/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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 Softwarechang
+ * along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
package jalview.gui;
import java.awt.*;
import java.awt.datatransfer.*;
+import java.awt.dnd.*;
import java.awt.event.*;
import java.awt.print.*;
import javax.swing.*;
+import javax.swing.event.MenuEvent;
import jalview.analysis.*;
+import jalview.commands.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
-import jalview.commands.*;
import jalview.ws.*;
-import java.awt.dnd.*;
-import javax.swing.event.ChangeListener;
-import javax.swing.event.ChangeEvent;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class AlignFrame extends GAlignFrame implements DropTargetListener
+public class AlignFrame extends GAlignFrame implements DropTargetListener,
+ IProgressIndicator
{
+
/** DOCUMENT ME!! */
public static final int DEFAULT_WIDTH = 700;
/** DOCUMENT ME!! */
public static final int DEFAULT_HEIGHT = 500;
+
public AlignmentPanel alignPanel;
AlignViewport viewport;
Vector alignPanels = new Vector();
-
- /** DOCUMENT ME!! */
+ /**
+ * Last format used to load or save alignments in this window
+ */
String currentFileFormat = null;
+ /**
+ * Current filename for this alignment
+ */
String fileName = null;
-
/**
- * Creates a new AlignFrame object.
- *
- * @param al DOCUMENT ME!
+ * Creates a new AlignFrame object with specific width and height.
+ *
+ * @param al
+ * @param width
+ * @param height
*/
public AlignFrame(AlignmentI al, int width, int height)
{
this(al, null, width, height);
}
+ /**
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
+ * @param al
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ */
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId)
+ {
+ this(al, null, width, height, sequenceSetId);
+ }
+
+ /**
+ * Creates a new AlignFrame object with specific width, height and
+ * sequenceSetId
+ *
+ * @param al
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * @param viewId
+ */
+ public AlignFrame(AlignmentI al, int width, int height,
+ String sequenceSetId, String viewId)
+ {
+ this(al, null, width, height, sequenceSetId, viewId);
+ }
/**
* new alignment window with hidden columns
- * @param al AlignmentI
- * @param hiddenColumns ColumnSelection or null
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection or null
+ * @param width
+ * Width of alignment frame
+ * @param height
+ * height of frame.
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height)
+ {
+ this(al, hiddenColumns, width, height, null);
+ }
+
+ /**
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * (may be null)
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ int width, int height, String sequenceSetId)
+ {
+ this(al, hiddenColumns, width, height, sequenceSetId, null);
+ }
+
+ /**
+ * Create alignment frame for al with hiddenColumns, a specific width and
+ * height, and specific sequenceId
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param width
+ * @param height
+ * @param sequenceSetId
+ * (may be null)
+ * @param viewId
+ * (may be null)
*/
public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
- int width, int height)
+ int width, int height, String sequenceSetId, String viewId)
{
- this.setSize(width, height);
- viewport = new AlignViewport(al, hiddenColumns);
+ setSize(width, height);
+ viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
alignPanel = new AlignmentPanel(this, viewport);
- if(al.getDataset()==null)
+ if (al.getDataset() == null)
{
al.setDataset(null);
}
/**
* Make a new AlignFrame from exisiting alignmentPanels
- * @param ap AlignmentPanel
- * @param av AlignViewport
+ *
+ * @param ap
+ * AlignmentPanel
+ * @param av
+ * AlignViewport
*/
public AlignFrame(AlignmentPanel ap)
{
init();
}
+ /**
+ * initalise the alignframe from the underlying viewport data and the
+ * configurations
+ */
void init()
{
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
-
if (viewport.conservation == null)
{
BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
- // PIDColour.setEnabled(false);
- // abovePIDThreshold.setEnabled(false);
- // modifyPID.setEnabled(false);
+ // PIDColour.setEnabled(false);
+ // abovePIDThreshold.setEnabled(false);
+ // modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ "No sort");
if (sortby.equals("Id"))
+ {
sortIDMenuItem_actionPerformed(null);
+ }
else if (sortby.equals("Pairwise Identity"))
+ {
sortPairwiseMenuItem_actionPerformed(null);
+ }
if (Desktop.desktop != null)
- {
- addServiceListeners();
- setGUINucleotide(viewport.alignment.isNucleotide());
- }
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide(viewport.alignment.isNucleotide());
+ }
- setMenusFromViewport(viewport);
+ setMenusFromViewport(viewport);
+ buildSortByAnnotationScoresMenu();
+ if (viewport.wrapAlignment)
+ {
+ wrapMenuItem_actionPerformed(null);
+ }
- if (viewport.wrapAlignment)
- {
- wrapMenuItem_actionPerformed(null);
- }
+ if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ {
+ this.overviewMenuItem_actionPerformed(null);
+ }
- addKeyListener();
+ addKeyListener();
}
+ /**
+ * Change the filename and format for the alignment, and enable the 'reload'
+ * button functionality.
+ *
+ * @param file
+ * valid filename
+ * @param format
+ * format of file
+ */
public void setFileName(String file, String format)
{
- fileName = file;
- currentFileFormat = format;
- reload.setEnabled(true);
+ fileName = file;
+ currentFileFormat = format;
+ reload.setEnabled(true);
}
void addKeyListener()
{
- addKeyListener(new KeyAdapter()
+ addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
{
- 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());
+
+ switch (evt.getKeyCode())
{
- if (viewport.cursorMode
- && evt.getKeyCode() >= KeyEvent.VK_0
- && evt.getKeyCode() <= KeyEvent.VK_9)
- {
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
- }
- switch (evt.getKeyCode())
- {
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed(null);
+ break;
- break;
+ case KeyEvent.VK_DOWN:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(false);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, 1);
+ break;
- case KeyEvent.VK_DOWN:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, 1);
- }
- else
- moveSelectedSequences(false);
- break;
+ case KeyEvent.VK_UP:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(true);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, -1);
- case KeyEvent.VK_UP:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, -1);
- }
- else
- moveSelectedSequences(true);
- break;
+ break;
- case KeyEvent.VK_LEFT:
- if (viewport.cursorMode)
- {
- 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);
- case KeyEvent.VK_RIGHT:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(1, 0);
- }
- break;
+ 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)
- {
- cut_actionPerformed(null);
- }
- else
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown());
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ break;
- break;
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (!viewport.cursorMode)
+ {
+ cut_actionPerformed(null);
+ }
+ else
+ {
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
- case KeyEvent.VK_S:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRow();
- }
- break;
- case KeyEvent.VK_C:
- if (viewport.cursorMode && !evt.isControlDown())
- {
- alignPanel.seqPanel.setCursorColumn();
- }
- break;
- case KeyEvent.VK_P:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorPosition();
- }
- break;
+ 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_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ 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;
- }
- alignPanel.seqPanel.seqCanvas.repaint();
- 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_F1:
- try
- {
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+ 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;
+ }
+ alignPanel.seqPanel.seqCanvas.repaint();
+ break;
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- break
- ;
- case KeyEvent.VK_H:
- {
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
+ case KeyEvent.VK_F1:
+ try
+ {
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
+ "help/help");
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+ javax.help.HelpBroker hb = hs.createHelpBroker();
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ break;
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
- boolean hide = false;
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ // TODO: document ctrl-shift-h for show visible selected area and fix hack so columns for the current selected region get transferred.
+ 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.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.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) {
+ invertSequenceMenuItem_actionPerformed(null);
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
- SequenceGroup sg = viewport.getSelectionGroup();
- if (toggleSeqs)
+ if (sg!=null && sg.getStartRes()>=0 && sg.getStartRes()<=sg.getEndRes()&& (viewport.colSel==null || viewport.colSel.getSelected()==null || viewport.colSel.getSelected().size()==0))
+ {
+ // synthesize a column selection if none exists. this happens if a single region has been selected rather than whole columns.
+ if (viewport.colSel==null)
{
- if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
- {
- hideSelSequences_actionPerformed(null);
- hide = true;
- }
- else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
- showAllSeqs_actionPerformed(null);
+ viewport.colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) {
+ viewport.colSel.addElement(cspos);
}
+ }
+ // finally invert the column selection and get the new sequence selection.
+ invertColSel_actionPerformed(null);
+ toggleCols = true;
+ }
+ }
+
+ if (toggleSeqs)
+ {
+ if (sg != null
+ && sg.getSize() != viewport.alignment.getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ {
+ showAllSeqs_actionPerformed(null);
+ }
+ }
- if (toggleCols)
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
{
- if (viewport.colSel.getSelected().size() > 0)
- {
- hideSelColumns_actionPerformed(null);
- if (!toggleSeqs)
- viewport.selectionGroup = sg;
- }
- else if (!hide)
- showAllColumns_actionPerformed(null);
+ viewport.selectionGroup = sg;
}
- 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;
+ else if (!hide)
+ {
+ showAllColumns_actionPerformed(null);
+ }
}
+ 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;
+ }
+ }
+ public void keyReleased(KeyEvent evt)
+ {
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ break;
+
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ break;
+ }
+ }
+ });
+ }
- public void addAlignmentPanel(final AlignmentPanel ap,
- boolean newPanel)
+ public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
{
ap.alignFrame = this;
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
- if (aSize == 1 && ap.av.viewName==null)
+ if (aSize == 1 && ap.av.viewName == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
ap.setVisible(false);
}
- if(newPanel)
+ if (newPanel)
{
if (ap.av.padGaps)
+ {
ap.av.alignment.padGaps();
+ }
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
}
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
- tabbedPane.addTab(first.av.viewName,first);
+ tabbedPane.addTab(first.av.viewName, first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
-
public AlignViewport getViewport()
{
return viewport;
final java.beans.PropertyChangeListener thisListener;
// Do this once to get current state
BuildWebServiceMenu();
- Desktop.discoverer.addPropertyChangeListener(
- thisListener = new java.beans.PropertyChangeListener()
- {
- public void propertyChange(PropertyChangeEvent evt)
- {
- // System.out.println("Discoverer property change.");
- if (evt.getPropertyName().equals("services"))
- {
- // System.out.println("Rebuilding web service menu");
- BuildWebServiceMenu();
- }
- }
- });
+ Desktop.discoverer
+ .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // System.out.println("Discoverer property change.");
+ if (evt.getPropertyName().equals("services"))
+ {
+ // System.out.println("Rebuilding web service menu");
+ BuildWebServiceMenu();
+ }
+ }
+ });
- addInternalFrameListener(new javax.swing.event.
- InternalFrameAdapter()
+ addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ javax.swing.event.InternalFrameEvent evt)
{
// System.out.println("deregistering discoverer listener");
Desktop.discoverer.removePropertyChangeListener(thisListener);
closeMenuItem_actionPerformed(true);
- }
- ;
+ };
});
}
public void setGUINucleotide(boolean nucleotide)
{
- showTranslation.setVisible( nucleotide );
- conservationMenuItem.setEnabled( !nucleotide );
- modifyConservation.setEnabled( !nucleotide );
+ showTranslation.setVisible(nucleotide);
+ conservationMenuItem.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide);
- //Remember AlignFrame always starts as protein
- if(!nucleotide)
+ // Remember AlignFrame always starts as protein
+ if (!nucleotide)
{
- calculateMenu.remove(calculateMenu.getItemCount()-2);
+ calculateMenu.remove(calculateMenu.getItemCount() - 2);
}
}
/**
- * Need to call this method when tabs are selected for multiple views,
- * or when loading from Jalview2XML.java
- * @param av AlignViewport
+ * set up menus for the currently viewport. This may be called after any
+ * operation that affects the data in the current view (selection changed,
+ * etc) to update the menus to reflect the new state.
+ */
+ public void setMenusForViewport()
+ {
+ setMenusFromViewport(viewport);
+ }
+
+ /**
+ * Need to call this method when tabs are selected for multiple views, or when
+ * loading from Jalview2XML.java
+ *
+ * @param av
+ * AlignViewport
*/
void setMenusFromViewport(AlignViewport av)
{
conservationMenuItem.setSelected(av.getConservationSelected());
seqLimits.setSelected(av.getShowJVSuffix());
idRightAlign.setSelected(av.rightAlignIds);
+ centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
renderGapsMenuItem.setSelected(av.renderGaps);
wrapMenuItem.setSelected(av.wrapAlignment);
+ scaleAbove.setVisible(av.wrapAlignment);
+ scaleLeft.setVisible(av.wrapAlignment);
+ scaleRight.setVisible(av.wrapAlignment);
annotationPanelMenuItem.setState(av.showAnnotation);
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
-
- setColourSelected(ColourSchemeProperty.
- getColourName(av.getGlobalColourScheme()));
+ showUnconservedMenuItem.setSelected(av.showUnconserved);
+ showGroupConsensus.setSelected(av.showGroupConsensus);
+ showGroupConservation.setSelected(av.showGroupConservation);
+ setColourSelected(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
showSeqFeatures.setSelected(av.showSequenceFeatures);
hiddenMarkers.setState(av.showHiddenMarkers);
applyToAllGroups.setState(av.colourAppliesToAllGroups);
+ showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
+ showDbRefsMenuitem.setSelected(av.isShowDbRefs());
+
+ setShowProductsEnabled();
updateEditMenuBar();
}
+ Hashtable progressBars, progressBarHandlers;
- Hashtable progressBars;
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
public void setProgressBar(String message, long id)
{
- if(progressBars == null)
+ if (progressBars == null)
+ {
progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
+ }
JPanel progressPanel;
GridLayout layout = (GridLayout) statusPanel.getLayout();
- if(progressBars.get( new Long(id) )!=null)
- {
- progressPanel = (JPanel)progressBars.get( new Long(id) );
- statusPanel.remove(progressPanel);
- progressBars.remove( progressPanel );
- progressPanel = null;
- if(message!=null)
- statusBar.setText(message);
-
- layout.setRows(layout.getRows() - 1);
- }
+ if (progressBars.get(new Long(id)) != null)
+ {
+ progressPanel = (JPanel) progressBars.get(new Long(id));
+ statusPanel.remove(progressPanel);
+ progressBars.remove(progressPanel);
+ progressPanel = null;
+ if (message != null)
+ {
+ statusBar.setText(message);
+ }
+ if (progressBarHandlers.contains(new Long(id)))
+ {
+ progressBarHandlers.remove(new Long(id));
+ }
+ layout.setRows(layout.getRows() - 1);
+ }
else
{
progressPanel = new JPanel(new BorderLayout(10, 5));
progressBars.put(new Long(id), progressPanel);
}
-
+ // update GUI
+ setMenusForViewport();
validate();
}
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton("Cancel");
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar("Cancelled "
+ + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+ /**
+ *
+ * @return true if any progress bars are still active
+ */
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
+ return true;
+ }
+ return false;
+ }
/*
- Added so Castor Mapping file can obtain Jalview Version
- */
+ * Added so Castor Mapping file can obtain Jalview Version
+ */
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return jalview.bin.Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
}
-
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
public void reload_actionPerformed(ActionEvent e)
{
- if(fileName!=null)
+ if (fileName != null)
{
- if(currentFileFormat.equals("Jalview"))
+ if (currentFileFormat.equals("Jalview"))
{
- JInternalFrame [] frames = Desktop.desktop.getAllFrames();
- for(int i=0; i<frames.length; i++)
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int i = 0; i < frames.length; i++)
{
- if (frames[i] instanceof AlignFrame
- && frames[i] != this
- && ( (AlignFrame) frames[i]).fileName.equals(fileName))
+ if (frames[i] instanceof AlignFrame && frames[i] != this
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
- try{
+ try
+ {
frames[i].setSelected(true);
Desktop.instance.closeAssociatedWindows();
- }catch(java.beans.PropertyVetoException ex){}
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
}
}
Desktop.instance.closeAssociatedWindows();
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";
+ loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
else
{
- viewport.alignment.deleteAllGroups();
- viewport.sequenceColours=null;
- while (viewport.alignment.getHeight() > 0)
- {
- viewport.alignment.deleteSequence(0);
- }
+ Rectangle bounds = this.getBounds();
- viewport.historyList.clear();
- viewport.redoList.clear();
- Alignment dset = viewport.alignment.getDataset();
- while (dset.getHeight() > 0)
- {
- dset.deleteSequence(0);
- }
+ FileLoader loader = new FileLoader();
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";
+ AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
+ protocol, currentFileFormat);
- firePropertyChange("Alignment", null, viewport.alignment.getSequences());
+ newframe.setBounds(bounds);
- updateEditMenuBar();
+ this.closeMenuItem_actionPerformed(true);
}
-
- FileLoader loader = new FileLoader();
- String protocol = fileName.startsWith("http:")? "URL":"File";
- loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
-
}
}
-
public void addFromText_actionPerformed(ActionEvent e)
{
Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
-
public void save_actionPerformed(ActionEvent e)
{
- if(fileName==null
- || currentFileFormat==null
- || fileName.startsWith("http")
- )
+ if (fileName == null
+ || (currentFileFormat == null || !jalview.io.FormatAdapter
+ .isValidIOFormat(currentFileFormat, true))
+ || fileName.startsWith("http"))
+ {
saveAs_actionPerformed(null);
+ }
else
+ {
saveAlignment(fileName, currentFileFormat);
+ }
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void saveAs_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty( "LAST_DIRECTORY"),
- new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
- new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
- currentFileFormat,
- false);
-
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"),
+ jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
+ jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
+ currentFileFormat, false);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Alignment to file");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- currentFileFormat = chooser.getSelectedFormat();
- if (currentFileFormat == null)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "You must select a file format before saving!",
- "File format not specified",
- JOptionPane.WARNING_MESSAGE);
- value = chooser.showSaveDialog(this);
- return;
- }
+ currentFileFormat = chooser.getSelectedFormat();
+ if (currentFileFormat == null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "You must select a file format before saving!",
+ "File format not specified", JOptionPane.WARNING_MESSAGE);
+ value = chooser.showSaveDialog(this);
+ return;
+ }
- fileName = chooser.getSelectedFile().getPath();
+ fileName = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
- currentFileFormat);
+ currentFileFormat);
jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
-
+ if (currentFileFormat.indexOf(" ") > -1)
+ {
+ currentFileFormat = currentFileFormat.substring(0,
+ currentFileFormat.indexOf(" "));
+ }
saveAlignment(fileName, currentFileFormat);
}
}
if (shortName.indexOf(java.io.File.separatorChar) > -1)
{
- shortName = shortName.substring(shortName.lastIndexOf(
- java.io.File.separatorChar) + 1);
+ shortName = shortName.substring(shortName
+ .lastIndexOf(java.io.File.separatorChar) + 1);
}
success = new Jalview2XML().SaveAlignment(this, file, shortName);
- statusBar.setText("Successfully saved to file: "
- +fileName+" in "
- +format +" format.");
+ statusBar.setText("Successfully saved to file: " + fileName + " in "
+ + format + " format.");
}
else
{
+ if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
+ {
+ warningMessage("Cannot save file " + fileName + " using format "
+ + format, "Alignment output format not supported");
+ saveAs_actionPerformed(null);
+ // JBPNote need to have a raise_gui flag here
+ return false;
+ }
String[] omitHidden = null;
if (viewport.hasHiddenColumns)
{
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "The Alignment contains hidden columns."
- + "\nDo you want to save only the visible alignment?",
- "Save / Omit Hidden Columns",
- JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+ int reply = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ "The Alignment contains hidden columns."
+ + "\nDo you want to save only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
if (reply == JOptionPane.YES_OPTION)
+ {
omitHidden = viewport.getViewAsString(false);
+ }
}
-
- String output = new FormatAdapter().formatSequences(
- format,
- viewport.alignment.getSequencesArray(),
- omitHidden);
+ FormatAdapter f = new FormatAdapter();
+ String output = f.formatSequences(format,
+ (Alignment) viewport.alignment, // class cast exceptions will
+ // occur in the distant future
+ omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
if (output == null)
{
try
{
java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
+ new java.io.FileWriter(file));
out.print(output);
out.close();
this.setTitle(file);
- statusBar.setText("Successfully saved to file: "
- + fileName + " in "
- + format + " format.");
- }
- catch (Exception ex)
+ statusBar.setText("Successfully saved to file: " + fileName
+ + " in " + format + " format.");
+ } catch (Exception ex)
{
success = false;
ex.printStackTrace();
}
if (!success)
- JOptionPane.showInternalMessageDialog(
- this, "Couldn't save file: " + fileName,
- "Error Saving File",
- JOptionPane.WARNING_MESSAGE);
+ {
+ JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
+ + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
+ }
return success;
}
+ private void warningMessage(String warning, String title)
+ {
+ if (new jalview.util.Platform().isHeadless())
+ {
+ System.err.println("Warning: " + title + "\nWarning: " + warning);
+
+ }
+ else
+ {
+ JOptionPane.showInternalMessageDialog(this, warning, title,
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void outputText_actionPerformed(ActionEvent e)
{
- String [] omitHidden = null;
+ String[] omitHidden = null;
- if(viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns)
{
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "The Alignment contains hidden columns."
- +"\nDo you want to output only the visible alignment?",
- "Save / Omit Hidden Columns",
- JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
-
- if(reply==JOptionPane.YES_OPTION)
+ int reply = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ "The Alignment contains hidden columns."
+ + "\nDo you want to output only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (reply == JOptionPane.YES_OPTION)
{
omitHidden = viewport.getViewAsString(false);
}
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap,
- "Alignment output - " + e.getActionCommand(), 600,
- 500);
+ Desktop.addInternalFrame(cap, "Alignment output - "
+ + e.getActionCommand(), 600, 500);
-
- cap.setText(new FormatAdapter().formatSequences(
- e.getActionCommand(),
- viewport.alignment.getSequencesArray(),
- omitHidden));
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ viewport.alignment, omitHidden, viewport.colSel));
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(viewport,
- alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
+ .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer());
}
public void createImageMap(File file, String image)
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void createPNG(File f)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
+ public void pageSetup_actionPerformed(ActionEvent e)
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
+ }
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void printMenuItem_actionPerformed(ActionEvent e)
{
- //Putting in a thread avoids Swing painting problems
- PrintThread thread = new PrintThread();
+ // Putting in a thread avoids Swing painting problems
+ PrintThread thread = new PrintThread(alignPanel);
thread.start();
}
new AnnotationExporter().exportFeatures(alignPanel);
}
-
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(
- alignPanel,
- viewport.alignment.getAlignmentAnnotation()
- );
+ new AnnotationExporter().exportAnnotations(alignPanel,
+ viewport.showAnnotation ? viewport.alignment
+ .getAlignmentAnnotation() : null, viewport.alignment
+ .getGroups(),
+ ((Alignment) viewport.alignment).alignmentProperties);
}
-
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Load Jalview Annotations or Features File");
chooser.setToolTipText("Load Jalview Annotations / Features file");
}
-
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Close the current view or all views in the alignment frame. If the frame
+ * only contains one view then the alignment will be removed from memory.
+ *
+ * @param closeAllTabs
*/
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
- if(alignPanels!=null && alignPanels.size()<2)
+ if (alignPanels != null && alignPanels.size() < 2)
+ {
closeAllTabs = true;
+ }
try
{
- if(alignPanels!=null)
+ if (alignPanels != null)
{
if (closeAllTabs)
- for (int i = 0; i < alignPanels.size(); i++)
+ {
+ if (this.isClosed())
{
- AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
- PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(ap);
+ // really close all the windows - otherwise wait till
+ // setClosed(true) is called
+ for (int i = 0; i < alignPanels.size(); i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ ap.closePanel();
+ }
}
+ }
else
{
- int index = tabbedPane.getSelectedIndex();
-
- alignPanels.removeElement(alignPanel);
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(alignPanel);
- alignPanel = null;
- viewport = null;
-
- tabbedPane.removeTabAt(index);
- tabbedPane.validate();
-
- if(index==tabbedPane.getTabCount())
- index --;
-
- this.tabSelectionChanged(index);
+ closeView(alignPanel);
}
}
if (closeAllTabs)
+ {
this.setClosed(true);
- }
- catch (Exception ex)
+ }
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
+ /**
+ * close alignPanel2 and shuffle tabs appropriately.
+ *
+ * @param alignPanel2
+ */
+ public void closeView(AlignmentPanel alignPanel2)
+ {
+ int index = tabbedPane.getSelectedIndex();
+ int closedindex = tabbedPane.indexOfComponent(alignPanel2);
+ alignPanels.removeElement(alignPanel2);
+ // Unnecessary
+ // if (viewport == alignPanel2.av)
+ // {
+ // viewport = null;
+ // }
+ alignPanel2.closePanel();
+ alignPanel2 = null;
+
+ tabbedPane.removeTabAt(closedindex);
+ tabbedPane.validate();
+
+ if (index > closedindex || index == tabbedPane.getTabCount())
+ {
+ // modify currently selected tab index if necessary.
+ index--;
+ }
+
+ this.tabSelectionChanged(index);
+ }
/**
* DOCUMENT ME!
}
}
-
public void addHistoryItem(CommandI command)
{
- if(command.getSize()>0)
+ if (command.getSize() > 0)
{
viewport.historyList.push(command);
viewport.redoList.clear();
}
}
-
+ /**
+ *
+ * @return alignment objects for all views
+ */
+ AlignmentI[] getViewAlignments()
+ {
+ if (alignPanels != null)
+ {
+ Enumeration e = alignPanels.elements();
+ AlignmentI[] als = new AlignmentI[alignPanels.size()];
+ for (int i = 0; e.hasMoreElements(); i++)
+ {
+ als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
+ }
+ return als;
+ }
+ if (viewport != null)
+ {
+ return new AlignmentI[]
+ { viewport.alignment };
+ }
+ return null;
+ }
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
- CommandI command = (CommandI)viewport.historyList.pop();
+ if (viewport.historyList.empty())
+ return;
+ CommandI command = (CommandI) viewport.historyList.pop();
viewport.redoList.push(command);
- command.undoCommand();
+ command.undoCommand(getViewAlignments());
AlignViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
- if(originalSource!=null)
+ if (originalSource != null)
{
originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
- originalSource.firePropertyChange("alignment",
- null,
- originalSource.alignment.getSequences());
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.alignment.getSequences());
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
- if(viewport.redoList.size()<1)
+ if (viewport.redoList.size() < 1)
+ {
return;
+ }
CommandI command = (CommandI) viewport.redoList.pop();
viewport.historyList.push(command);
- command.doCommand();
+ command.doCommand(getViewAlignments());
AlignViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
- if(originalSource!=null)
+ if (originalSource != null)
{
originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
- originalSource.firePropertyChange("alignment",
- null,
- originalSource.alignment.getSequences());
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.alignment.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
- AlignmentI al=null;
+ // 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.alignment)
{
- originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
break;
}
}
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);
+ }
originalSource = viewport;
}
/**
* DOCUMENT ME!
- *
- * @param up DOCUMENT ME!
+ *
+ * @param up
+ * DOCUMENT ME!
*/
public void moveSelectedSequences(boolean up)
{
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(false).contains(seq))
+ if (!sg.getSequences(null).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.getSequences(false).contains(temp))
+ if (sg.getSequences(null).contains(temp))
{
continue;
}
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(false).contains(seq))
+ if (!sg.getSequences(null).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.getSequences(false).contains(temp))
+ if (sg.getSequences(null).contains(temp))
{
continue;
}
}
}
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
+ synchronized void slideSequences(boolean right, int size)
+ {
+ Vector sg = new Vector();
+ if (viewport.cursorMode)
+ {
+ sg.addElement(viewport.alignment
+ .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport.alignment
+ .getHeight())
+ {
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.hiddenRepSequences);
+ }
+
+ if (sg.size() < 1)
+ {
+ return;
+ }
+
+ Vector invertGroup = new Vector();
+
+ for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ {
+ if (!sg.contains(viewport.alignment.getSequenceAt(i)))
+ invertGroup.add(viewport.alignment.getSequenceAt(i));
+ }
+
+ SequenceI[] seqs1 = new SequenceI[sg.size()];
+ for (int i = 0; i < sg.size(); i++)
+ seqs1[i] = (SequenceI) sg.elementAt(i);
+
+ SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+ for (int i = 0; i < invertGroup.size(); i++)
+ seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+
+ SlideSequencesCommand ssc;
+ if (right)
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+ size, viewport.getGapCharacter());
+ else
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+ size, viewport.getGapCharacter());
+
+ int groupAdjustment = 0;
+ if (ssc.getGapsInsertedBegin() && right)
+ {
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(size, 0);
+ else
+ groupAdjustment = size;
+ }
+ else if (!ssc.getGapsInsertedBegin() && !right)
+ {
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(-size, 0);
+ else
+ groupAdjustment = -size;
+ }
+
+ if (groupAdjustment != 0)
+ {
+ viewport.getSelectionGroup().setStartRes(
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().setEndRes(
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ }
+
+ boolean appendHistoryItem = false;
+ if (viewport.historyList != null && viewport.historyList.size() > 0
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ {
+ appendHistoryItem = ssc
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .peek());
+ }
+ if (!appendHistoryItem)
+ addHistoryItem(ssc);
+
+ repaint();
+ }
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void copy_actionPerformed(ActionEvent e)
{
{
return;
}
-
- SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+ // TODO: preserve the ordering of displayed alignment annotation in any
+ // internal paste (particularly sequence associated annotation)
+ SequenceI[] seqs = viewport.getSelectionAsNewSequence();
String[] omitHidden = null;
if (viewport.hasHiddenColumns)
omitHidden = viewport.getViewAsString(true);
}
- String output = new FormatAdapter().formatSequences(
- "Fasta",
- seqs,
- omitHidden);
+ String output = new FormatAdapter().formatSequences("Fasta", seqs,
+ omitHidden);
StringSelection ss = new StringSelection(output);
try
{
- //Its really worth setting the clipboard contents
- //to empty before setting the large StringSelection!!
- Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(""), null);
-
- Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(ss, Desktop.instance);
- }
- catch (OutOfMemoryError er)
+ jalview.gui.Desktop.internalCopy = true;
+ // Its really worth setting the clipboard contents
+ // to empty before setting the large StringSelection!!
+ Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
+ new StringSelection(""), null);
+
+ Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
+ Desktop.instance);
+ } catch (OutOfMemoryError er)
{
- er.printStackTrace();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory copying region!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
+ new OOMWarning("copying region", er);
return;
}
Vector hiddenColumns = null;
- if(viewport.hasHiddenColumns)
+ if (viewport.hasHiddenColumns)
{
- hiddenColumns =new Vector();
+ hiddenColumns = 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);
- hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
- region[1]-hiddenOffset});
+ hiddenColumns.addElement(new int[]
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
-
-
- Desktop.jalviewClipboard = new Object[]{ seqs,
- viewport.alignment.getDataset(),
- hiddenColumns};
- statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+ Desktop.jalviewClipboard = new Object[]
+ { seqs, viewport.alignment.getDataset(), hiddenColumns };
+ statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void pasteNew_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void pasteThis_actionPerformed(ActionEvent e)
{
}
/**
- * DOCUMENT ME!
- *
- * @param newAlignment DOCUMENT ME!
+ * Paste contents of Jalview clipboard
+ *
+ * @param newAlignment
+ * true to paste to a new alignment, otherwise add to this.
*/
void paste(boolean newAlignment)
{
+ boolean externalPaste = true;
try
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
{
str = (String) contents.getTransferData(DataFlavor.stringFlavor);
if (str.length() < 1)
+ {
return;
+ }
format = new IdentifyFile().Identify(str, "Paste");
- }
- catch (OutOfMemoryError er)
+ } catch (OutOfMemoryError er)
{
- er.printStackTrace();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory pasting sequences!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
+ new OOMWarning("Out of memory pasting sequences!!", er);
return;
}
SequenceI[] sequences;
+ boolean annotationAdded = false;
+ AlignmentI alignment = null;
+ if (Desktop.jalviewClipboard != null)
+ {
+ // The clipboard was filled from within Jalview, we must use the
+ // sequences
+ // And dataset from the copied alignment
+ SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+ // be doubly sure that we create *new* sequence objects.
+ sequences = new SequenceI[newseq.length];
+ for (int i = 0; i < newseq.length; i++)
+ {
+ sequences[i] = new Sequence(newseq[i]);
+ }
+ alignment = new Alignment(sequences);
+ externalPaste = false;
+ }
+ else
+ {
+ // parse the clipboard as an alignment.
+ alignment = new FormatAdapter().readFile(str, "Paste", format);
+ sequences = alignment.getSequencesArray();
+ }
- if(Desktop.jalviewClipboard!=null)
- {
- // The clipboard was filled from within Jalview, we must use the sequences
- // And dataset from the copied alignment
- sequences = (SequenceI[])Desktop.jalviewClipboard[0];
- }
- else
- {
- sequences = new FormatAdapter().readFile(str, "Paste", format).getSequencesArray();
- }
-
- AlignmentI alignment = null;
+ int alwidth = 0;
if (newAlignment)
{
- alignment = new Alignment(sequences);
- if (Desktop.jalviewClipboard != null)
- alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
- else
- alignment.setDataset(null);
+ if (Desktop.jalviewClipboard != null)
+ {
+ // dataset is inherited
+ alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+ }
+ else
+ {
+ // new dataset is constructed
+ alignment.setDataset(null);
+ }
+ alwidth = alignment.getWidth() + 1;
}
else
{
+ AlignmentI pastedal = alignment; // preserve pasted alignment object
+ // Add pasted sequences and dataset into existing alignment.
alignment = viewport.getAlignment();
+ alwidth = alignment.getWidth() + 1;
+ // decide if we need to import sequences from an existing dataset
+ boolean importDs = Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[1] != alignment.getDataset();
+ // importDs==true instructs us to copy over new dataset sequences from
+ // an existing alignment
+ Vector newDs = (importDs) ? new Vector() : null; // used to create
+ // minimum dataset set
- //!newAlignment
- SequenceI [] newseqs = new SequenceI[sequences.length];
for (int i = 0; i < sequences.length; i++)
{
- newseqs[i] = new Sequence(sequences[i].getName(),
- sequences[i].getSequence(), sequences[i].getStart(),
- sequences[i].getEnd());
+ if (importDs)
+ {
+ newDs.addElement(null);
+ }
+ SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
+ // paste
+ if (importDs && ds != null)
+ {
+ if (!newDs.contains(ds))
+ {
+ newDs.setElementAt(ds, i);
+ ds = new Sequence(ds);
+ // update with new dataset sequence
+ sequences[i].setDatasetSequence(ds);
+ }
+ else
+ {
+ ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
+ }
+ }
+ else
+ {
+ // copy and derive new dataset sequence
+ sequences[i] = sequences[i].deriveSequence();
+ alignment.getDataset().addSequence(
+ sequences[i].getDatasetSequence());
+ // TODO: avoid creation of duplicate dataset sequences with a
+ // 'contains' method using SequenceI.equals()/SequenceI.contains()
+ }
+ alignment.addSequence(sequences[i]); // merges dataset
+ }
+ if (newDs != null)
+ {
+ newDs.clear(); // tidy up
+ }
+ if (pastedal.getAlignmentAnnotation() != null)
+ {
+ // Add any annotation attached to alignment.
+ AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
+ for (int i = 0; i < alann.length; i++)
+ {
+ annotationAdded = true;
+ if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
+ {
+ AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+ newann.padAnnotation(alwidth);
+ alignment.addAnnotation(newann);
+ }
+ }
+ }
+ }
+ if (!newAlignment)
+ {
+ // /////
+ // ADD HISTORY ITEM
+ //
+ addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ sequences, 0, alignment.getWidth(), alignment));
+ }
+ // Add any annotations attached to sequences
+ for (int i = 0; i < sequences.length; i++)
+ {
+ if (sequences[i].getAnnotation() != null)
+ {
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+ {
+ annotationAdded = true;
+ sequences[i].getAnnotation()[a].adjustForAlignment();
+ sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+ alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
+ // was
+ // duplicated
+ // earlier
+ alignment
+ .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
+ }
+ }
+ }
+ if (!newAlignment)
+ {
- alignment.addSequence(newseqs[i]);
+ // propagate alignment changed.
+ viewport.setEndSeq(alignment.getHeight());
+ if (annotationAdded)
+ {
+ // Duplicate sequence annotation in all views.
+ AlignmentI[] alview = this.getViewAlignments();
+ for (int i = 0; i < sequences.length; i++)
+ {
+ AlignmentAnnotation sann[] = sequences[i].getAnnotation();
+ if (sann == null)
+ continue;
+ for (int avnum = 0; avnum < alview.length; avnum++)
+ {
+ if (alview[avnum] != alignment)
+ {
+ // duplicate in a view other than the one with input focus
+ int avwidth = alview[avnum].getWidth() + 1;
+ // this relies on sann being preserved after we
+ // modify the sequence's annotation array for each duplication
+ for (int a = 0; a < sann.length; a++)
+ {
+ AlignmentAnnotation newann = new AlignmentAnnotation(
+ sann[a]);
+ sequences[i].addAlignmentAnnotation(newann);
+ newann.padAnnotation(avwidth);
+ alview[avnum].addAnnotation(newann); // annotation was
+ // duplicated earlier
+ alview[avnum].setAnnotationIndex(newann, a);
+ }
+ }
+ }
+ }
+ buildSortByAnnotationScoresMenu();
}
+ viewport.firePropertyChange("alignment", null, alignment
+ .getSequences());
+
+ }
+ else
+ {
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = new String("Copied sequences");
- /*
- //ADD HISTORY ITEM
- */
- addHistoryItem(new EditCommand(
- "Add sequences",
- EditCommand.PASTE,
- newseqs,
- 0,
- alignment.getWidth(),
- alignment)
- );
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
+ {
+ Vector hc = (Vector) Desktop.jalviewClipboard[2];
+ for (int i = 0; i < hc.size(); i++)
+ {
+ int[] region = (int[]) hc.elementAt(i);
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+ .transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
- viewport.setEndSeq(alignment.getHeight());
- alignment.getWidth();
- viewport.firePropertyChange("alignment", null, alignment.getSequences());
- }
+ // TODO: maintain provenance of an alignment, rather than just make the
+ // title a concatenation of operations.
+ if (!externalPaste)
+ {
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+ }
+ else
+ {
+ newtitle = new String("Pasted sequences");
+ }
+ Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
- // Add any annotations attached to sequences
- for (int i = 0; i < sequences.length; i++)
- {
- if (sequences[i].getAnnotation() != null)
- {
- for (int a = 0; a < sequences[i].getAnnotation().length; a++)
- {
- AlignmentAnnotation newAnnot =
- new AlignmentAnnotation(
- sequences[i].getAnnotation()[a].label,
- sequences[i].getAnnotation()[a].description,
- sequences[i].getAnnotation()[a].annotations,
- sequences[i].getAnnotation()[a].graphMin,
- sequences[i].getAnnotation()[a].graphMax,
- sequences[i].getAnnotation()[a].graph);
-
- sequences[i].getAnnotation()[a] = newAnnot;
- newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
- sequenceMapping;
- newAnnot.sequenceRef = sequences[i];
- newAnnot.adjustForAlignment();
- alignment.addAnnotation(newAnnot);
- alignment.setAnnotationIndex(newAnnot, a);
- }
-
- alignPanel.annotationPanel.adjustPanelHeight();
- }
- }
-
- if(newAlignment)
- {
- AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- String newtitle = new String("Copied sequences");
-
- if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
- {
- Vector hc = (Vector)Desktop.jalviewClipboard[2];
- for(int i=0; i<hc.size(); i++)
- {
- int [] region = (int[]) hc.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
-
-
- //>>>This is a fix for the moment, until a better solution is found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
-
-
- if (title.startsWith("Copied sequences"))
- {
- newtitle = title;
- }
- else
- {
- newtitle = newtitle.concat("- from " + title);
- }
-
- Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
-
- }
-
-
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
- System.out.println("Exception whilst pasting: "+ex);
- // could be anything being pasted in here
+ System.out.println("Exception whilst pasting: " + ex);
+ // could be anything being pasted in here
}
-
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void cut_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void delete_actionPerformed(ActionEvent evt)
{
Vector seqs = new Vector();
SequenceI seq;
- for (int i = 0; i < sg.getSize(false); i++)
+ for (int i = 0; i < sg.getSize(); i++)
{
seq = sg.getSequenceAt(i);
seqs.addElement(seq);
}
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize() == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize(false) == viewport.alignment.getHeight())
- {
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
-
-
- SequenceI [] cut = new SequenceI[seqs.size()];
- for(int i=0; i<seqs.size(); i++)
- cut[i] = (SequenceI)seqs.elementAt(i);
-
+ SequenceI[] cut = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ cut[i] = (SequenceI) seqs.elementAt(i);
+ }
/*
- //ADD HISTORY ITEM
- */
- addHistoryItem(new EditCommand("Cut Sequences",
- EditCommand.CUT,
- cut,
- sg.getStartRes(),
- sg.getEndRes()-sg.getStartRes()+1,
- viewport.alignment));
-
+ * //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.alignment));
viewport.setSelectionGroup(null);
+ viewport.sendSelection();
viewport.alignment.deleteGroup(sg);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
-
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
if (viewport.getAlignment().getHeight() < 1)
{
try
{
this.setClosed(true);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.repaint();
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup();
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
sg.setEndRes(viewport.alignment.getWidth() - 1);
viewport.setSelectionGroup(sg);
- alignPanel.repaint();
+ viewport.sendSelection();
+ alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
alignPanel.seqPanel.keyboardNo1 = null;
alignPanel.seqPanel.keyboardNo2 = null;
viewport.setSelectionGroup(null);
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
alignPanel.idPanel.idCanvas.searchResults = null;
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
return;
}
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
}
- alignPanel.repaint();
-
+ alignPanel.paintAlignment(true);
+ viewport.sendSelection();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
- trimAlignment(false);
+ trimAlignment(false);
}
void trimAlignment(boolean trimLeft)
if (colSel.size() > 0)
{
- if(trimLeft)
+ if (trimLeft)
+ {
column = colSel.getMin();
+ }
else
+ {
column = colSel.getMax();
+ }
- SequenceI [] seqs;
- if(viewport.getSelectionGroup()!=null)
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
+ }
else
+ {
seqs = viewport.alignment.getSequencesArray();
-
+ }
TrimRegionCommand trimRegion;
- if(trimLeft)
+ if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
+ TrimRegionCommand.TRIM_LEFT, seqs, column,
+ viewport.alignment, viewport.colSel,
+ viewport.selectionGroup);
viewport.setStartRes(0);
}
- else
- {
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
- }
-
- statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,
+ viewport.alignment, viewport.colSel,
+ viewport.selectionGroup);
+ }
+ statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
addHistoryItem(trimRegion);
{
SequenceGroup sg = (SequenceGroup) groups.get(i);
- if ( (trimLeft && !sg.adjustForRemoveLeft(column))
- || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
{
viewport.alignment.deleteGroup(sg);
}
}
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
- int start = 0, end = viewport.alignment.getWidth()-1;
+ int start = 0, end = viewport.alignment.getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
+ {
seqs = viewport.alignment.getSequencesArray();
+ }
-
- RemoveGapColCommand removeGapCols =
- new RemoveGapColCommand("Remove Gapped Columns",
- seqs,
- start, end,
- viewport.getGapCharacter());
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+ "Remove Gapped Columns", seqs, start, end, viewport.alignment);
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
+ // This is to maintain viewport position on first residue
+ // of first sequence
SequenceI seq = viewport.alignment.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.setStartRes(seq.findIndex(startRes)-1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ // ShiftList shifts;
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ // edit.alColumnChanges=shifts.getInverse();
+ // if (viewport.hasHiddenColumns)
+ // viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
- int start = 0, end = viewport.alignment.getWidth()-1;
+ int start = 0, end = viewport.alignment.getWidth() - 1;
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
else
+ {
seqs = viewport.alignment.getSequencesArray();
+ }
- //This is to maintain viewport position on first residue
- //of first sequence
+ // This is to maintain viewport position on first residue
+ // of first sequence
SequenceI seq = viewport.alignment.getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
- addHistoryItem(new RemoveGapsCommand("Remove Gaps",
- seqs,
- start, end,
- viewport.getGapCharacter()));
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+ viewport.alignment));
- viewport.setStartRes(seq.findIndex(startRes)-1);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.padGaps = padGapsMenuitem.isSelected();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+ }
- viewport.firePropertyChange("alignment",
- null,
- viewport.getAlignment().getSequences());
+ // else
+ {
+ // if (justifySeqs>0)
+ {
+ // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
+ }
}
+ // }
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void findMenuItem_actionPerformed(ActionEvent e)
{
public void newView_actionPerformed(ActionEvent e)
{
- AlignmentPanel newap =
- new Jalview2XML().copyAlignPanel(alignPanel, true);
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
+ true);
+
+ newap.av.gatherViewsHere = false;
if (viewport.viewName == null)
+ {
viewport.viewName = "Original";
+ }
newap.av.historyList = viewport.historyList;
newap.av.redoList = viewport.redoList;
int index = Desktop.getViewCount(viewport.getSequenceSetId());
- String newViewName = "View " +index;
+ String newViewName = "View " + index;
- Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
Vector existingNames = new Vector();
- for(int i=0; i<comps.size(); i++)
+ for (int i = 0; i < comps.size(); i++)
{
- if(comps.elementAt(i) instanceof AlignmentPanel)
+ if (comps.elementAt(i) instanceof AlignmentPanel)
{
- AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
- if(!existingNames.contains(ap.av.viewName))
+ AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
+ if (!existingNames.contains(ap.av.viewName))
+ {
existingNames.addElement(ap.av.viewName);
+ }
}
}
- while(existingNames.contains(newViewName))
+ while (existingNames.contains(newViewName))
{
- newViewName = "View "+ (++index);
+ newViewName = "View " + (++index);
}
newap.av.viewName = newViewName;
- addAlignmentPanel(newap, false);
+ addAlignmentPanel(newap, true);
- if(alignPanels.size()==2)
+ if (alignPanels.size() == 2)
{
viewport.gatherViewsHere = true;
}
public void expandViews_actionPerformed(ActionEvent e)
{
- Desktop.instance.explodeViews(this);
+ Desktop.instance.explodeViews(this);
}
public void gatherViews_actionPerformed(ActionEvent e)
Desktop.instance.gatherViews(this);
}
-
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.setShowJVSuffix(seqLimits.isSelected());
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
- alignPanel.repaint();
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+ .calculateIdWidth());
+ alignPanel.paintAlignment(true);
}
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.rightAlignIds = idRightAlign.isSelected();
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
+ public void centreColumnLabels_actionPerformed(ActionEvent e)
+ {
+ viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+ alignPanel.paintAlignment(true);
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
+ */
+ protected void followHighlight_actionPerformed()
+ {
+ if (viewport.followHighlight = this.followHighlightMenuItem.getState())
+ {
+ alignPanel.scrollToPosition(
+ alignPanel.seqPanel.seqCanvas.searchResults, false);
+ }
+ }
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
public void hiddenMarkers_actionPerformed(ActionEvent e)
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
-
public FeatureSettings featureSettings;
+
public void featureSettings_actionPerformed(ActionEvent e)
{
- if(featureSettings !=null )
+ if (featureSettings != null)
{
featureSettings.close();
featureSettings = null;
}
/**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
+ .isSelected());
+ if (viewport.getShowSequenceFeaturesHeight())
+ {
+ // ensure we're actually displaying features
+ viewport.setShowSequenceFeatures(true);
+ showSeqFeatures.setSelected(true);
+ }
+ alignPanel.paintAlignment(true);
if (alignPanel.getOverviewPanel() != null)
{
alignPanel.getOverviewPanel().updateOverviewImage();
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void overviewMenuItem_actionPerformed(ActionEvent e)
+ public void alignmentProperties()
{
- if (alignPanel.overviewPanel != null)
+ JEditorPane editPane = new JEditorPane("text/html", "");
+ editPane.setEditable(false);
+ StringBuffer contents = new StringBuffer("<html>");
+
+ float avg = 0;
+ int min = Integer.MAX_VALUE, max = 0;
+ for (int i = 0; i < viewport.alignment.getHeight(); i++)
{
- return;
+ int size = viewport.alignment.getSequenceAt(i).getEnd()
+ - viewport.alignment.getSequenceAt(i).getStart();
+ avg += size;
+ if (size > max)
+ max = size;
+ if (size < min)
+ min = size;
}
+ avg = avg / (float) viewport.alignment.getHeight();
- JInternalFrame frame = new JInternalFrame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
- frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
- frame.getWidth(), frame.getHeight());
- frame.pack();
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ contents.append("<br>Sequences: " + viewport.alignment.getHeight());
+ contents.append("<br>Minimum Sequence Length: " + min);
+ contents.append("<br>Maximum Sequence Length: " + max);
+ contents.append("<br>Average Length: " + (int) avg);
+
+ if (((Alignment) viewport.alignment).getProperties() != null)
{
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
+ Hashtable props = ((Alignment) viewport.alignment).getProperties();
+ Enumeration en = props.keys();
+ contents.append("<br><br><table border=\"1\">");
+ while (en.hasMoreElements())
{
- alignPanel.setOverviewPanel(null);
+ String key = en.nextElement().toString();
+ StringBuffer val = new StringBuffer();
+ String vals = props.get(key).toString();
+ int pos = 0, npos;
+ do
+ {
+ npos = vals.indexOf("\n", pos);
+ if (npos == -1)
+ {
+ val.append(vals.substring(pos));
+ }
+ else
+ {
+ val.append(vals.substring(pos, npos));
+ val.append("<br>");
+ }
+ pos = npos + 1;
+ } while (npos != -1);
+ contents
+ .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
}
- ;
- });
+ contents.append("</table>");
+ }
+ editPane.setText(contents.toString() + "</html>");
+ JInternalFrame frame = new JInternalFrame();
+ frame.getContentPane().add(new JScrollPane(editPane));
+
+ Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
+ + getTitle(), 500, 400);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void overviewMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (alignPanel.overviewPanel != null)
+ {
+ return;
+ }
+
+ JInternalFrame frame = new JInternalFrame();
+ OverviewPanel overview = new OverviewPanel(alignPanel);
+ frame.setContentPane(overview);
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
+ .getWidth(), frame.getHeight());
+ frame.pack();
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame
+ .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
alignPanel.setOverviewPanel(overview);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void clustalColour_actionPerformed(ActionEvent e)
{
changeColour(new ClustalxColourScheme(
- viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+ viewport.alignment.getSequences(), viewport.alignment
+ .getWidth()));
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void zappoColour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void taylorColour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void helixColour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void strandColour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void turnColour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void buriedColour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void nucleotideColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param cs DOCUMENT ME!
+ *
+ * @param cs
+ * DOCUMENT ME!
*/
public void changeColour(ColourSchemeI cs)
{
int threshold = 0;
- if(cs!=null)
+ if (cs != null)
{
if (viewport.getAbovePIDThreshold())
{
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
+ "Background");
- cs.setThreshold(threshold,
- viewport.getIgnoreGapsConsensus());
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
viewport.setGlobalColourScheme(cs);
}
Alignment al = (Alignment) viewport.alignment;
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);
cs.setConservation(c);
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
- "Background"));
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs, "Background"));
}
else
{
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(
- sg.getSequences(true), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(sg
+ .getSequences(viewport.hiddenRepSequences), sg.getWidth());
}
else if (cs instanceof UserColourScheme)
{
- sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
+ sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
}
else
{
try
{
sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
+ || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
{
- sg.cs.setThreshold(threshold,
- viewport.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(true), sg.getStartRes(),
- sg.getEndRes()+1));
- }
+ sg.cs.setConsensus(AAFrequency.calculate(sg
+ .getSequences(viewport.hiddenRepSequences), sg
+ .getStartRes(), sg.getEndRes() + 1));
+ }
else
+ {
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-
+ }
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(true),
- sg.getStartRes(),
- sg.getEndRes()+1);
+ ResidueProperties.propHash, 3, sg
+ .getSequences(viewport.hiddenRepSequences), sg
+ .getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
sg.cs.setConservation(c);
}
else
+ {
sg.cs.setConservation(null);
+ }
}
}
alignPanel.getOverviewPanel().updateOverviewImage();
}
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void modifyPID_actionPerformed(ActionEvent e)
{
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+ if (viewport.getAbovePIDThreshold()
+ && viewport.globalColourScheme != null)
{
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setPIDSliderSource(alignPanel, viewport
+ .getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void modifyConservation_actionPerformed(ActionEvent e)
{
- if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+ if (viewport.getConservationSelected()
+ && viewport.globalColourScheme != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.globalColourScheme,
- "Background");
+ viewport.globalColourScheme, "Background");
SliderPanel.showConservationSlider();
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void userDefinedColour_actionPerformed(ActionEvent e)
{
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.
- getUserColourSchemes().get(e.getActionCommand());
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
changeColour(udc);
}
int i, iSize = menuItems.length;
for (i = 0; i < iSize; i++)
{
- if (menuItems[i].getName() != null &&
- menuItems[i].getName().equals("USER_DEFINED"))
+ if (menuItems[i].getName() != null
+ && menuItems[i].getName().equals("USER_DEFINED"))
{
colourMenu.remove(menuItems[i]);
iSize--;
}
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
while (userColours.hasMoreElements())
{
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
- nextElement().toString());
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ userColours.nextElement().toString());
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isControlDown()
+ || SwingUtilities.isRightMouseButton(evt))
{
- public void mousePressed(MouseEvent evt)
- {
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem
+ .removeActionListener(radioItem.getActionListeners()[0]);
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+ int option = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop,
"Remove from default list?",
"Remove user defined colour",
JOptionPane.YES_NO_OPTION);
- if(option == JOptionPane.YES_OPTION)
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
{
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
+ userDefinedColour_actionPerformed(evt);
}
- else
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
+ });
}
- });
+ }
+ }
+ });
radioItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void PIDColour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(),
- viewport.getAlignment().getSequenceAt(0));
- addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
- alignPanel.repaint();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0), null);
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void sortLengthMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.alignment));
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
- if ( (viewport.getSelectionGroup() == null) ||
- (viewport.getSelectionGroup().getSize(false) < 2))
+ if ((viewport.getSelectionGroup() == null)
+ || (viewport.getSelectionGroup().getSize() < 2))
{
JOptionPane.showInternalMessageDialog(this,
- "You must select at least 2 sequences.",
- "Invalid Selection",
- JOptionPane.WARNING_MESSAGE);
+ "You must select at least 2 sequences.", "Invalid Selection",
+ JOptionPane.WARNING_MESSAGE);
}
else
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
- if ( ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize(false) < 4) &&
- (viewport.getSelectionGroup().getSize(false) > 0)) ||
- (viewport.getAlignment().getHeight() < 4))
+ if (((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() < 4) && (viewport
+ .getSelectionGroup().getSize() > 0))
+ || (viewport.getAlignment().getHeight() < 4))
{
JOptionPane.showInternalMessageDialog(this,
- "Principal component analysis must take\n" +
- "at least 4 input sequences.",
- "Sequence selection insufficient",
- JOptionPane.WARNING_MESSAGE);
+ "Principal component analysis must take\n"
+ + "at least 4 input sequences.",
+ "Sequence selection insufficient",
+ JOptionPane.WARNING_MESSAGE);
return;
}
- new PCAPanel(alignPanel);
+ new PCAPanel(alignPanel);
}
-
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if(viewport.autoCalculateConsensus)
+ if (viewport.autoCalculateConsensus)
{
- viewport.firePropertyChange("alignment",
- null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
}
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param type DOCUMENT ME!
- * @param pwType DOCUMENT ME!
- * @param title DOCUMENT ME!
+ *
+ * @param type
+ * DOCUMENT ME!
+ * @param pwType
+ * DOCUMENT ME!
+ * @param title
+ * DOCUMENT ME!
*/
void NewTreePanel(String type, String pwType, String title)
{
TreePanel tp;
- if (viewport.getSelectionGroup() != null) {
- if (viewport.getSelectionGroup().getSize(false) < 3) {
- JOptionPane.showMessageDialog(Desktop.desktop,
- "You need to have more than two sequences selected to build a tree!",
- "Not enough sequences",
- JOptionPane.WARNING_MESSAGE);
+ if (viewport.getSelectionGroup() != null)
+ {
+ if (viewport.getSelectionGroup().getSize() < 3)
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "You need to have more than two sequences selected to build a tree!",
+ "Not enough sequences", JOptionPane.WARNING_MESSAGE);
return;
}
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.getSize(false))
+ while (s < sg.getSize())
{
- if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
- sg.getEndRes())
+ if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
+ .getEndRes())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "The selected region to create a tree may\nonly contain residues or gaps.\n" +
- "Try using the Pad function in the edit menu,\n" +
- "or one of the multiple sequence alignment web services.",
- "Sequences in selection are not aligned",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "The selected region to create a tree may\nonly contain residues or gaps.\n"
+ + "Try using the Pad function in the edit menu,\n"
+ + "or one of the multiple sequence alignment web services.",
+ "Sequences in selection are not aligned",
+ JOptionPane.WARNING_MESSAGE);
return;
}
}
else
{
- //are the sequences aligned?
+ // are the sequences aligned?
if (!viewport.alignment.isAligned())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "The sequences must be aligned before creating a tree.\n" +
- "Try using the Pad function in the edit menu,\n" +
- "or one of the multiple sequence alignment web services.",
- "Sequences not aligned",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "The sequences must be aligned before creating a tree.\n"
+ + "Try using the Pad function in the edit menu,\n"
+ + "or one of the multiple sequence alignment web services.",
+ "Sequences not aligned",
+ JOptionPane.WARNING_MESSAGE);
return;
}
- if(viewport.alignment.getHeight()<2)
+ if (viewport.alignment.getHeight() < 2)
+ {
return;
+ }
tp = new TreePanel(alignPanel, type, pwType);
}
title += " from ";
- if(viewport.viewName!=null)
- title+= viewport.viewName+" of ";
+ if (viewport.viewName != null)
+ {
+ title += viewport.viewName + " of ";
+ }
title += this.title;
/**
* DOCUMENT ME!
- *
- * @param title DOCUMENT ME!
- * @param order DOCUMENT ME!
+ *
+ * @param title
+ * DOCUMENT ME!
+ * @param order
+ * DOCUMENT ME!
*/
- public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
+ public void addSortByOrderMenuItem(String title,
+ final AlignmentOrder order)
{
final JMenuItem item = new JMenuItem("by " + title);
sort.add(item);
{
public void actionPerformed(ActionEvent e)
{
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+ // TODO: JBPNote - have to map order entries to curent SequenceI
+ // pointers
AlignmentSorter.sortBy(viewport.getAlignment(), order);
- addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder,
+ viewport.alignment));
+
+ alignPanel.paintAlignment(true);
+ }
+ });
+ }
- alignPanel.repaint();
+ /**
+ * Add a new sort by annotation score menu item
+ *
+ * @param sort
+ * the menu to add the option to
+ * @param scoreLabel
+ * the label used to retrieve scores for each sequence on the
+ * alignment
+ */
+ public void addSortByAnnotScoreMenuItem(JMenu sort,
+ final String scoreLabel)
+ {
+ final JMenuItem item = new JMenuItem(scoreLabel);
+ sort.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
+ .getAlignment());// ,viewport.getSelectionGroup());
+ addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
}
});
}
/**
- * Maintain the Order by->Displayed Tree menu.
- * Creates a new menu item for a TreePanel with an appropriate
- * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
- * to remove the menu item when the treePanel is closed, and adjust
- * the tree leaf to sequence mapping when the alignment is modified.
- * @param treePanel Displayed tree window.
- * @param title SortBy menu item title.
+ * last hash for alignment's annotation array - used to minimise cost of
+ * rebuild.
+ */
+ protected int _annotationScoreVectorHash;
+
+ /**
+ * search the alignment and rebuild the sort by annotation score submenu the
+ * last alignment annotation vector hash is stored to minimize cost of
+ * rebuilding in subsequence calls.
+ *
+ */
+ public void buildSortByAnnotationScoresMenu()
+ {
+ if (viewport.alignment.getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+
+ if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
+ {
+ sortByAnnotScore.removeAll();
+ // almost certainly a quicker way to do this - but we keep it simple
+ Hashtable scoreSorts = new Hashtable();
+ AlignmentAnnotation aann[];
+ Enumeration sq = viewport.alignment.getSequences().elements();
+ while (sq.hasMoreElements())
+ {
+ aann = ((SequenceI) sq.nextElement()).getAnnotation();
+ for (int i = 0; aann != null && i < aann.length; i++)
+ {
+ if (aann[i].hasScore() && aann[i].sequenceRef != null)
+ {
+ scoreSorts.put(aann[i].label, aann[i].label);
+ }
+ }
+ }
+ Enumeration labels = scoreSorts.keys();
+ while (labels.hasMoreElements())
+ {
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
+ .nextElement());
+ }
+ sortByAnnotScore.setVisible(scoreSorts.size() > 0);
+ scoreSorts.clear();
+
+ _annotationScoreVectorHash = viewport.alignment
+ .getAlignmentAnnotation().hashCode();
+ }
+ }
+
+ /**
+ * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
+ * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
+ * call. Listeners are added to remove the menu item when the treePanel is
+ * closed, and adjust the tree leaf to sequence mapping when the alignment is
+ * modified.
+ *
+ * @param treePanel
+ * Displayed tree window.
+ * @param title
+ * SortBy menu item title.
*/
public void buildTreeMenu()
{
sortByTreeMenu.removeAll();
- Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
Vector treePanels = new Vector();
int i, iSize = comps.size();
- for(i=0; i<iSize; i++)
+ for (i = 0; i < iSize; i++)
{
- if(comps.elementAt(i) instanceof TreePanel)
+ if (comps.elementAt(i) instanceof TreePanel)
{
treePanels.add(comps.elementAt(i));
}
iSize = treePanels.size();
- if(iSize<1)
+ if (iSize < 1)
{
sortByTreeMenu.setVisible(false);
return;
sortByTreeMenu.setVisible(true);
- for(i=0; i<treePanels.size(); i++)
+ for (i = 0; i < treePanels.size(); i++)
{
- TreePanel tp = (TreePanel)treePanels.elementAt(i);
+ TreePanel tp = (TreePanel) treePanels.elementAt(i);
final JMenuItem item = new JMenuItem(tp.getTitle());
- final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
+ final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment()
+ .getSequencesArray();
AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
- addHistoryItem(new OrderCommand("Tree Sort",
- oldOrder,
- viewport.alignment));
+ addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
+ viewport.alignment));
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
});
}
/**
- * Work out whether the whole set of sequences
- * or just the selected set will be submitted for multiple alignment.
- *
+ * Work out whether the whole set of sequences or just the selected set will
+ * be submitted for multiple alignment.
+ *
*/
- private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
+ public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
{
// Now, check we have enough sequences
AlignmentView msa = null;
- if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize(false) > 1))
+ if ((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() > 1))
{
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
- /*SequenceGroup seqs = viewport.getSelectionGroup();
- int sz;
- msa = new SequenceI[sz = seqs.getSize(false)];
-
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- } */
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
+ // some common interface!
+ /*
+ * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
+ * SequenceI[sz = seqs.getSize(false)];
+ *
+ * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
+ * seqs.getSequenceAt(i); }
+ */
msa = viewport.getAlignmentView(true);
}
else
{
- /*Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1)
- {
- msa = new SequenceI[seqs.size()];
-
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
- }*/
+ /*
+ * Vector seqs = viewport.getAlignment().getSequences();
+ *
+ * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
+ *
+ * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
+ * seqs.elementAt(i); } }
+ */
msa = viewport.getAlignmentView(false);
}
return msa;
}
/**
- * Decides what is submitted to a secondary structure prediction service,
- * the currently selected sequence, or the currently selected alignment
- * (where the first sequence in the set is the one that the prediction
- * will be for).
+ * Decides what is submitted to a secondary structure prediction service: the
+ * first sequence in the alignment, or in the current selection, or, if the
+ * alignment is 'aligned' (ie padded with gaps), then the currently selected
+ * region or the whole alignment. (where the first sequence in the set is the
+ * one that the prediction will be for).
*/
- AlignmentView gatherSeqOrMsaForSecStrPrediction()
+ public AlignmentView gatherSeqOrMsaForSecStrPrediction()
{
- AlignmentView seqs = null;
+ AlignmentView seqs = null;
- if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize(false) > 0))
+ if ((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() > 0))
{
seqs = viewport.getAlignmentView(true);
}
{
seqs = viewport.getAlignmentView(false);
}
- // limit sequences - JBPNote in future - could spawn multiple prediction jobs
- // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+ // limit sequences - JBPNote in future - could spawn multiple prediction
+ // jobs
+ // TODO: viewport.alignment.isAligned is a global state - the local
+ // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
if (!viewport.alignment.isAligned())
{
- seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
+ seqs.setSequences(new SeqCigar[]
+ { seqs.getSequences()[0] });
}
return seqs;
}
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Select a newick-like tree file");
chooser.setToolTipText("Load a tree file");
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-
+ jalview.io.NewickFile fin = null;
try
{
- jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
- "File");
+ fin = new jalview.io.NewickFile(choice, "File");
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "Problem reading tree file",
- ex.getMessage(),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop, fin
+ .getWarningMessage(), "Possible problem with tree file",
+ JOptionPane.WARNING_MESSAGE);
+ }
}
}
-
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
- return ShowNewickTree(nf,title,600,500,4,5);
+ return ShowNewickTree(nf, title, 600, 500, 4, 5);
}
- public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title,
+ AlignmentView input)
{
- return ShowNewickTree(nf,title, input, 600,500,4,5);
+ return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
}
- public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
+ int h, int x, int y)
+ {
return ShowNewickTree(nf, title, null, w, h, x, y);
}
+
/**
- * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
- *
- * @param nf the tree
- * @param title tree viewer title
- * @param input Associated alignment input data (or null)
- * @param w width
- * @param h height
- * @param x position
- * @param y position
+ * Add a treeviewer for the tree extracted from a newick file object to the
+ * current alignment view
+ *
+ * @param nf
+ * the tree
+ * @param title
+ * tree viewer title
+ * @param input
+ * Associated alignment input data (or null)
+ * @param w
+ * width
+ * @param h
+ * height
+ * @param x
+ * position
+ * @param y
+ * position
* @return TreePanel handle
*/
- public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
+ public TreePanel ShowNewickTree(NewickFile nf, String title,
+ AlignmentView input, int w, int h, int x, int y)
+ {
TreePanel tp = null;
try
if (nf.getTree() != null)
{
- tp = new TreePanel(alignPanel,
- "FromFile",
- title,
- nf, input);
-
- tp.setSize(w,h);
+ tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
- if(x>0 && y>0)
- tp.setLocation(x,y);
+ tp.setSize(w, h);
+ if (x > 0 && y > 0)
+ {
+ tp.setLocation(x, y);
+ }
Desktop.addInternalFrame(tp, title, w, h);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
return tp;
}
- class PrintThread
- extends Thread
- {
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
- printJob.setPrintable(alignPanel, pf);
-
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- }
- catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
- }
- }
-
/**
* Generates menu items and listener event actions for web service clients
- *
+ *
*/
public void BuildWebServiceMenu()
{
- if ( (Discoverer.services != null)
- && (Discoverer.services.size() > 0))
+ // TODO: add support for context dependent disabling of services based on
+ // alignment and current selection
+ // TODO: add additional serviceHandle parameter to specify abstract handler
+ // class independently of AbstractName
+ // TODO: add in rediscovery GUI function to restart discoverer
+ // TODO: group services by location as well as function and/or introduce
+ // object broker mechanism.
+ if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
{
+ // TODO: refactor to allow list of AbstractName/Handler bindings to be
+ // stored or retrieved from elsewhere
Vector msaws = (Vector) Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
+ Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
+ // TODO: move GUI generation code onto service implementation - so a
+ // client instance attaches itself to the GUI with method call like
+ // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
+ // alignframe)
Vector wsmenu = new Vector();
- final AlignFrame af = this;
+ final IProgressIndicator af = this;
if (msaws != null)
{
// Add any Multiple Sequence Alignment Services
final JMenu msawsmenu = new JMenu("Alignment");
for (int i = 0, j = msaws.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
- get(i);
- final JMenuItem method = new JMenuItem(sh.getName());
- method.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = gatherSequencesForAlignment();
- new jalview.ws.MsaWSClient(sh, title, msa,
- false, true, viewport.getAlignment().getDataset(), af);
-
- }
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
+ .get(i);
+ jalview.ws.WSClient impl = jalview.ws.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(msawsmenu, this);
- });
- msawsmenu.add(method);
- // Deal with services that we know accept partial alignments.
- if (sh.getName().indexOf("lustal") > -1)
- {
- // We know that ClustalWS can accept partial alignments for refinement.
- final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
- methodR.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = gatherSequencesForAlignment();
- new jalview.ws.MsaWSClient(sh, title, msa,
- true, true, viewport.getAlignment().getDataset(), af);
-
- }
-
- });
- msawsmenu.add(methodR);
-
- }
}
wsmenu.add(msawsmenu);
}
final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
- secstrpr.get(i);
- final JMenuItem method = new JMenuItem(sh.getName());
- method.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
- if (msa.getSequences().length == 1)
- {
- // Single Sequence prediction
- new jalview.ws.JPredClient(sh, title, false, msa, af, true);
- }
- else
- {
- if (msa.getSequences().length > 1)
- {
- // Sequence profile based prediction
- new jalview.ws.JPredClient(sh,
- title, true, msa, af, true);
- }
- }
- }
- });
- secstrmenu.add(method);
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ .get(i);
+ jalview.ws.WSClient impl = jalview.ws.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(secstrmenu, this);
}
wsmenu.add(secstrmenu);
}
- this.webService.removeAll();
+ if (seqsrch != null)
+ {
+ // Add any sequence search services
+ final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
+ for (int i = 0, j = seqsrch.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
+ .elementAt(i);
+ jalview.ws.WSClient impl = jalview.ws.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(seqsrchmenu, this);
+ }
+ // finally, add the whole shebang onto the webservices menu
+ wsmenu.add(seqsrchmenu);
+ }
+ resetWebServiceMenu();
for (int i = 0, j = wsmenu.size(); i < j; i++)
{
- webService.add( (JMenu) wsmenu.get(i));
+ webService.add((JMenu) wsmenu.get(i));
}
}
else
{
- this.webService.removeAll();
+ resetWebServiceMenu();
this.webService.add(this.webServiceNoServices);
}
- // TODO: add in rediscovery function
- // TODO: reduce code redundancy.
- // TODO: group services by location as well as function.
}
- /* public void vamsasStore_actionPerformed(ActionEvent e)
+ /**
+ * empty the web service menu and add any ad-hoc functions not dynamically
+ * discovered.
+ *
+ */
+ private void resetWebServiceMenu()
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Export to Vamsas file");
- chooser.setToolTipText("Export");
+ webService.removeAll();
+ build_fetchdbmenu(webService);
+ }
- int value = chooser.showSaveDialog(this);
+ /*
+ * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
+ * chooser = new JalviewFileChooser(jalview.bin.Cache.
+ * getProperty("LAST_DIRECTORY"));
+ *
+ * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
+ * to Vamsas file"); chooser.setToolTipText("Export");
+ *
+ * int value = chooser.showSaveDialog(this);
+ *
+ * if (value == JalviewFileChooser.APPROVE_OPTION) {
+ * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+ * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
+ * chooser.getSelectedFile().getAbsolutePath(), this); } }
+ */
+ /**
+ * prototype of an automatically enabled/disabled analysis function
+ *
+ */
+ protected void setShowProductsEnabled()
+ {
+ SequenceI[] selection = viewport.getSequenceSelection();
+ if (canShowProducts(selection, viewport.getSelectionGroup() != null,
+ viewport.getAlignment().getDataset()))
+ {
+ showProducts.setEnabled(true);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ }
+ else
{
- jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
- //vs.store(chooser.getSelectedFile().getAbsolutePath() );
- vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+ showProducts.setEnabled(false);
}
- }*/
-
+ }
+ /**
+ * search selection for sequence xRef products and build the show products
+ * menu.
+ *
+ * @param selection
+ * @param dataset
+ * @return true if showProducts menu should be enabled.
+ */
+ public boolean canShowProducts(SequenceI[] selection,
+ boolean isRegionSelection, Alignment dataset)
+ {
+ boolean showp = false;
+ try
+ {
+ showProducts.removeAll();
+ final boolean dna = viewport.getAlignment().isNucleotide();
+ final Alignment ds = dataset;
+ String[] ptypes = (selection == null || selection.length == 0) ? null
+ : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
+ // Object[] prods =
+ // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
+ // selection, dataset, true);
+ final SequenceI[] sel = selection;
+ for (int t = 0; ptypes != null && t < ptypes.length; t++)
+ {
+ showp = true;
+ final boolean isRegSel = isRegionSelection;
+ final AlignFrame af = this;
+ final String source = ptypes[t];
+ JMenuItem xtype = new JMenuItem(ptypes[t]);
+ xtype.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: new thread for this call with vis-delay
+ af.showProductsFor(af.viewport.getSequenceSelection(), ds,
+ isRegSel, dna, source);
+ }
-public void showTranslation_actionPerformed(ActionEvent e)
-{
- SequenceI [] selection = viewport.getSelectionAsNewSequence();
- String [] seqstring = viewport.getViewAsString(true);
-
- int s, sSize = selection.length;
- SequenceI [] newSeq = new SequenceI[sSize];
-
- int res, resSize;
- StringBuffer protein;
- String seq;
- for(s=0; s<sSize; s++)
- {
- protein = new StringBuffer();
- seq = AlignSeq.extractGaps("-. ", seqstring[s]);
- resSize = seq.length();
- resSize -= resSize%3;
-
- for(res = 0; res < resSize; res+=3)
- {
- String codon = seq.substring(res, res+3);
- codon = codon.replace('U', 'T');
- String aa = ResidueProperties.codonTranslate(codon);
- if(aa==null)
- protein.append(viewport.getGapCharacter());
- else if(aa.equals("STOP"))
- protein.append("X");
- else
- protein.append( aa );
+ });
+ showProducts.add(xtype);
+ }
+ showProducts.setVisible(showp);
+ showProducts.setEnabled(showp);
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log
+ .warn(
+ "canTranslate threw an exception - please report to help@jalview.org",
+ e);
+ return false;
}
- newSeq[s] = new Sequence(selection[s].getName(),
- protein.toString());
+ return showp;
}
-
- AlignmentI al = new Alignment(newSeq);
- al.setDataset(null);
-
-
- ////////////////////////////////
- // Copy annotations across
- jalview.datamodel.AlignmentAnnotation[] annotations
- = viewport.alignment.getAlignmentAnnotation();
- int a, aSize;
- if(annotations!=null)
+ protected void showProductsFor(SequenceI[] sel, Alignment ds,
+ boolean isRegSel, boolean dna, String source)
{
- for (int i = 0; i < annotations.length; i++)
+ final boolean fisRegSel = isRegSel;
+ final boolean fdna = dna;
+ final String fsrc = source;
+ final AlignFrame ths = this;
+ final SequenceI[] fsel = sel;
+ Runnable foo = new Runnable()
{
- if (annotations[i].label.equals("Quality") ||
- annotations[i].label.equals("Conservation") ||
- annotations[i].label.equals("Consensus"))
- {
- continue;
- }
-
- aSize = viewport.alignment.getWidth() / 3;
- jalview.datamodel.Annotation[] anots =
- new jalview.datamodel.Annotation[aSize];
- for (a = 0; a < viewport.alignment.getWidth(); a++)
+ public void run()
{
- if (annotations[i].annotations[a] == null
- || annotations[i].annotations[a] == null)
- continue;
-
- anots[a / 3] = new Annotation(
- annotations[i].annotations[a].displayCharacter,
- annotations[i].annotations[a].description,
- annotations[i].annotations[a].secondaryStructure,
- annotations[i].annotations[a].value,
- annotations[i].annotations[a].colour);
+ final long sttime = System.currentTimeMillis();
+ ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+ try
+ {
+ Alignment ds = ths.getViewport().alignment.getDataset(); // update
+ // our local
+ // dataset
+ // reference
+ Alignment prods = CrossRef
+ .findXrefSequences(fsel, fdna, fsrc, ds);
+ if (prods != null)
+ {
+ SequenceI[] sprods = new SequenceI[prods.getHeight()];
+ for (int s = 0; s < sprods.length; s++)
+ {
+ sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+ if (ds.getSequences() == null
+ || !ds.getSequences().contains(
+ sprods[s].getDatasetSequence()))
+ ds.addSequence(sprods[s].getDatasetSequence());
+ sprods[s].updatePDBIds();
+ }
+ Alignment al = new Alignment(sprods);
+ AlignedCodonFrame[] cf = prods.getCodonFrames();
+ al.setDataset(ds);
+ for (int s = 0; cf != null && s < cf.length; s++)
+ {
+ al.addCodonFrame(cf[s]);
+ cf[s] = null;
+ }
+ AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
+ + " for " + ((fisRegSel) ? "selected region of " : "")
+ + getTitle();
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+ else
+ {
+ System.err.println("No Sequences generated for xRef type "
+ + fsrc);
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.error(
+ "Exception when finding crossreferences", e);
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning("whilst fetching crossreferences", e);
+ } catch (Error e)
+ {
+ jalview.bin.Cache.log.error("Error when finding crossreferences",
+ e);
+ }
+ ths.setProgressBar("Finished searching for sequences from " + fsrc,
+ sttime);
}
- jalview.datamodel.AlignmentAnnotation aa
- = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
- annotations[i].description, anots);
- al.addAnnotation(aa);
- }
+ };
+ Thread frunner = new Thread(foo);
+ frunner.start();
}
- AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
- DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ public boolean canShowTranslationProducts(SequenceI[] selection,
+ AlignmentI alignment)
+ {
+ // old way
+ try
+ {
+ return (jalview.analysis.Dna.canTranslate(selection, viewport
+ .getViewAsVisibleContigs(true)));
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log
+ .warn(
+ "canTranslate threw an exception - please report to help@jalview.org",
+ e);
+ return false;
+ }
+ }
+ public void showProducts_actionPerformed(ActionEvent e)
+ {
+ // /////////////////////////////
+ // Collect Data to be translated/transferred
+ SequenceI[] selection = viewport.getSequenceSelection();
+ AlignmentI al = null;
+ try
+ {
+ al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
+ .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
+ viewport.getAlignment().getDataset());
+ } catch (Exception ex)
+ {
+ al = null;
+ jalview.bin.Cache.log.debug("Exception during translation.", ex);
+ }
+ if (al == null)
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+ "Translation Failed", JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+ DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ }
+ }
+ public void showTranslation_actionPerformed(ActionEvent e)
+ {
+ // /////////////////////////////
+ // Collect Data to be translated/transferred
-}
+ SequenceI[] selection = viewport.getSequenceSelection();
+ String[] seqstring = viewport.getViewAsString(true);
+ AlignmentI al = null;
+ try
+ {
+ al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
+ viewport.getViewAsVisibleContigs(true), viewport
+ .getGapCharacter(), viewport.alignment
+ .getAlignmentAnnotation(), viewport.alignment
+ .getWidth(), viewport.getAlignment().getDataset());
+ } catch (Exception ex)
+ {
+ al = null;
+ jalview.bin.Cache.log.debug("Exception during translation.", ex);
+ }
+ if (al == null)
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+ "Translation Failed", JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
+ DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ }
+ }
-/**
- * DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
- */
-public boolean parseFeaturesFile(String file, String type)
-{
+ /**
+ * Try to load a features file onto the alignment.
+ *
+ * @param file
+ * contents or path to retrieve file
+ * @param type
+ * access mode of file (see jalview.io.AlignFile)
+ * @return true if features file was parsed corectly.
+ */
+ public boolean parseFeaturesFile(String file, String type)
+ {
boolean featuresFile = false;
- try{
- featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
- alignPanel.seqPanel.seqCanvas.
- getFeatureRenderer().featureColours,
- false);
- }
- catch(Exception ex)
+ try
+ {
+ featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
+ .getDataset(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().featureColours, false);
+ } catch (Exception ex)
{
ex.printStackTrace();
}
- if(featuresFile)
+ if (featuresFile)
{
viewport.showSequenceFeatures = true;
showSeqFeatures.setSelected(true);
- alignPanel.repaint();
+ if (alignPanel.seqPanel.seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ }
+ alignPanel.paintAlignment(true);
}
return featuresFile;
-}
+ }
-public void dragEnter(DropTargetDragEvent evt)
-{}
+ public void dragEnter(DropTargetDragEvent evt)
+ {
+ }
-public void dragExit(DropTargetEvent evt)
-{}
+ public void dragExit(DropTargetEvent evt)
+ {
+ }
-public void dragOver(DropTargetDragEvent evt)
-{}
+ public void dragOver(DropTargetDragEvent evt)
+ {
+ }
-public void dropActionChanged(DropTargetDragEvent evt)
-{}
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {
+ }
-public void drop(DropTargetDropEvent evt)
-{
+ public void drop(DropTargetDropEvent evt)
+ {
Transferable t = evt.getTransferable();
java.util.List files = null;
try
{
- DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+ DataFlavor uriListFlavor = new DataFlavor(
+ "text/uri-list;class=java.lang.String");
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
- //Works on Windows and MacOSX
+ // Works on Windows and MacOSX
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+ files = (java.util.List) t
+ .getTransferData(DataFlavor.javaFileListFlavor);
}
else if (t.isDataFlavorSupported(uriListFlavor))
{
String data = (String) t.getTransferData(uriListFlavor);
files = new java.util.ArrayList(1);
for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data,
- "\r\n");
- st.hasMoreTokens(); )
+ data, "\r\n"); st.hasMoreTokens();)
{
String s = st.nextToken();
if (s.startsWith("#"))
}
java.net.URI uri = new java.net.URI(s);
- java.io.File file = new java.io.File(uri);
- files.add(file);
+ // check to see if we can handle this kind of URI
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ files.add(file.toString());
+ }
}
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
{
loadJalviewDataFile(files.get(i).toString());
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
-}
+ }
- // This method will attempt to load a "dropped" file first by testing
- // whether its and Annotation file, then features file. If both are
- // false then the user may have dropped an alignment file onto this
- // AlignFrame
- public void loadJalviewDataFile(String file)
+ /**
+ * Attempt to load a "dropped" file or URL string: First by testing whether
+ * it's and Annotation file, then a JNet file, and finally a features file. If
+ * all are false then the user may have dropped an alignment file onto this
+ * AlignFrame.
+ *
+ * @param file
+ * either a filename or a URL string.
+ */
+ public void loadJalviewDataFile(String file)
{
- try{
- String protocol = "File";
-
- if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ try
+ {
+ String protocol = jalview.io.FormatAdapter.FILE;
+ String f = file.toLowerCase();
+ if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
+ || f.indexOf("file:") == 0)
{
- protocol = "URL";
+ protocol = jalview.io.FormatAdapter.URL;
}
- boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
- alignment, file);
+ boolean isAnnotation = new AnnotationFile().readAnnotationFile(
+ viewport.alignment, file, protocol);
if (!isAnnotation)
{
- boolean isGroupsFile = parseFeaturesFile(file,protocol);
- if (!isGroupsFile)
+ // try to see if its a JNet 'concise' style annotation file *before* we
+ // try to parse it as a features file
+ String format = new IdentifyFile().Identify(file, protocol);
+ if (format.equalsIgnoreCase("JnetFile"))
{
- String format = new IdentifyFile().Identify(file, protocol);
-
- if(format.equalsIgnoreCase("JnetFile"))
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
+ protocol);
+ new JnetAnnotationMaker().add_annotation(predictions, viewport
+ .getAlignment(), 0, false);
+ isAnnotation = true;
+ }
+ else
+ {
+ // try to parse it as a features file
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);
+ // if it wasn't a features file then we just treat it as a general
+ // alignment file to load into the current view.
+ if (!isGroupsFile)
{
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- file, protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
- viewport.getAlignment(),
- 0, false);
- alignPanel.adjustAnnotationHeight();
- alignPanel.repaint();
+ new FileLoader().LoadFile(viewport, file, protocol, format);
}
else
- new FileLoader().LoadFile(viewport, file, protocol, format);
+ {
+ alignPanel.paintAlignment(true);
+ }
}
}
- else
+ if (isAnnotation)
{
- // (isAnnotation)
+
alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true);
}
-
- }catch(Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
public void tabbedPane_mousePressed(MouseEvent e)
{
- if(SwingUtilities.isRightMouseButton(e))
+ if (SwingUtilities.isRightMouseButton(e))
{
String reply = JOptionPane.showInternalInputDialog(this,
- "Enter View Name",
- "Edit View Name",
- JOptionPane.QUESTION_MESSAGE);
+ "Enter View Name", "Edit View Name",
+ JOptionPane.QUESTION_MESSAGE);
if (reply != null)
{
viewport.viewName = reply;
- tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+ tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
}
}
-
public AlignViewport getCurrentView()
{
return viewport;
}
+
+ /**
+ * Open the dialog for regex description parsing.
+ */
+ protected void extractScores_actionPerformed(ActionEvent e)
+ {
+ ParseProperties pp = new jalview.analysis.ParseProperties(
+ viewport.alignment);
+ // TODO: verify regex and introduce GUI dialog for version 2.5
+ // if (pp.getScoresFromDescription("col", "score column ",
+ // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
+ // true)>0)
+ if (pp.getScoresFromDescription("description column",
+ "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ protected void showDbRefs_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ protected void showNpFeats_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
+ }
+
+ /**
+ * find the viewport amongst the tabs in this alignment frame and close that
+ * tab
+ *
+ * @param av
+ */
+ public boolean closeView(AlignViewport av)
+ {
+ if (viewport == av)
+ {
+ this.closeMenuItem_actionPerformed(false);
+ return true;
+ }
+ Component[] comp = tabbedPane.getComponents();
+ for (int i = 0; comp != null && i < comp.length; i++)
+ {
+ if (comp[i] instanceof AlignmentPanel)
+ {
+ if (((AlignmentPanel) comp[i]).av == av)
+ {
+ // close the view.
+ closeView((AlignmentPanel) comp[i]);
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ protected void build_fetchdbmenu(JMenu webService)
+ {
+ // Temporary hack - DBRef Fetcher always top level ws entry.
+ // TODO We probably want to store a sequence database checklist in
+ // preferences and have checkboxes.. rather than individual sources selected
+ // here
+ JMenu rfetch = new JMenu("Fetch DB References");
+ rfetch
+ .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ webService.add(rfetch);
+
+ JMenuItem fetchr = new JMenuItem("Standard Databases");
+ fetchr
+ .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame)
+ .fetchDBRefs(false);
+ }
+ }).start();
+
+ }
+
+ });
+ rfetch.add(fetchr);
+ JMenu dfetch = new JMenu();
+ rfetch.add(dfetch);
+ jalview.ws.SequenceFetcher sf = SequenceFetcher
+ .getSequenceFetcherSingleton(this);
+ String[] otherdb = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ int comp = 0, mcomp = 15;
+ String mname = null;
+ if (otherdb != null && otherdb.length > 0)
+ {
+ for (int i = 0; i < otherdb.length; i++)
+ {
+ String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
+ if (mname == null)
+ {
+ mname = "from '" + dbname + "'";
+ }
+ fetchr = new JMenuItem(otherdb[i]);
+ final String[] dassource = new String[]
+ { otherdb[i] };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame,
+ dassource).fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText("Retrieve from " + dbname);
+ dfetch.add(fetchr);
+ if (comp++ == mcomp || i == (otherdb.length - 1))
+ {
+ dfetch.setText(mname + " to '" + dbname + "'");
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
+ }
+ }
+ }
+
+ /**
+ * Left justify the whole alignment.
+ */
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(false);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ /**
+ * Right justify the whole alignment.
+ */
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ AlignmentI al = viewport.getAlignment();
+ al.justify(true);
+ viewport.firePropertyChange("alignment", null, al);
+ }
+
+ public void setShowSeqFeatures(boolean b)
+ {
+ showSeqFeatures.setSelected(true);
+ viewport.setShowSequenceFeatures(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
+ * awt.event.ActionEvent)
+ */
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation();
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getSelectionGroup() != null)
+ {
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(), viewport.getAlignmentView(
+ true).getSequenceStrings(viewport.getGapCharacter()),
+ viewport.alignment.getGroups());
+ viewport.alignment.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].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols());
+ viewport.alignment.addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255), (int) (Math
+ .random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (Enumeration sq = gps[g].getSequences(null).elements(); sq
+ .hasMoreElements(); viewport.setSequenceColour(
+ (SequenceI) sq.nextElement(), col))
+ ;
+ }
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
+}
+
+class PrintThread extends Thread
+{
+ AlignmentPanel ap;
+
+ public PrintThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ static PageFormat pf;
+
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+
+ if (pf != null)
+ {
+ printJob.setPrintable(ap, pf);
+ }
+ else
+ {
+ printJob.setPrintable(ap);
+ }
+
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ } catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
}