X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2e6ea520d9cc36b90a79628e16b083ceb5bfc2de;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=a714ce64a710e12380afdb571e061f1ffa514724;hpb=10b27a2672c66e9c927194065d187cc744105867;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a714ce6..2e6ea52 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Softwarechang
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.gui;
@@ -40,60 +39,136 @@ import jalview.ws.*;
/**
* 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();
-
- /**
- * Last format used to load or save alignments in this window
+ /**
+ * 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);
}
@@ -104,8 +179,11 @@ public class AlignFrame
/**
* Make a new AlignFrame from exisiting alignmentPanels
- * @param ap AlignmentPanel
- * @param av AlignViewport
+ *
+ * @param ap
+ * AlignmentPanel
+ * @param av
+ * AlignViewport
*/
public AlignFrame(AlignmentPanel ap)
{
@@ -115,6 +193,10 @@ public class AlignFrame
init();
}
+ /**
+ * initalise the alignframe from the underlying viewport data and the
+ * configurations
+ */
void init()
{
if (viewport.conservation == null)
@@ -122,12 +204,13 @@ public class AlignFrame
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"))
{
@@ -139,274 +222,238 @@ public class AlignFrame
}
if (Desktop.desktop != null)
- {
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
- setGUINucleotide(viewport.alignment.isNucleotide());
- }
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide(viewport.alignment.isNucleotide());
+ }
- setMenusFromViewport(viewport);
- buildSortByAnnotationScoresMenu();
- if (viewport.wrapAlignment)
- {
- wrapMenuItem_actionPerformed(null);
- }
+ setMenusFromViewport(viewport);
+ buildSortByAnnotationScoresMenu();
+ if (viewport.wrapAlignment)
+ {
+ wrapMenuItem_actionPerformed(null);
+ }
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
+ 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)
- ||
- (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
- evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
- )
- && Character.isDigit(evt.getKeyChar()))
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-
- switch (evt.getKeyCode())
- {
-
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed(null);
-
- break;
- case KeyEvent.VK_DOWN:
- if (evt.isAltDown() || !viewport.cursorMode)
- moveSelectedSequences(false);
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, 1);
- break;
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
- case KeyEvent.VK_UP:
- if (evt.isAltDown() || !viewport.cursorMode)
- moveSelectedSequences(true);
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(0, -1);
+ 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_LEFT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor( -1, 0);
-
-
- 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_UP:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(true);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, -1);
- 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_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(-1, 0);
- break;
+ 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_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(1, 0);
+ break;
- case KeyEvent.VK_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ 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_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_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;
+ 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_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;
- 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_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
- boolean hide = false;
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
- SequenceGroup sg = viewport.getSelectionGroup();
- 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);
- }
- }
+ 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;
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- hideSelColumns_actionPerformed(null);
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- 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;
+ 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();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ 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())
+ 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;
+ 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;
@@ -416,9 +463,9 @@ public class AlignFrame
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);
}
@@ -436,7 +483,7 @@ public class AlignFrame
ap.setVisible(false);
}
- if(newPanel)
+ if (newPanel)
{
if (ap.av.padGaps)
{
@@ -453,11 +500,10 @@ public class AlignFrame
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;
@@ -469,54 +515,61 @@ public class AlignFrame
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 );
-
- //Remember AlignFrame always starts as protein
- if(!nucleotide)
+ showTranslation.setVisible(nucleotide);
+ conservationMenuItem.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide);
+ showGroupConservation.setEnabled(!nucleotide);
+ // Remember AlignFrame always starts as protein
+ if (!nucleotide)
{
- calculateMenu.remove(calculateMenu.getItemCount()-2);
+ calculateMenu.remove(calculateMenu.getItemCount() - 2);
}
- setShowProductsEnabled();
}
-
+ /**
+ * 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
+ * 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)
{
@@ -526,6 +579,7 @@ public class AlignFrame
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);
@@ -534,41 +588,59 @@ public class AlignFrame
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);
+ showConsensusHistogram.setSelected(av.showConsensusHistogram);
+ showSequenceLogo.setSelected(av.showSequenceLogo);
+ 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;
+ Long lId = new Long(id);
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)
+ if (progressBars.get(lId) != null)
+ {
+ progressPanel = (JPanel) progressBars.get(new Long(id));
+ statusPanel.remove(progressPanel);
+ progressBars.remove(lId);
+ progressPanel = null;
+ if (message != null)
{
- statusBar.setText(message);
+ statusBar.setText(message);
}
-
- layout.setRows(layout.getRows() - 1);
- }
+ if (progressBarHandlers.contains(lId))
+ {
+ progressBarHandlers.remove(lId);
+ }
+ layout.setRows(layout.getRows() - 1);
+ }
else
{
progressPanel = new JPanel(new BorderLayout(10, 5));
@@ -582,21 +654,60 @@ public class AlignFrame
layout.setRows(layout.getRows() + 1);
statusPanel.add(progressPanel);
- progressBars.put(new Long(id), progressPanel);
+ progressBars.put(lId, 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()
@@ -604,7 +715,6 @@ public class AlignFrame
return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
}
-
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
@@ -617,31 +727,32 @@ public class AlignFrame
public void reload_actionPerformed(ActionEvent e)
{
- if(fileName!=null)
+ if (fileName != null)
{
- if(currentFileFormat.equals("Jalview"))
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
+ if (currentFileFormat.equals("Jalview"))
{
- JInternalFrame [] frames = Desktop.desktop.getAllFrames();
- for(int i=0; i-1)
+ if (currentFileFormat.indexOf(" ") > -1)
{
- currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" "));
+ currentFileFormat = currentFileFormat.substring(0,
+ currentFileFormat.indexOf(" "));
}
saveAlignment(fileName, currentFileFormat);
}
@@ -745,41 +869,50 @@ public class AlignFrame
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);
- }
+ }
}
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);
+ 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)
{
@@ -790,16 +923,14 @@ public class AlignFrame
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();
@@ -809,33 +940,50 @@ public class AlignFrame
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);
+ 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)
+ if (reply == JOptionPane.YES_OPTION)
{
omitHidden = viewport.getViewAsString(false);
}
@@ -843,27 +991,24 @@ public class AlignFrame
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,
- omitHidden, viewport.colSel));
+ 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(alignPanel,
- 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)
@@ -873,8 +1018,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void createPNG(File f)
{
@@ -883,15 +1029,15 @@ public class AlignFrame
/**
* 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();
@@ -900,12 +1046,13 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void printMenuItem_actionPerformed(ActionEvent e)
{
- //Putting in a thread avoids Swing painting problems
+ // Putting in a thread avoids Swing painting problems
PrintThread thread = new PrintThread(alignPanel);
thread.start();
}
@@ -915,24 +1062,20 @@ public class AlignFrame
new AnnotationExporter().exportFeatures(alignPanel);
}
-
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(
- alignPanel,
- viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
- viewport.alignment.getGroups(),
- ((Alignment)viewport.alignment).alignmentProperties
- );
+ 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");
@@ -948,71 +1091,81 @@ public class AlignFrame
}
-
/**
- * 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);
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(ap.seqPanel, null);
- PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(ap);
- ap.av.alignment = null;
+ // 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);
- viewport.alignment = null;
- 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!
@@ -1046,73 +1199,79 @@ public class AlignFrame
}
}
-
public void addHistoryItem(CommandI command)
{
- if(command.getSize()>0)
+ if (command.getSize() > 0)
{
viewport.historyList.push(command);
viewport.redoList.clear();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
}
}
/**
- *
+ *
* @return alignment objects for all views
*/
AlignmentI[] getViewAlignments()
{
- if (alignPanels!=null)
+ if (alignPanels != null)
{
Enumeration e = alignPanels.elements();
AlignmentI[] als = new AlignmentI[alignPanels.size()];
- for (int i=0; e.hasMoreElements(); i++)
+ for (int i = 0; e.hasMoreElements(); i++)
{
als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
}
return als;
}
- if (viewport!=null)
+ if (viewport != null)
{
- return new AlignmentI[] { viewport.alignment };
+ return new AlignmentI[]
+ { viewport.alignment };
}
return null;
}
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.historyList.empty())
return;
- CommandI command = (CommandI)viewport.historyList.pop();
+ CommandI command = (CommandI) viewport.historyList.pop();
viewport.redoList.push(command);
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.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
+ 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;
}
@@ -1124,36 +1283,37 @@ public class AlignFrame
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.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
+ 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;
}
}
@@ -1162,8 +1322,8 @@ public class AlignFrame
if (originalSource == null)
{
- //The original view is closed, we must validate
- //the current view against the closed view first
+ // The original view is closed, we must validate
+ // the current view against the closed view first
if (al != null)
{
PaintRefresher.validateSequences(al, viewport.alignment);
@@ -1177,8 +1337,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param up DOCUMENT ME!
+ *
+ * @param up
+ * DOCUMENT ME!
*/
public void moveSelectedSequences(boolean up)
{
@@ -1237,25 +1398,23 @@ public class AlignFrame
alignPanel.paintAlignment(true);
}
-
-
-
synchronized void slideSequences(boolean right, int size)
{
Vector sg = new Vector();
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
+ {
+ sg.addElement(viewport.alignment
+ .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport.alignment
+ .getHeight())
{
- sg.addElement(viewport.alignment.getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.hiddenRepSequences);
}
- else if(viewport.getSelectionGroup()!=null
- && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
- {
- sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
- }
- if(sg.size()<1)
+ if (sg.size() < 1)
{
return;
}
@@ -1264,8 +1423,8 @@ public class AlignFrame
for (int i = 0; i < viewport.alignment.getHeight(); i++)
{
- if(!sg.contains(viewport.alignment.getSequenceAt(i)))
- invertGroup.add(viewport.alignment.getSequenceAt(i));
+ if (!sg.contains(viewport.alignment.getSequenceAt(i)))
+ invertGroup.add(viewport.alignment.getSequenceAt(i));
}
SequenceI[] seqs1 = new SequenceI[sg.size()];
@@ -1278,15 +1437,11 @@ public class AlignFrame
SlideSequencesCommand ssc;
if (right)
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs2, seqs1, size,
- viewport.getGapCharacter()
- );
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+ size, viewport.getGapCharacter());
else
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs1, seqs2, size,
- viewport.getGapCharacter()
- );
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+ size, viewport.getGapCharacter());
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
@@ -1299,7 +1454,7 @@ public class AlignFrame
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor( -size, 0);
+ alignPanel.seqPanel.moveCursor(-size, 0);
else
groupAdjustment = -size;
}
@@ -1307,33 +1462,31 @@ public class AlignFrame
if (groupAdjustment != 0)
{
viewport.getSelectionGroup().setStartRes(
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
viewport.getSelectionGroup().setEndRes(
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
-
boolean appendHistoryItem = false;
- if(viewport.historyList!=null
- && viewport.historyList.size()>0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ if (viewport.historyList != null && viewport.historyList.size() > 0
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)
{
- appendHistoryItem = ssc.appendSlideCommand(
- (SlideSequencesCommand)viewport.historyList.peek())
- ;
+ appendHistoryItem = ssc
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .peek());
}
- if(!appendHistoryItem)
+ if (!appendHistoryItem)
addHistoryItem(ssc);
repaint();
}
-
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void copy_actionPerformed(ActionEvent e)
{
@@ -1342,8 +1495,9 @@ public class AlignFrame
{
return;
}
- // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
- 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)
@@ -1351,72 +1505,53 @@ public class AlignFrame
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
{
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);
+ // 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)
+ 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});
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
Desktop.jalviewClipboard = new Object[]
- {
- seqs,
- viewport.alignment.getDataset(),
- hiddenColumns};
- statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
+ { 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)
{
@@ -1425,8 +1560,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void pasteThis_actionPerformed(ActionEvent e)
{
@@ -1434,13 +1570,14 @@ public class AlignFrame
}
/**
- * 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;
+ boolean externalPaste = true;
try
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -1462,23 +1599,9 @@ public class AlignFrame
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;
}
@@ -1486,56 +1609,58 @@ public class AlignFrame
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>>This is a fix for the moment, until a better solution is found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
-
- // 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);
-
- }
-
-
- }
- catch (Exception ex)
+ }
+ 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)
+ {
+
+ // 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");
+
+ 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());
+
+ // 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);
+
+ }
+
+ } 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)
{
@@ -1714,8 +1852,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -1734,46 +1873,38 @@ public class AlignFrame
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);
- }
-
-
- SequenceI [] cut = new SequenceI[seqs.size()];
- for(int i=0; i 0)
{
- if(trimLeft)
+ if (trimLeft)
{
column = colSel.getMin();
}
@@ -1905,43 +2041,35 @@ public class AlignFrame
column = colSel.getMax();
}
- SequenceI [] seqs;
- if(viewport.getSelectionGroup()!=null)
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ 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);
@@ -1951,32 +2079,33 @@ public class AlignFrame
{
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(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
@@ -1985,46 +2114,44 @@ public class AlignFrame
seqs = viewport.alignment.getSequencesArray();
}
-
- RemoveGapColCommand removeGapCols =
- new RemoveGapColCommand("Remove Gapped Columns",
- seqs,
- start, end,
- viewport.alignment);
+ 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(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
@@ -2033,41 +2160,49 @@ public class AlignFrame
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.alignment));
+ 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)
{
@@ -2076,8 +2211,8 @@ public class AlignFrame
public void newView_actionPerformed(ActionEvent e)
{
- AlignmentPanel newap =
- new Jalview2XML().copyAlignPanel(alignPanel, true);
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
+ true);
newap.av.gatherViewsHere = false;
@@ -2090,33 +2225,33 @@ public class AlignFrame
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 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;
+
+ }
+ viewport.expandColSelection(sg, true);
+ // 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 (viewport.colSel.getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ {
+ viewport.selectionGroup = sg;
+ }
+ }
+ else if (!hide)
+ {
+ showAllColumns_actionPerformed(null);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
+ * event.ActionEvent)
+ */
+ public void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ toggleHiddenRegions(false, false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ public void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ public void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
@@ -2223,8 +2488,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void scaleAbove_actionPerformed(ActionEvent e)
{
@@ -2234,8 +2500,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void scaleLeft_actionPerformed(ActionEvent e)
{
@@ -2245,8 +2512,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void scaleRight_actionPerformed(ActionEvent e)
{
@@ -2256,8 +2524,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
@@ -2267,8 +2536,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
@@ -2278,8 +2548,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
@@ -2287,22 +2558,29 @@ public class AlignFrame
alignPanel.paintAlignment(true);
}
-
public FeatureSettings featureSettings;
+
public void featureSettings_actionPerformed(ActionEvent e)
{
- if(featureSettings !=null )
+ if (featureSettings != null)
{
featureSettings.close();
featureSettings = null;
}
+ if (!showSeqFeatures.isSelected())
+ {
+ // make sure features are actually displayed
+ showSeqFeatures.setSelected(true);
+ showSeqFeatures_actionPerformed(null);
+ }
featureSettings = new FeatureSettings(this);
}
/**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ * Set or clear 'Show Sequence Features'
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
@@ -2315,9 +2593,33 @@ public class AlignFrame
}
/**
+ * 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)
{
@@ -2327,67 +2629,72 @@ public class AlignFrame
public void alignmentProperties()
{
- JEditorPane editPane = new JEditorPane("text/html","");
+ JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
StringBuffer contents = new StringBuffer("");
- float avg = 0;
- int min=Integer.MAX_VALUE, max=0;
- for(int i=0; imax)
+ if (size > max)
max = size;
- if(sizeSequences: "+ viewport.alignment.getHeight());
- contents.append("
Minimum Sequence Length: "+min);
- contents.append("
Maximum Sequence Length: "+max);
- contents.append("
Average Length: "+(int)avg);
+ contents.append("
Sequences: " + viewport.alignment.getHeight());
+ contents.append("
Minimum Sequence Length: " + min);
+ contents.append("
Maximum Sequence Length: " + max);
+ contents.append("
Average Length: " + (int) avg);
- if (((Alignment)viewport.alignment).getProperties() != null)
+ if (((Alignment) viewport.alignment).getProperties() != null)
{
- Hashtable props = ((Alignment)viewport.alignment).getProperties();
+ Hashtable props = ((Alignment) viewport.alignment).getProperties();
Enumeration en = props.keys();
contents.append("
");
- while(en.hasMoreElements())
+ while (en.hasMoreElements())
{
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)
+ int pos = 0, npos;
+ do
+ {
+ npos = vals.indexOf("\n", pos);
+ if (npos == -1)
{
val.append(vals.substring(pos));
- } else {
+ }
+ else
+ {
val.append(vals.substring(pos, npos));
val.append("
");
}
- pos = npos+1;
- } while (npos!=-1);
- contents.append(""+key+" | "+val+" |
");
+ pos = npos + 1;
+ } while (npos != -1);
+ contents
+ .append("" + key + " | " + val + " |
");
}
contents.append("
");
}
- editPane.setText(contents.toString()+"");
+ editPane.setText(contents.toString() + "