X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=f5a14949410c5a03ad721f035ba0df2712c310ad;hb=50ad147ba0eb763fae29b364c80632abc1155e9c;hp=ae814c19943ded422aa2191bbb3403741ad52e3e;hpb=dcf795defdc686708f6b5a00f9089855a68a7733;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ae814c1..f5a1494 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,19 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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;
@@ -28,6 +28,7 @@ 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.*;
@@ -39,49 +40,113 @@ 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();
- /** 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)
+ 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,
+ 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);
@@ -96,8 +161,11 @@ 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)
{
@@ -106,22 +174,23 @@ public class AlignFrame
addAlignmentPanel(ap, false);
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"))
{
@@ -134,18 +203,19 @@ public class AlignFrame
if (Desktop.desktop != null)
{
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
addServiceListeners();
setGUINucleotide(viewport.alignment.isNucleotide());
}
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);
}
@@ -154,6 +224,15 @@ public class AlignFrame
}
+ /**
+ * 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;
@@ -168,219 +247,225 @@ public class AlignFrame
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
- && evt.getKeyCode() >= KeyEvent.VK_0
- && evt.getKeyCode() <= KeyEvent.VK_9)
- {
+ && ((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);
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed(null);
- break;
+ break;
- case KeyEvent.VK_DOWN:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, 1);
- }
- else
- {
- moveSelectedSequences(false);
- }
- break;
+ case KeyEvent.VK_DOWN:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(false);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, 1);
+ break;
- case KeyEvent.VK_UP:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, -1);
- }
- else
- {
- moveSelectedSequences(true);
- }
- break;
+ case KeyEvent.VK_UP:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ moveSelectedSequences(true);
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(0, -1);
- case KeyEvent.VK_LEFT:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor( -1, 0);
- }
- break;
+ break;
- case KeyEvent.VK_RIGHT:
- 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_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_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ 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_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_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_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
+ 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_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_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_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ 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_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
- javax.help.HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
- hb.setDisplayed(true);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- break
- ;
- case KeyEvent.VK_H:
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText("Keyboard editing mode is "
+ + (viewport.cursorMode ? "on" : "off"));
+ if (viewport.cursorMode)
{
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ alignPanel.seqPanel.seqCanvas.repaint();
+ break;
- boolean hide = false;
+ 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();
- 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);
- }
- }
+ boolean hide = false;
- 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)
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (toggleSeqs)
+ {
+ if (sg != null
+ && sg.getSize() != viewport.alignment.getHeight())
{
- alignPanel.scrollUp(true);
+ hideSelSequences_actionPerformed(null);
+ hide = true;
}
- else
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
{
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ showAllSeqs_actionPerformed(null);
}
- break;
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
{
- alignPanel.scrollUp(false);
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ {
+ viewport.selectionGroup = sg;
+ }
}
- else
+ else if (!hide)
{
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ showAllColumns_actionPerformed(null);
}
- break;
+ }
+ 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;
@@ -442,31 +527,29 @@ 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);
- }
- ;
+ };
});
}
@@ -476,7 +559,7 @@ public class AlignFrame
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
- //Remember AlignFrame always starts as protein
+ // Remember AlignFrame always starts as protein
if (!nucleotide)
{
calculateMenu.remove(calculateMenu.getItemCount() - 2);
@@ -484,9 +567,21 @@ public class AlignFrame
}
/**
- * 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)
{
@@ -496,6 +591,7 @@ 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);
@@ -505,17 +601,27 @@ public class AlignFrame
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
- setColourSelected(ColourSchemeProperty.
- getColourName(av.getGlobalColourScheme()));
+ 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;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
public void setProgressBar(String message, long id)
{
if (progressBars == null)
@@ -553,12 +659,26 @@ public class AlignFrame
progressBars.put(new Long(id), progressPanel);
}
-
+ // update GUI
+ setMenusForViewport();
validate();
}
+ /**
+ *
+ * @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()
{
@@ -589,24 +709,23 @@ public class AlignFrame
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
{
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";
+ String protocol = fileName.startsWith("http:") ? "URL" : "File";
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
else
@@ -615,8 +734,8 @@ public class AlignFrame
FileLoader loader = new FileLoader();
String protocol = fileName.startsWith("http:") ? "URL" : "File";
- AlignFrame newframe =
- loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
+ AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
+ protocol, currentFileFormat);
newframe.setBounds(bounds);
@@ -638,9 +757,9 @@ public class AlignFrame
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
- || currentFileFormat == null
- || fileName.startsWith("http")
- )
+ || (currentFileFormat == null
+ || !jalview.io.FormatAdapter.isValidIOFormat(currentFileFormat, true))
+ || fileName.startsWith("http"))
{
saveAs_actionPerformed(null);
}
@@ -652,19 +771,17 @@ public class AlignFrame
/**
* 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");
@@ -678,9 +795,8 @@ public class AlignFrame
if (currentFileFormat == null)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "You must select a file format before saving!",
- "File format not specified",
- JOptionPane.WARNING_MESSAGE);
+ "You must select a file format before saving!",
+ "File format not specified", JOptionPane.WARNING_MESSAGE);
value = chooser.showSaveDialog(this);
return;
}
@@ -688,10 +804,14 @@ public class AlignFrame
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);
}
}
@@ -706,40 +826,52 @@ 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))
+ {
+ // JBPNote need to have a raise_gui flag here
+ JOptionPane.showInternalMessageDialog(this, "Cannot save file "
+ + fileName + " using format " + format,
+ "Alignment output format not supported",
+ JOptionPane.WARNING_MESSAGE);
+ saveAs_actionPerformed(null);
+ 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)
{
@@ -750,16 +882,14 @@ 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();
@@ -769,10 +899,8 @@ 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;
@@ -780,8 +908,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void outputText_actionPerformed(ActionEvent e)
{
@@ -789,11 +918,14 @@ public class AlignFrame
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)
{
@@ -803,26 +935,24 @@ 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.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)
@@ -832,8 +962,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void createPNG(File f)
{
@@ -842,8 +973,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void createEPS(File f)
{
@@ -858,12 +990,13 @@ 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();
}
@@ -875,19 +1008,18 @@ public class AlignFrame
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(
- alignPanel,
- viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
- viewport.alignment.getGroups()
- );
+ 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");
@@ -904,9 +1036,10 @@ 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)
{
@@ -924,31 +1057,21 @@ public class AlignFrame
for (int i = 0; i < alignPanels.size(); i++)
{
AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ jalview.structure.StructureSelectionManager ssm =
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager();
+ ssm.removeStructureViewerListener(ap.seqPanel, null);
+ ssm.removeSelectionListener(ap.seqPanel);
PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
PaintRefresher.RemoveComponent(ap);
+ ap.av.alignment = null;
}
}
else
{
- int index = tabbedPane.getSelectedIndex();
-
- alignPanels.removeElement(alignPanel);
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
- PaintRefresher.RemoveComponent(alignPanel);
- alignPanel = null;
+ closeView(alignPanel);
viewport = null;
-
- tabbedPane.removeTabAt(index);
- tabbedPane.validate();
-
- if (index == tabbedPane.getTabCount())
- {
- index--;
- }
-
- this.tabSelectionChanged(index);
}
}
@@ -956,13 +1079,40 @@ public class AlignFrame
{
this.setClosed(true);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
+ public void closeView(AlignmentPanel alignPanel2)
+ {
+ int index = tabbedPane.getSelectedIndex();
+ int closedindex = tabbedPane.indexOfComponent(alignPanel2);
+ alignPanels.removeElement(alignPanel2);
+ PaintRefresher.RemoveComponent(alignPanel2.seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(alignPanel2.idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(alignPanel2);
+ alignPanel2.av.alignment = null;
+
+ if (viewport == alignPanel2.av)
+ {
+ viewport = null;
+ }
+ 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!
*/
@@ -1007,15 +1157,42 @@ public class AlignFrame
}
/**
+ *
+ * @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)
{
+ 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();
@@ -1023,16 +1200,16 @@ public class AlignFrame
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)
{
@@ -1043,7 +1220,7 @@ public class AlignFrame
CommandI command = (CommandI) viewport.redoList.pop();
viewport.historyList.push(command);
- command.doCommand();
+ command.doCommand(getViewAlignments());
AlignViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
@@ -1051,33 +1228,32 @@ public class AlignFrame
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
+ // 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;
}
}
@@ -1086,8 +1262,8 @@ 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);
@@ -1101,8 +1277,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param up DOCUMENT ME!
+ *
+ * @param up
+ * DOCUMENT ME!
*/
public void moveSelectedSequences(boolean up)
{
@@ -1158,13 +1335,98 @@ public class AlignFrame
}
}
- 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)
{
@@ -1173,7 +1435,8 @@ public class AlignFrame
{
return;
}
-
+ // TODO: preserve the ordering of displayed alignment annotation in any
+ // internal paste (particularly sequence associated annotation)
SequenceI[] seqs = viewport.getSelectionAsNewSequence();
String[] omitHidden = null;
@@ -1182,40 +1445,24 @@ 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);
-
- Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(ss, Desktop.instance);
- }
- catch (OutOfMemoryError er)
+ // 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;
}
@@ -1224,30 +1471,27 @@ public class AlignFrame
{
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};
+ { 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)
{
@@ -1256,8 +1500,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void pasteThis_actionPerformed(ActionEvent e)
{
@@ -1265,12 +1510,14 @@ 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;
try
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -1292,88 +1539,130 @@ 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;
}
SequenceI[] sequences;
+ boolean annotationAdded = false;
+ AlignmentI alignment = null;
if (Desktop.jalviewClipboard != null)
{
- // The clipboard was filled from within Jalview, we must use the sequences
+ // The clipboard was filled from within Jalview, we must use the
+ // sequences
// And dataset from the copied alignment
- sequences = (SequenceI[]) Desktop.jalviewClipboard[0];
+ 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
{
- sequences = new FormatAdapter().readFile(str, "Paste", format).
- getSequencesArray();
+ // parse the clipboard as an alignment.
+ alignment = new FormatAdapter().readFile(str, "Paste", format);
+ sequences = alignment.getSequencesArray();
}
- AlignmentI alignment = null;
+ int alwidth = 0;
if (newAlignment)
{
- alignment = new Alignment(sequences);
if (Desktop.jalviewClipboard != null)
{
- alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
+ // 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());
-
- alignment.addSequence(newseqs[i]);
+ 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);
+ }
+ }
}
-
- /*
- //ADD HISTORY ITEM
- */
- addHistoryItem(new EditCommand(
- "Add sequences",
- EditCommand.PASTE,
- newseqs,
- 0,
- alignment.getWidth(),
- alignment)
- );
-
- viewport.setEndSeq(alignment.getHeight());
- alignment.getWidth();
- viewport.firePropertyChange("alignment", null, alignment.getSequences());
}
-
+ 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++)
{
@@ -1381,34 +1670,67 @@ public class AlignFrame
{
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);
+ 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);
}
-
- alignPanel.annotationPanel.adjustPanelHeight();
}
}
+ if (!newAlignment)
+ {
- 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);
+ AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
- if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null)
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
{
Vector hc = (Vector) Desktop.jalviewClipboard[2];
for (int i = 0; i < hc.size(); i++)
@@ -1418,26 +1740,36 @@ public class AlignFrame
}
}
- //>>>This is a fix for the moment, until a better solution is found!!<<<
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ // >>>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"))
+ // TODO: maintain provenance of an alignment, rather than just make the
+ // title a concatenation of operations.
+ if (!externalPaste)
{
- newtitle = title;
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
}
else
{
- newtitle = newtitle.concat("- from " + title);
+ newtitle = new String("Pasted sequences");
}
Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ DEFAULT_HEIGHT);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
System.out.println("Exception whilst pasting: " + ex);
@@ -1448,8 +1780,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void cut_actionPerformed(ActionEvent e)
{
@@ -1459,8 +1792,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -1483,7 +1817,7 @@ public class AlignFrame
if (sg.getSize() == viewport.alignment.getHeight())
{
viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
+ sg.getEndRes() + 1);
}
SequenceI[] cut = new SequenceI[seqs.size()];
@@ -1493,28 +1827,24 @@ public class AlignFrame
}
/*
- //ADD HISTORY ITEM
+ * //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences",
- EditCommand.CUT,
- cut,
- sg.getStartRes(),
- sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.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)
{
}
}
@@ -1522,8 +1852,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void deleteGroups_actionPerformed(ActionEvent e)
{
@@ -1531,34 +1862,36 @@ public class AlignFrame
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.repaint();
+ 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)
{
@@ -1572,14 +1905,15 @@ public class AlignFrame
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)
{
@@ -1592,27 +1926,27 @@ public class AlignFrame
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)
{
@@ -1621,8 +1955,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
@@ -1648,8 +1983,8 @@ public class AlignFrame
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
}
else
{
@@ -1660,23 +1995,17 @@ public class AlignFrame
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);
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,
+ viewport.alignment, viewport.colSel,
+ viewport.selectionGroup);
}
statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
@@ -1689,22 +2018,23 @@ 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)
{
@@ -1713,8 +2043,8 @@ public class AlignFrame
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();
}
@@ -1723,35 +2053,34 @@ 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.getColumnSelection().compensateForEdits(shifts);
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 removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
@@ -1760,8 +2089,8 @@ public class AlignFrame
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();
}
@@ -1770,41 +2099,40 @@ 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.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());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void findMenuItem_actionPerformed(ActionEvent e)
{
@@ -1813,8 +2141,10 @@ 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;
if (viewport.viewName == null)
{
@@ -1827,8 +2157,8 @@ public class AlignFrame
int index = Desktop.getViewCount(viewport.getSequenceSetId());
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++)
{
@@ -1849,7 +2179,7 @@ public class AlignFrame
newap.av.viewName = newViewName;
- addAlignmentPanel(newap, false);
+ addAlignmentPanel(newap, true);
if (alignPanels.size() == 2)
{
@@ -1870,8 +2200,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void font_actionPerformed(ActionEvent e)
{
@@ -1880,38 +2211,58 @@ public class AlignFrame
/**
* 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)
{
@@ -1936,13 +2287,13 @@ public class AlignFrame
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)
@@ -1953,71 +2304,78 @@ public class AlignFrame
/**
* 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)
@@ -2030,13 +2388,14 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @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();
@@ -2045,8 +2404,9 @@ public class AlignFrame
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
@@ -2054,10 +2414,74 @@ public class AlignFrame
alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
}
+ public void alignmentProperties()
+ {
+ 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; i < viewport.alignment.getHeight(); i++)
+ {
+ 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();
+
+ 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)
+ {
+ Hashtable props = ((Alignment) viewport.alignment).getProperties();
+ Enumeration en = props.keys();
+ contents.append("
" + key + " | " + val + " |
jalview.analysis.AlignmentSorter
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 jalview.analysis.AlignmentSorter
+ * 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++)
@@ -2810,19 +3352,19 @@ public class AlignFrame
{
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);
}
});
@@ -2831,58 +3373,57 @@ public class AlignFrame
}
/**
- * 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() > 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;
- if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() > 0))
+ if ((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() > 0))
{
seqs = viewport.getAlignmentView(true);
}
@@ -2890,27 +3431,29 @@ public class AlignFrame
{
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.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");
@@ -2921,21 +3464,23 @@ public class AlignFrame
{
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);
+ }
}
}
@@ -2945,32 +3490,39 @@ public class AlignFrame
}
public TreePanel ShowNewickTree(NewickFile nf, String title,
- AlignmentView input)
+ AlignmentView input)
{
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)
+ AlignmentView input, int w, int h, int x, int y)
{
TreePanel tp = null;
@@ -2980,10 +3532,7 @@ public class AlignFrame
if (nf.getTree() != null)
{
- tp = new TreePanel(alignPanel,
- "FromFile",
- title,
- nf, input);
+ tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
tp.setSize(w, h);
@@ -2994,8 +3543,7 @@ public class AlignFrame
Desktop.addInternalFrame(tp, title, w, h);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -3005,61 +3553,42 @@ public class AlignFrame
/**
* 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);
}
@@ -3069,183 +3598,348 @@ public class AlignFrame
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)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty("LAST_DIRECTORY"));
+ /**
+ * empty the web service menu and add any ad-hoc functions not dynamically
+ * discovered.
+ *
+ */
+ private void resetWebServiceMenu()
+ {
+ webService.removeAll();
+ // Temporary hack - DBRef Fetcher always top level ws entry.
+ JMenuItem rfetch = new JMenuItem("Fetch DB References");
+ rfetch
+ .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ webService.add(rfetch);
+ rfetch.addActionListener(new ActionListener()
+ {
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Export to Vamsas file");
- chooser.setToolTipText("Export");
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
- int value = chooser.showSaveDialog(this);
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame)
+ .fetchDBRefs(false);
+ }
+ }).start();
- 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);
- }
- }*/
+ }
+ });
+ }
+ /*
+ * 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);
+ }
+ else
+ {
+ showProducts.setEnabled(false);
+ }
+ }
- public void showTranslation_actionPerformed(ActionEvent e)
+ /**
+ * 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)
{
- SequenceI[] selection = viewport.getSelectionAsNewSequence();
- String[] seqstring = viewport.getViewAsString(true);
+ boolean showp = false;
+ try
+ {
+ showProducts.removeAll();
+ final boolean dna = viewport.getAlignment().isNucleotide();
+ final Alignment ds = dataset;
+ String[] ptypes = 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()
+ {
- int s, sSize = selection.length;
- SequenceI[] newSeq = new SequenceI[sSize];
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: new thread for this call with vis-delay
+ af.showProductsFor(af.viewport.getSequenceSelection(), ds,
+ isRegSel, dna, source);
+ }
+
+ });
+ 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;
+ }
+ return showp;
+ }
- int res, resSize;
- StringBuffer protein;
- String seq;
- for (s = 0; s < sSize; s++)
+ protected void showProductsFor(SequenceI[] sel, Alignment ds,
+ boolean isRegSel, boolean dna, String source)
+ {
+ final boolean fisRegSel = isRegSel;
+ final boolean fdna = dna;
+ final String fsrc = source;
+ final AlignFrame ths = this;
+ final SequenceI[] fsel = sel;
+ Runnable foo = new Runnable()
{
- protein = new StringBuffer();
- seq = AlignSeq.extractGaps("-. ", seqstring[s]);
- resSize = seq.length();
- resSize -= resSize % 3;
- for (res = 0; res < resSize; res += 3)
+ public void run()
{
- String codon = seq.substring(res, res + 3);
- codon = codon.replace('U', 'T');
- String aa = ResidueProperties.codonTranslate(codon);
- if (aa == null)
+ final long sttime = System.currentTimeMillis();
+ ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+ try
{
- protein.append(viewport.getGapCharacter());
- }
- else if (aa.equals("STOP"))
+ 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)
{
- protein.append("X");
- }
- else
+ jalview.bin.Cache.log.error(
+ "Exception when finding crossreferences", e);
+ } catch (OutOfMemoryError e)
{
- protein.append(aa);
+ 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);
}
- newSeq[s] = new Sequence(selection[s].getName(),
- protein.toString());
- }
- AlignmentI al = new Alignment(newSeq);
- al.setDataset(null);
+ };
+ Thread frunner = new Thread(foo);
+ frunner.start();
+ }
- ////////////////////////////////
- // Copy annotations across
- jalview.datamodel.AlignmentAnnotation[] annotations
- = viewport.alignment.getAlignmentAnnotation();
- int a, aSize;
- if (annotations != null)
+ public boolean canShowTranslationProducts(SequenceI[] selection,
+ AlignmentI alignment)
+ {
+ // old way
+ try
{
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] == viewport.quality ||
- annotations[i] == viewport.conservation ||
- annotations[i] == viewport.consensus)
- {
- System.out.println("COPT HERE");
- continue;
- }
-
- aSize = viewport.alignment.getWidth() / 3;
- jalview.datamodel.Annotation[] anots =
- new jalview.datamodel.Annotation[aSize];
-
- for (a = 0; a < viewport.alignment.getWidth(); a++)
- {
- if (annotations[i].annotations[a] == null
- || annotations[i].annotations[a] == null)
- {
- continue;
- }
+ 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;
+ }
+ }
- 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);
- }
+ public void showProducts_actionPerformed(ActionEvent e)
+ {
+ // /////////////////////////////
+ // Collect Data to be translated/transferred
- jalview.datamodel.AlignmentAnnotation aa
- = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
- annotations[i].description, anots);
- al.addAnnotation(aa);
- }
+ 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);
}
+ }
- 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!
+ * 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)
+ featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
+ .getDataset(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().featureColours, false);
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -3254,23 +3948,27 @@ public class AlignFrame
{
viewport.showSequenceFeatures = true;
showSeqFeatures.setSelected(true);
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
return featuresFile;
}
public void dragEnter(DropTargetDragEvent evt)
- {}
+ {
+ }
public void dragExit(DropTargetEvent evt)
- {}
+ {
+ }
public void dragOver(DropTargetDragEvent evt)
- {}
+ {
+ }
public void dropActionChanged(DropTargetDragEvent evt)
- {}
+ {
+ }
public void drop(DropTargetDropEvent evt)
{
@@ -3280,13 +3978,13 @@ public class AlignFrame
try
{
DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
+ "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))
{
@@ -3295,9 +3993,7 @@ public class AlignFrame
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("#"))
@@ -3311,8 +4007,7 @@ public class AlignFrame
files.add(file);
}
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
@@ -3325,18 +4020,22 @@ public class AlignFrame
{
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
+ /**
+ * Attempt to load a "dropped" file: 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
@@ -3348,40 +4047,47 @@ public class AlignFrame
protocol = "URL";
}
- boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
- alignment, file, protocol);
+ 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();
}
@@ -3402,9 +4108,8 @@ public class AlignFrame
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)
{
@@ -3418,18 +4123,80 @@ public class AlignFrame
{
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)
+ * @see jalview.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