
- viewport.getAlignment().getSequenceAt(0));
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0), null);
+
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
public void sortIDMenuItem_actionPerformed()
{
- // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
- // HistoryItem.SORT));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortLengthMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
public void sortGroupMenuItem_actionPerformed()
{
- // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
- // HistoryItem.SORT));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -2137,24 +2463,24 @@ public class AlignFrame
public void pairwiseAlignmentMenuItem_actionPerformed()
{
if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() > 1)
+ && viewport.getSelectionGroup().getSize() > 1)
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
+ 500);
}
}
public void PCAMenuItem_actionPerformed()
{
- //are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
@@ -2166,10 +2492,10 @@ public class AlignFrame
alignPanel.paintAlignment(true);
}
- if ( (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize() < 4 &&
- viewport.getSelectionGroup().getSize() > 0)
- || viewport.getAlignment().getHeight() < 4)
+ if ((viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() < 4 && viewport
+ .getSelectionGroup().getSize() > 0)
+ || viewport.getAlignment().getHeight() < 4)
{
return;
}
@@ -2177,8 +2503,7 @@ public class AlignFrame
try
{
new PCAPanel(viewport);
- }
- catch (java.lang.OutOfMemoryError ex)
+ } catch (java.lang.OutOfMemoryError ex)
{
}
@@ -2206,14 +2531,13 @@ public class AlignFrame
void NewTreePanel(String type, String pwType, String title)
{
- //are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
@@ -2226,14 +2550,11 @@ public class AlignFrame
}
- if ( (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize() > 1)
- || (viewport.getSelectionGroup() == null
- && viewport.alignment.getHeight() > 1))
+ if ((viewport.getSelectionGroup() != null && viewport
+ .getSelectionGroup().getSize() > 1)
+ || (viewport.getAlignment().getHeight() > 1))
{
- final TreePanel tp = new TreePanel(viewport,
- type,
- pwType);
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);
addTreeMenuItem(tp, title);
@@ -2253,31 +2574,65 @@ public class AlignFrame
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(viewport,
- treeFile,
- "From File - ",
- tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
- void addTreeMenuItem(final TreePanel treePanel, String title)
+ /**
+ * sort the alignment using the given treePanel
+ *
+ * @param treePanel
+ * tree used to sort view
+ * @param title
+ * string used for undo event name
+ */
+ public void sortByTree(TreePanel treePanel, String title)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ // HistoryItem.SORT));
+ addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Do any automatic reordering of the alignment and add the necessary bits to
+ * the menu structure for the new tree
+ *
+ * @param treePanel
+ * @param title
+ */
+ protected void addTreeMenuItem(final TreePanel treePanel,
+ final String title)
{
final MenuItem item = new MenuItem(title);
sortByTreeMenu.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
- // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- // HistoryItem.SORT));
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
- alignPanel.paintAlignment(true);
+ sortByTree(treePanel, title); // treePanel.getTitle());
}
});
treePanel.addWindowListener(new WindowAdapter()
{
+ @Override
+ public void windowOpened(WindowEvent e)
+ {
+ if (viewport.sortByTree)
+ {
+ sortByTree(treePanel, title);
+ }
+ super.windowOpened(e);
+ }
+
+ @Override
public void windowClosing(WindowEvent e)
{
sortByTreeMenu.remove(item);
@@ -2285,23 +2640,45 @@ public class AlignFrame
});
}
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ if (viewport.applet.debug)
+ {
+ System.err.println("Sorting " + alorder.getOrder().size()
+ + " in alignment '" + getTitle() + "'");
+ }
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.getAlignment()));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
protected void documentation_actionPerformed()
{
- showURL("http://www.jalview.org/help.html", "HELP");
+ alignPanel.av.applet.openJalviewHelpUrl();
}
protected void about_actionPerformed()
{
- class AboutPanel
- extends Canvas
+ class AboutPanel extends Canvas
{
String version;
- public AboutPanel(String version)
+
+ String builddate;
+
+ public AboutPanel(String version, String builddate)
{
this.version = version;
+ this.builddate = builddate;
}
+ @Override
public void paint(Graphics g)
{
g.setColor(Color.white);
@@ -2311,163 +2688,254 @@ public class AlignFrame
int fh = fm.getHeight();
int y = 5, x = 7;
g.setColor(Color.black);
+ // TODO: update this text for each release or centrally store it for
+ // lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString("Jalview - Release " + version, 200, y += fh);
+ g.drawString("JalviewLite - Release " + version, x, y += fh);
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));
+ g.drawString("Build date: " + builddate, x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
- x, y += fh * 2);
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
- x, y += fh);
g.drawString(
- "For any issues relating to Jalview, email help@jalview.org", x,
- y += fh);
- g.drawString("If you use JalView, please cite:", x, y += fh + 8);
- g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
- x, y += fh);
- g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
+ "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
+ x, y += fh * 1.5);
+ g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
+ g.drawString(
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+ x, y += fh);
+ g.drawString(
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+ x, y += fh);
+ g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
+ g.drawString(
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ x, y += fh);
+ g.drawString(
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+ x, y += fh);
+ g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
+ x, y += fh);
}
}
- String version = "test";
- java.net.URL url = getClass().getResource("/.build_properties");
- if (url != null)
+ Frame frame = new Frame();
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
+ .getBuildDate()));
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
+
+ }
+
+ public void showURL(String url, String target)
+ {
+ if (viewport.applet == null)
{
- try
- {
- BufferedReader reader = new BufferedReader(new InputStreamReader(
- url.openStream()));
- String line;
- while ( (line = reader.readLine()) != null)
- {
- if (line.indexOf("VERSION") > -1)
- {
- version = line.substring(line.indexOf("=") + 1);
- }
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ System.out.println("Not running as applet - no browser available.");
+ }
+ else
+ {
+ viewport.applet.showURL(url, target);
}
+ }
- Frame frame = new Frame();
- frame.add(new AboutPanel(version));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
+ // ////////////////////////////////////////////////////////////////////////////////
+ // JBuilder Graphics here
+
+ MenuBar alignFrameMenuBar = new MenuBar();
+
+ Menu fileMenu = new Menu("File");
+
+ MenuItem loadApplication = new MenuItem("View in Full Application");
+
+ MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+
+ MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
+
+ MenuItem outputFeatures = new MenuItem("Export Features ...");
+
+ MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+
+ MenuItem closeMenuItem = new MenuItem("Close");
+
+ Menu editMenu = new Menu("Edit");
+
+ Menu viewMenu = new Menu("View");
+
+ Menu colourMenu = new Menu("Colour");
+
+ Menu calculateMenu = new Menu("Calculate");
+
+ MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+
+ MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+
+ MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
+
+ MenuItem remove2LeftMenuItem = new MenuItem();
+
+ MenuItem remove2RightMenuItem = new MenuItem();
+
+ MenuItem removeGappedColumnMenuItem = new MenuItem();
+
+ MenuItem removeAllGapsMenuItem = new MenuItem();
+
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+
+ MenuItem sortPairwiseMenuItem = new MenuItem();
+
+ MenuItem sortIDMenuItem = new MenuItem();
+
+ MenuItem sortLengthMenuItem = new MenuItem();
+
+ MenuItem sortGroupMenuItem = new MenuItem();
+
+ MenuItem removeRedundancyMenuItem = new MenuItem();
+
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+
+ MenuItem PCAMenuItem = new MenuItem();
+
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();
- }
+ MenuItem neighbourTreeMenuItem = new MenuItem();
- public void showURL(String url, String target)
- {
- if (viewport.applet == null)
- {
- System.out.println("Not running as applet - no browser available.");
- }
- else
- {
- try
- {
- System.out.println("Show url: " + url);
- viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
- target);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-
- //////////////////////////////////////////////////////////////////////////////////
- //JBuilder Graphics here
-
- MenuBar alignFrameMenuBar = new MenuBar();
- Menu fileMenu = new Menu("File");
- MenuItem loadApplication = new MenuItem("View in Full Application");
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");
- MenuItem loadAnnotations = new MenuItem(
- "Load Features/Annotations ...");
- MenuItem outputFeatures = new MenuItem("Export Features ...");
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
-
- MenuItem closeMenuItem = new MenuItem("Close");
- Menu editMenu = new Menu("Edit");
- Menu viewMenu = new Menu("View");
- Menu colourMenu = new Menu("Colour");
- Menu calculateMenu = new Menu("Calculate");
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
- MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
- MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
- MenuItem remove2LeftMenuItem = new MenuItem();
- MenuItem remove2RightMenuItem = new MenuItem();
- MenuItem removeGappedColumnMenuItem = new MenuItem();
- MenuItem removeAllGapsMenuItem = new MenuItem();
- CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
- CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
- MenuItem sortPairwiseMenuItem = new MenuItem();
- MenuItem sortIDMenuItem = new MenuItem();
- MenuItem sortGroupMenuItem = new MenuItem();
- MenuItem removeRedundancyMenuItem = new MenuItem();
- MenuItem pairwiseAlignmentMenuItem = new MenuItem();
- MenuItem PCAMenuItem = new MenuItem();
- MenuItem averageDistanceTreeMenuItem = new MenuItem();
- MenuItem neighbourTreeMenuItem = new MenuItem();
BorderLayout borderLayout1 = new BorderLayout();
+
public Label statusBar = new Label();
- Menu outputTextboxMenu = new Menu();
- MenuItem clustalColour = new MenuItem();
- MenuItem zappoColour = new MenuItem();
- MenuItem taylorColour = new MenuItem();
- MenuItem hydrophobicityColour = new MenuItem();
- MenuItem helixColour = new MenuItem();
- MenuItem strandColour = new MenuItem();
- MenuItem turnColour = new MenuItem();
- MenuItem buriedColour = new MenuItem();
- MenuItem userDefinedColour = new MenuItem();
- MenuItem PIDColour = new MenuItem();
- MenuItem BLOSUM62Colour = new MenuItem();
+
+ Menu outputTextboxMenu = new Menu();
+
+ MenuItem clustalColour = new MenuItem();
+
+ MenuItem zappoColour = new MenuItem();
+
+ MenuItem taylorColour = new MenuItem();
+
+ MenuItem hydrophobicityColour = new MenuItem();
+
+ MenuItem helixColour = new MenuItem();
+
+ MenuItem strandColour = new MenuItem();
+
+ MenuItem turnColour = new MenuItem();
+
+ MenuItem buriedColour = new MenuItem();
+
+ MenuItem purinePyrimidineColour = new MenuItem();
+
+ MenuItem RNAHelixColour = new MenuItem();
+
+ MenuItem userDefinedColour = new MenuItem();
+
+ MenuItem PIDColour = new MenuItem();
+
+ MenuItem BLOSUM62Colour = new MenuItem();
+
+ MenuItem tcoffeeColour = new MenuItem();
+
MenuItem njTreeBlosumMenuItem = new MenuItem();
+
MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
- CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
- CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
- MenuItem alProperties = new MenuItem("Alignment Properties...");
+
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
+
+ MenuItem alProperties = new MenuItem("Alignment Properties...");
+
MenuItem overviewMenuItem = new MenuItem();
- MenuItem undoMenuItem = new MenuItem();
- MenuItem redoMenuItem = new MenuItem();
- CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+ MenuItem undoMenuItem = new MenuItem();
+
+ MenuItem redoMenuItem = new MenuItem();
+
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
MenuItem noColourmenuItem = new MenuItem();
- CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
- CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
MenuItem findMenuItem = new MenuItem();
- CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
- MenuItem nucleotideColour = new MenuItem();
+
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+
+ MenuItem nucleotideColour = new MenuItem();
+
MenuItem deleteGroups = new MenuItem();
+
+ MenuItem grpsFromSelection = new MenuItem();
+
MenuItem delete = new MenuItem();
+
MenuItem copy = new MenuItem();
+
MenuItem cut = new MenuItem();
+
Menu pasteMenu = new Menu();
+
MenuItem pasteNew = new MenuItem();
+
MenuItem pasteThis = new MenuItem();
- CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
- MenuItem font = new MenuItem();
- CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
- CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
- CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+
+ MenuItem font = new MenuItem();
+
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+
MenuItem modifyPID = new MenuItem();
+
MenuItem modifyConservation = new MenuItem();
- CheckboxMenuItem autoCalculate
- = new CheckboxMenuItem("Autocalculate Consensus", true);
- Menu sortByTreeMenu = new Menu();
+
+ CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
+ "Autocalculate Consensus", true);
+
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+ "Sort Alignment With New Tree", true);
+
+ Menu sortByTreeMenu = new Menu();
+
Menu sort = new Menu();
+
Menu calculate = new Menu();
+
MenuItem inputText = new MenuItem();
+
Menu helpMenu = new Menu();
+
MenuItem documentation = new MenuItem();
+
MenuItem about = new MenuItem();
- CheckboxMenuItem seqLimits = new CheckboxMenuItem();
- private void jbInit()
- throws Exception
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
+
+ CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
+
+ Menu autoAnnMenu = new Menu();
+
+ CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
+
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
+
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
+
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
+
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
+
+ CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
+
+ private void jbInit() throws Exception
{
setMenuBar(alignFrameMenuBar);
@@ -2475,14 +2943,15 @@ public class AlignFrame
MenuItem item;
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
- i++)
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+ item = new MenuItem(
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
@@ -2519,6 +2988,8 @@ public class AlignFrame
sortPairwiseMenuItem.addActionListener(this);
sortIDMenuItem.setLabel("by ID");
sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel("by Length");
+ sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel("by Group");
sortGroupMenuItem.addActionListener(this);
removeRedundancyMenuItem.setLabel("Remove Redundancy...");
@@ -2527,8 +2998,8 @@ public class AlignFrame
pairwiseAlignmentMenuItem.addActionListener(this);
PCAMenuItem.setLabel("Principal Component Analysis");
PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem.setLabel(
- "Average Distance Using % Identity");
+ averageDistanceTreeMenuItem
+ .setLabel("Average Distance Using % Identity");
averageDistanceTreeMenuItem.addActionListener(this);
neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
neighbourTreeMenuItem.addActionListener(this);
@@ -2553,14 +3024,22 @@ public class AlignFrame
turnColour.addActionListener(this);
buriedColour.setLabel("Buried Index");
buriedColour.addActionListener(this);
+ purinePyrimidineColour.setLabel("Purine/Pyrimidine");
+ purinePyrimidineColour.addActionListener(this);
+ RNAHelixColour.setLabel("by RNA Helices");
+ RNAHelixColour.addActionListener(this);
userDefinedColour.setLabel("User Defined...");
userDefinedColour.addActionListener(this);
PIDColour.setLabel("Percentage Identity");
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel("BLOSUM62 Score");
BLOSUM62Colour.addActionListener(this);
- avDistanceTreeBlosumMenuItem.setLabel(
- "Average Distance Using BLOSUM62");
+ tcoffeeColour.setLabel("T-Coffee Scores");
+ tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
+ // provided
+ tcoffeeColour.addActionListener(this);
+ avDistanceTreeBlosumMenuItem
+ .setLabel("Average Distance Using BLOSUM62");
avDistanceTreeBlosumMenuItem.addActionListener(this);
njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
njTreeBlosumMenuItem.addActionListener(this);
@@ -2568,6 +3047,8 @@ public class AlignFrame
annotationPanelMenuItem.addItemListener(this);
colourTextMenuItem.setLabel("Colour Text");
colourTextMenuItem.addItemListener(this);
+ displayNonconservedMenuItem.setLabel("Show nonconserved");
+ displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
overviewMenuItem.setLabel("Overview Window");
overviewMenuItem.addActionListener(this);
@@ -2594,6 +3075,8 @@ public class AlignFrame
nucleotideColour.addActionListener(this);
deleteGroups.setLabel("Undefine Groups");
deleteGroups.addActionListener(this);
+ grpsFromSelection.setLabel("Make Groups for selection");
+ grpsFromSelection.addActionListener(this);
copy.setLabel("Copy");
copy.addActionListener(this);
cut.setLabel("Cut");
@@ -2630,9 +3113,13 @@ public class AlignFrame
sort.setLabel("Sort");
calculate.setLabel("Calculate Tree");
autoCalculate.addItemListener(this);
+ sortByTree.addItemListener(this);
inputText.setLabel("Input from textbox");
inputText.addActionListener(this);
-
+ centreColumnLabelFlag.setLabel("Centre column labels");
+ centreColumnLabelFlag.addItemListener(this);
+ followMouseOverFlag.setLabel("Automatic Scrolling");
+ followMouseOverFlag.addItemListener(this);
helpMenu.setLabel("Help");
documentation.setLabel("Documentation");
documentation.addActionListener(this);
@@ -2657,11 +3144,33 @@ public class AlignFrame
menu2.setLabel("Hide");
hideColumns.setLabel("Selected Columns");
hideSequences.setLabel("Selected Sequences");
+ hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
+ hideAllSelection.setLabel("Selected Region");
+ showAllHidden.setLabel("All Sequences and Columns");
+ showGroupConsensus.setLabel("Group Consensus");
+ showGroupConservation.setLabel("Group Conservation");
+ showConsensusHistogram.setLabel("Show Consensus Histogram");
+ showSequenceLogo.setLabel("Show Consensus Logo");
+ normSequenceLogo.setLabel("Normalise Consensus Logo");
+ applyAutoAnnotationSettings.setLabel("Apply to all groups");
+ applyAutoAnnotationSettings.setState(true);
+ autoAnnMenu.setLabel("Autocalculated Annotation");
+
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
showSeqs.addActionListener(this);
hideColumns.addActionListener(this);
hideSequences.addActionListener(this);
+ hideAllButSelection.addActionListener(this);
+ hideAllSelection.addActionListener(this);
+ showAllHidden.addActionListener(this);
+ showGroupConsensus.addItemListener(this);
+ showGroupConservation.addItemListener(this);
+ showConsensusHistogram.addItemListener(this);
+ showSequenceLogo.addItemListener(this);
+ normSequenceLogo.addItemListener(this);
+
+ applyAutoAnnotationSettings.addItemListener(this);
formatMenu.setLabel("Format");
selectMenu.setLabel("Select");
newView.setLabel("New View");
@@ -2709,7 +3218,16 @@ public class AlignFrame
viewMenu.add(menu1);
viewMenu.add(menu2);
viewMenu.addSeparator();
+ viewMenu.add(followMouseOverFlag);
viewMenu.add(annotationPanelMenuItem);
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ viewMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
viewMenu.add(featureSettings);
@@ -2731,6 +3249,8 @@ public class AlignFrame
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
@@ -2738,16 +3258,19 @@ public class AlignFrame
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
+ colourMenu.add(RNAHelixColour);
calculateMenu.add(sort);
calculateMenu.add(calculate);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.add(autoCalculate);
+ calculateMenu.add(sortByTree);
this.add(statusBar, BorderLayout.SOUTH);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
sort.add(sortByTreeMenu);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
@@ -2759,8 +3282,11 @@ public class AlignFrame
helpMenu.add(about);
menu1.add(showColumns);
menu1.add(showSeqs);
+ menu1.add(showAllHidden);
menu2.add(hideColumns);
menu2.add(hideSequences);
+ menu2.add(hideAllSelection);
+ menu2.add(hideAllButSelection);
formatMenu.add(font);
formatMenu.add(seqLimits);
formatMenu.add(wrapMenuItem);
@@ -2770,72 +3296,459 @@ public class AlignFrame
formatMenu.add(viewBoxesMenuItem);
formatMenu.add(viewTextMenuItem);
formatMenu.add(colourTextMenuItem);
+ formatMenu.add(displayNonconservedMenuItem);
formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelFlag);
selectMenu.add(findMenuItem);
selectMenu.addSeparator();
selectMenu.add(selectAllSequenceMenuItem);
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
+ selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+
}
+
MenuItem featureSettings = new MenuItem();
+
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
+
MenuItem annotationColour = new MenuItem();
+
MenuItem invertColSel = new MenuItem();
+
Menu menu1 = new Menu();
+
MenuItem showColumns = new MenuItem();
+
MenuItem showSeqs = new MenuItem();
+
Menu menu2 = new Menu();
+
MenuItem hideColumns = new MenuItem();
+
MenuItem hideSequences = new MenuItem();
+
+ MenuItem hideAllButSelection = new MenuItem();
+
+ MenuItem hideAllSelection = new MenuItem();
+
+ MenuItem showAllHidden = new MenuItem();
+
Menu formatMenu = new Menu();
+
Menu selectMenu = new Menu();
+
MenuItem newView = new MenuItem();
/**
- * Attach the alignFrame panels after embedding menus, if necessary.
- * This used to be called setEmbedded, but is now creates the
- * dropdown menus in a platform independent manner
- * to avoid OSX/Mac menu appendage daftness.
- *
- * @param reallyEmbedded true to attach the view to the applet area on the page rather than in a new window
+ * Attach the alignFrame panels after embedding menus, if necessary. This used
+ * to be called setEmbedded, but is now creates the dropdown menus in a
+ * platform independent manner to avoid OSX/Mac menu appendage daftness.
+ *
+ * @param reallyEmbedded
+ * true to attach the view to the applet area on the page rather than
+ * in a new window
*/
public void createAlignFrameWindow(boolean reallyEmbedded, String title)
{
if (reallyEmbedded)
{
- //////
+ // ////
// Explicly build the embedded menu panel for the on-page applet
//
// view cannot be closed if its actually on the page
fileMenu.remove(closeMenuItem);
fileMenu.remove(3); // Remove Seperator
- embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", Font.PLAIN, 10, false); // use our own fonts.
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
+ Font.PLAIN, 10, false); // use our own fonts.
// and actually add the components to the applet area
viewport.applet.setLayout(new BorderLayout());
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
viewport.applet.add(statusBar, BorderLayout.SOUTH);
alignPanel.setSize(viewport.applet.getSize().width,
- viewport.applet.getSize().height
- - embeddedMenu.HEIGHT - statusBar.HEIGHT);
+ viewport.applet.getSize().height - embeddedMenu.HEIGHT
+ - statusBar.HEIGHT);
viewport.applet.add(alignPanel, BorderLayout.CENTER);
+ final AlignFrame me = this;
+ viewport.applet.addFocusListener(new FocusListener()
+ {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ if (me.viewport.applet.currentAlignFrame == me)
+ {
+ me.viewport.applet.currentAlignFrame = null;
+ }
+ }
+
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ me.viewport.applet.currentAlignFrame = me;
+ }
+ });
viewport.applet.validate();
- } else {
- ////////
+ }
+ else
+ {
+ // //////
// test and embed menu bar if necessary.
//
- if (embedMenuIfNeeded(alignPanel)) {
+ if (embedMenuIfNeeded(alignPanel))
+ {
// adjust for status bar height too
- alignPanel.setSize(getSize().width,
- getSize().height
+ alignPanel.setSize(getSize().width, getSize().height
- statusBar.HEIGHT);
}
add(statusBar, BorderLayout.SOUTH);
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ DEFAULT_HEIGHT);
+ }
+ }
+
+ /**
+ * create a new binding between structures in an existing jmol viewer instance
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,
+ * this does not open a new Jmol window, or modify the display of the
+ * structures in the original jmol window. Note This method doesn't work
+ * without an additional javascript library to exchange messages between the
+ * distinct applets. See http://issues.jalview.org/browse/JAL-621
+ *
+ * @param viewer
+ * JmolViewer instance
+ * @param sequenceIds
+ * - sequence Ids to search for associations
+ */
+ public SequenceStructureBinding addStructureViewInstance(
+ Object jmolviewer, String[] sequenceIds)
+ {
+ org.jmol.api.JmolViewer viewer = null;
+ try
+ {
+ viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ } catch (ClassCastException ex)
+ {
+ System.err.println("Unsupported viewer object :"
+ + jmolviewer.getClass());
+ }
+ if (viewer == null)
+ {
+ System.err.println("Can't use this object as a structure viewer:"
+ + jmolviewer.getClass());
+ return null;
+ }
+ SequenceI[] seqs = null;
+ if (sequenceIds == null || sequenceIds.length == 0)
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ Vector sqi = new Vector();
+ AlignmentI al = viewport.getAlignment();
+ for (int sid = 0; sid < sequenceIds.length; sid++)
+ {
+ SequenceI sq = al.findName(sequenceIds[sid]);
+ if (sq != null)
+ {
+ sqi.addElement(sq);
+ }
+ }
+ if (sqi.size() > 0)
+ {
+ seqs = new SequenceI[sqi.size()];
+ for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
+ {
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);
+ }
+ }
+ else
+ {
+ return null;
+ }
+ }
+ ExtJmol jmv = null;
+ // TODO: search for a jmv that involves viewer
+ if (jmv == null)
+ { // create a new viewer/jalview binding.
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
+ { seqs });
+ }
+ return jmv;
+
+ }
+
+ /**
+ * bind a pdb file to a sequence in the current view
+ *
+ * @param sequenceId
+ * - sequenceId within the dataset.
+ * @param pdbEntryString
+ * - the short name for the PDB file
+ * @param pdbFile
+ * - pdb file - either a URL or a valid PDB file.
+ * @return true if binding was as success TODO: consider making an exception
+ * structure for indicating when PDB parsing or sequenceId location
+ * fails.
+ */
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,
+ String pdbFile)
+ {
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
+ {
+ Vector pdbe = toaddpdb.getPDBId();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ // make a note of the access mode and add
+ if (pdbentry.getProperty() == null)
+ {
+ pdbentry.setProperty(new Hashtable());
+ }
+ pdbentry.getProperty().put("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ }
+ }
+ return true;
+ }
+
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
+ {
+ if (seqs != null)
+ {
+ Vector sequences = new Vector();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ sequences.addElement(new Object[]
+ { seqs[i], (chains != null) ? chains[i] : null });
+ }
+ }
+ seqs = new SequenceI[sequences.size()];
+ chains = new String[sequences.size()];
+ for (int i = 0, isize = sequences.size(); i < isize; i++)
+ {
+ Object[] oj = (Object[]) sequences.elementAt(i);
+
+ seqs[i] = (SequenceI) oj[0];
+ chains[i] = (String) oj[1];
+ }
+ }
+ return new Object[]
+ { seqs, chains };
+
+ }
+
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,
+ SequenceI[] seqs, String[] chains, String protocol)
+ {
+ // Scrub any null sequences from the array
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);
+ seqs = (SequenceI[]) sqch[0];
+ chains = (String[]) sqch[1];
+ if (seqs == null || seqs.length == 0)
+ {
+ System.err
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+ }
+ if (protocol == null || protocol.trim().length() == 0
+ || protocol.equals("null"))
+ {
+ protocol = (String) pdb.getProperty().get("protocol");
+ if (protocol == null)
+ {
+ System.err.println("Couldn't work out protocol to open structure: "
+ + pdb.getId());
+ return;
+ }
+ }
+ if (applet.useXtrnalSviewer)
+ {
+ // register the association(s) and quit, don't create any windows.
+ if (StructureSelectionManager.getStructureSelectionManager(applet)
+ .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ {
+ System.err.println("Failed to map " + pdb.getFile() + " ("
+ + protocol + ") to any sequences");
+ }
+ return;
+ }
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)
+ {
+ // can only do alignments with Jmol
+ // find the last jmol window assigned to this alignment
+ jalview.appletgui.AppletJmol ajm = null, tajm;
+ Vector jmols = applet
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)
+ {
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ if (tajm.ap.alignFrame == this)
+ {
+ ajm = tajm;
+ break;
+ }
+ }
+ if (ajm != null)
+ {
+ System.err
+ .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ // try and add the pdb structure
+ // ajm.addS
+ ajm = null;
+ }
+ }
+ // otherwise, create a new window
+ if (applet.jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ protocol);
+ applet.lastFrameX += 40;
+ applet.lastFrameY += 40;
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ }
+
+ }
+
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
+ SequenceI[][] seqs, String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
+ System.err.println("Aligned Structure View: Not yet implemented.");
+ }
+
+ /**
+ * modify the current selection, providing the user has not made a selection
+ * already.
+ *
+ * @param sel
+ * - sequences from this alignment
+ * @param csel
+ * - columns to be selected on the alignment
+ */
+ public void select(SequenceGroup sel, ColumnSelection csel)
+ {
+ alignPanel.seqPanel.selection(sel, csel, null);
+ }
+
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.seqPanel.scrollTo(row, column);
+ }
+
+ public void scrollToRow(int row)
+ {
+ alignPanel.seqPanel.scrollToRow(row);
+ }
+
+ public void scrollToColumn(int column)
+ {
+ alignPanel.seqPanel.scrollToColumn(column);
+ }
+
+ /**
+ * @return the alignments unique ID.
+ */
+ public String getSequenceSetId()
+ {
+ return viewport.getSequenceSetId();
+ }
+
+ /**
+ * Load the (T-Coffee) score file from the specified url
+ *
+ * @param source
+ * File/URL/T-COFFEE score file contents
+ * @throws IOException
+ * @return true if alignment was annotated with data from source
+ */
+ public boolean loadScoreFile(String source) throws IOException
+ {
+
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source,
+ AppletFormatAdapter.checkProtocol(source));
+ if (!file.isValid())
+ {
+ // TODO: raise dialog for gui
+ System.err.println("Problems parsing T-Coffee scores: "
+ + file.getWarningMessage());
+ System.err.println("Origin was:\n" + source);
+ return false;
+ }
+
+ /*
+ * check that the score matrix matches the alignment dimensions
+ */
+ AlignmentI aln;
+ if ((aln = viewport.getAlignment()) != null
+ && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
+ .getWidth()))
+ {
+ // TODO: raise a dialog box here rather than bomb out.
+ System.err
+ .println("The scores matrix does not match the alignment dimensions");
+
+ }
+
+ // TODO add parameter to indicate if matching should be done
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))
+ {
+ alignPanel.fontChanged();
+ tcoffeeColour.setEnabled(true);
+ // switch to this color
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ return true;
+ }
+ else
+ {
+ System.err.println("Problems resolving T-Coffee scores:");
+ if (file.getWarningMessage() != null)
+ {
+ System.err.println(file.getWarningMessage());
+ }
}
+ return false;
}
+
}