X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cc57961160589c5068f7df08939f9a45573cb9ef;hb=e3eb93bc131a0f088312fddde91b728dbebe40d4;hp=5fe31da9c53ba7073d94dcfa597f653a6cd23bac;hpb=3ad2eb8f66c9b73fb80b2c8e957e81b0e4969e3c;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5fe31da..cc57961 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -13,12 +13,13 @@
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
+ * along with this program; if not, write to the Free Softwarechang
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
package jalview.gui;
import java.beans.*;
+import java.io.*;
import java.util.*;
import java.awt.*;
@@ -26,7 +27,6 @@ import java.awt.datatransfer.*;
import java.awt.event.*;
import java.awt.print.*;
import javax.swing.*;
-import javax.swing.event.*;
import jalview.analysis.*;
import jalview.datamodel.*;
@@ -34,64 +34,270 @@ import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.ws.*;
+import java.awt.dnd.*;
+import org.biojava.dasobert.eventmodel.*;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
public class AlignFrame
- extends GAlignFrame
+ extends GAlignFrame implements DropTargetListener, FeatureListener
{
+ /** DOCUMENT ME!! */
public static final int NEW_WINDOW_WIDTH = 700;
+
+ /** DOCUMENT ME!! */
public static final int NEW_WINDOW_HEIGHT = 500;
- final AlignmentPanel alignPanel;
- final AlignViewport viewport;
- public String currentFileFormat = "Jalview";
+ AlignmentPanel alignPanel;
+ AlignViewport viewport;
+
+ /** DOCUMENT ME!! */
+ public String currentFileFormat = null;
Stack historyList = new Stack();
Stack redoList = new Stack();
private int treeCount = 0;
+
+ /**
+ * Creates a new AlignFrame object.
+ *
+ * @param al DOCUMENT ME!
+ */
public AlignFrame(AlignmentI al)
{
+
viewport = new AlignViewport(al);
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+
+ if(viewport.vconsensus==null)
+ {
+ //Out of memory calculating consensus.
+ BLOSUM62Colour.setEnabled(false);
+ PIDColour.setEnabled(false);
+ conservationMenuItem.setEnabled(false);
+ modifyConservation.setEnabled(false);
+ abovePIDThreshold.setEnabled(false);
+ modifyPID.setEnabled(false);
+ }
+
alignPanel = new AlignmentPanel(this, viewport);
- alignPanel.annotationPanel.adjustPanelHeight();
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
- annotationPanel.getPreferredSize());
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
- getPreferredSize());
- alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+ if(sortby.equals("Id"))
+ sortIDMenuItem_actionPerformed(null);
+ else if(sortby.equals("Pairwise Identity"))
+ sortPairwiseMenuItem_actionPerformed(null);
+
+ // remove(tabbedPane);
+ getContentPane().add(alignPanel, BorderLayout.CENTER);
+
+
+
+ // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
+
+ ///Dataset tab
+ /////////////////////////
+ if(al.getDataset()==null)
+ {
+ al.setDataset(null);
+ }
+ // AlignViewport ds = new AlignViewport(al.getDataset(), true);
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);
+ // tabbedPane.add("Dataset", dap);
+ // viewports.add(ds);
+ // alignPanels.add(dap);
+ /////////////////////////
+
+
+ viewport.addPropertyChangeListener(new PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ alignmentChanged();
+ }
+ }
+ });
+
+
+ if (Desktop.desktop != null)
+ {
+ addServiceListeners();
+ setGUINucleotide(al.isNucleotide());
+ }
+
+
+ if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+ {
+ wrapMenuItem.setSelected(true);
+ wrapMenuItem_actionPerformed(null);
+ }
+
+ }
+
+ public AlignViewport getViewport()
+ {
+ return viewport;
+ }
- addInternalFrameListener(new InternalFrameAdapter()
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */
+ private void addServiceListeners()
+ {
+ final java.beans.PropertyChangeListener thisListener;
+ // Do this once to get current state
+ BuildWebServiceMenu();
+ Desktop.discoverer.addPropertyChangeListener(
+ thisListener = new java.beans.PropertyChangeListener()
{
- public void internalFrameActivated(InternalFrameEvent evt)
+ public void propertyChange(PropertyChangeEvent evt)
{
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ // System.out.println("Discoverer property change.");
+ if (evt.getPropertyName().equals("services"))
{
- public void run()
- {
- alignPanel.requestFocus();
- }
- });
+ // System.out.println("Rebuilding web service menu");
+ BuildWebServiceMenu();
+ }
}
});
+ addInternalFrameListener(new javax.swing.event.
+ InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ // System.out.println("deregistering discoverer listener");
+ Desktop.discoverer.removePropertyChangeListener(thisListener);
+ closeMenuItem_actionPerformed(null);
+ }
+ ;
+ });
}
+ public void setGUINucleotide(boolean nucleotide)
+ {
+ showTranslation.setVisible( nucleotide );
+ //sequenceFeatures.setVisible(!nucleotide );
+ //featureSettings.setVisible( !nucleotide );
+ conservationMenuItem.setVisible( !nucleotide );
+ modifyConservation.setVisible( !nucleotide );
+
+ //Remember AlignFrame always starts as protein
+ if(!nucleotide)
+ {
+ calculateMenu.remove(calculateMenu.getItemCount()-2);
+ }
+ }
+
+ public void comeBackLater(FeatureEvent evt)
+ {}
+
+ public void newFeatures(FeatureEvent evt)
+ {
+ if (evt.getFeatures().length > 0)
+ {
+ alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
+ alignPanel.repaint();
+ if(featureSettings!=null)
+ featureSettings.setTableData();
+ }
+ }
+
+ Hashtable progressBars;
+ public void setProgressBar(String message, long id)
+ {
+ if(progressBars == null)
+ progressBars = new Hashtable();
+
+ JPanel progressPanel;
+ GridLayout layout = (GridLayout) statusPanel.getLayout();
+ if(progressBars.get( new Long(id) )!=null)
+ {
+ progressPanel = (JPanel)progressBars.get( new Long(id) );
+ statusPanel.remove(progressPanel);
+ progressBars.remove( progressPanel );
+ progressPanel = null;
+ if(message!=null)
+ statusBar.setText(message);
+
+ layout.setRows(layout.getRows() - 1);
+ }
+ else
+ {
+ progressPanel = new JPanel(new BorderLayout(10, 5));
+
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ layout.setRows(layout.getRows() + 1);
+ statusPanel.add(progressPanel);
+
+ progressBars.put(new Long(id), progressPanel);
+ }
+
+ validate();
+ }
+
+
+ /*
+ Added so Castor Mapping file can obtain Jalview Version
+ */
+ public String getVersion()
+ {
+ return jalview.bin.Cache.getProperty("VERSION");
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
+
+ public void fetchSequence_actionPerformed(ActionEvent e)
+ {
+ new SequenceFetcher(this);
+ }
+
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void saveAlignmentMenu_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"),
+ getProperty( "LAST_DIRECTORY"),
new String[]
- {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "jar"
- },
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
new String[]
- {
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
- }, currentFileFormat);
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+ currentFileFormat,
+ false);
+
- chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Alignment to file");
chooser.setToolTipText("Save");
@@ -100,73 +306,167 @@ public class AlignFrame
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- currentFileFormat = chooser.getSelectedFormat();
+ currentFileFormat = chooser.getSelectedFormat();
+
+ if (currentFileFormat == null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "You must select a file format before saving!",
+ "File format not specified",
+ JOptionPane.WARNING_MESSAGE);
+ value = chooser.showSaveDialog(this);
+ return;
+ }
+
jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
currentFileFormat);
- if (currentFileFormat.equals("Jalview"))
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+
+ saveAlignment(choice, currentFileFormat);
+ }
+ }
+
+ public boolean saveAlignment(String file, String format)
+ {
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ String shortName = title;
+
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)
{
- String shortName = title;
+ shortName = shortName.substring(shortName.lastIndexOf(
+ java.io.File.separatorChar) + 1);
+ }
- if (shortName.indexOf(java.io.File.separatorChar) > -1)
- {
- shortName = shortName.substring(shortName.lastIndexOf(
- java.io.File.separatorChar) + 1);
- }
+ new Jalview2XML().SaveAlignment(this, file, shortName);
- String choice = chooser.getSelectedFile().getPath();
- Jalview2XML.SaveAlignment(this, choice, shortName);
+ // USE Jalview2XML to save this file
+ return true;
+ }
+ else
+ {
- // USE Jalview2XML to save this file
- return;
+ 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);
+
+ if (reply == JOptionPane.YES_OPTION)
+ omitHidden = viewport.getViewAsString(false);
}
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ String output = new FormatAdapter().formatSequences(
+ format,
+ viewport.alignment.getSequencesArray(),
+ omitHidden);
- String output = FormatAdapter.formatSequences(currentFileFormat,
- viewport.getAlignment().getSequences());
+ if (output == null)
+ {
+ return false;
+ }
try
{
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
- FileWriter(
- choice));
- out.println(output);
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(file));
+
+ out.print(output);
out.close();
+ this.setTitle(file);
+ return true;
}
catch (Exception ex)
{
+ ex.printStackTrace();
}
}
+ return false;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void outputText_actionPerformed(ActionEvent e)
{
+ String [] omitHidden = null;
+
+ if(viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ +"\nDo you want to output only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if(reply==JOptionPane.YES_OPTION)
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+ }
+
CutAndPasteTransfer cap = new CutAndPasteTransfer();
Desktop.addInternalFrame(cap,
"Alignment output - " + e.getActionCommand(), 600,
500);
- cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
- viewport.getAlignment().
- getSequences()));
+
+
+ cap.setText(new FormatAdapter().formatSequences(
+ e.getActionCommand(),
+ viewport.alignment.getSequencesArray(),
+ omitHidden));
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(viewport);
+ new HTMLOutput(viewport,
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ }
+
+ public void createImageMap(File file, String image)
+ {
+ alignPanel.makePNGImageMap(file, image);
}
- protected void createPNG_actionPerformed(ActionEvent e)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void createPNG(File f)
{
- alignPanel.makePNG();
+ alignPanel.makePNG(f);
}
- protected void epsFile_actionPerformed(ActionEvent e)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void createEPS(File f)
{
- alignPanel.makeEPS();
+ alignPanel.makeEPS(f);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void printMenuItem_actionPerformed(ActionEvent e)
{
//Putting in a thread avoids Swing painting problems
@@ -174,10 +474,52 @@ public class AlignFrame
thread.start();
}
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportFeatures(alignPanel);
+ }
+
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportAnnotations(
+ alignPanel,
+ viewport.alignment.getAlignmentAnnotation()
+ );
+ }
+
+
+ public void associatedData_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ 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");
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(choice);
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void closeMenuItem_actionPerformed(ActionEvent e)
{
try
{
+ PaintRefresher.components.remove(viewport.alignment);
this.setClosed(true);
}
catch (Exception ex)
@@ -185,6 +527,9 @@ public class AlignFrame
}
}
+ /**
+ * DOCUMENT ME!
+ */
void updateEditMenuBar()
{
if (historyList.size() > 0)
@@ -214,79 +559,61 @@ public class AlignFrame
}
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param hi DOCUMENT ME!
+ */
public void addHistoryItem(HistoryItem hi)
{
historyList.push(hi);
updateEditMenuBar();
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
HistoryItem hi = (HistoryItem) historyList.pop();
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
HistoryItem.HIDE));
restoreHistoryItem(hi);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
HistoryItem hi = (HistoryItem) redoList.pop();
restoreHistoryItem(hi);
updateEditMenuBar();
- viewport.updateConsensus();
- alignPanel.repaint();
- alignPanel.repaint();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
// used by undo and redo
void restoreHistoryItem(HistoryItem hi)
{
- if (hi.getType() == HistoryItem.SORT)
- {
- for (int i = 0; i < hi.getSequences().size(); i++)
- {
- viewport.alignment.getSequences().setElementAt(hi.getSequences()
- .elementAt(i),
- i);
- }
- }
- else
- {
- for (int i = 0; i < hi.getSequences().size(); i++)
- {
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
- if (restore.getLength() == 0)
- {
- restore.setSequence(hi.getHidden().elementAt(i).toString());
- viewport.alignment.getSequences().insertElementAt(restore,
- hi.getAlignIndex(i));
- }
- else
- {
- restore.setSequence(hi.getHidden().elementAt(i).toString());
- }
- }
-
- if (hi.getType() == HistoryItem.PASTE)
- {
- for (int i = viewport.alignment.getHeight() - 1;
- i > (hi.getSequences().size() - 1); i--)
- {
- viewport.alignment.deleteSequence(i);
- }
- }
- }
+ hi.restore();
updateEditMenuBar();
- viewport.updateConsensus();
- viewport.updateConservation();
- alignPanel.repaint();
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param up DOCUMENT ME!
+ */
public void moveSelectedSequences(boolean up)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -302,14 +629,14 @@ public class AlignFrame
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.sequences.contains(seq))
+ if (!sg.getSequences(false).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.sequences.contains(temp))
+ if (sg.getSequences(false).contains(temp))
{
continue;
}
@@ -324,14 +651,14 @@ public class AlignFrame
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.sequences.contains(seq))
+ if (!sg.getSequences(false).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.sequences.contains(temp))
+ if (sg.getSequences(false).contains(temp))
{
continue;
}
@@ -344,6 +671,13 @@ public class AlignFrame
alignPanel.repaint();
}
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void copy_actionPerformed(ActionEvent e)
{
if (viewport.getSelectionGroup() == null)
@@ -351,56 +685,58 @@ public class AlignFrame
return;
}
- SequenceGroup sg = viewport.getSelectionGroup();
+ SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+ String[] omitHidden = null;
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- StringBuffer buffer = new StringBuffer();
-
- Hashtable orderedSeqs = new Hashtable();
-
- for (int i = 0; i < sg.getSize(); i++)
+ if (viewport.hasHiddenColumns)
{
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
- orderedSeqs.put(index + "", seq);
+ omitHidden = viewport.getViewAsString(true);
}
- int index = 0;
+ String output = new FormatAdapter().formatSequences(
+ "Fasta",
+ seqs,
+ omitHidden);
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI seq = null;
- while (seq == null)
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
+
+ Vector hiddenColumns = null;
+ if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)
+ {
+ hiddenColumns =new Vector();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ for(int i=0; i>>This is a fix for the moment, until a better solution is found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+ NEW_WINDOW_HEIGHT);
+
+ }
+
+
}
catch (Exception ex)
{
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: "+ex);
+ // could be anything being pasted in here
}
- // could be anything being pasted in here
+
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void cut_actionPerformed(ActionEvent e)
{
copy_actionPerformed(null);
delete_actionPerformed(null);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void delete_actionPerformed(ActionEvent e)
{
- boolean seqsdeleted = false;
if (viewport.getSelectionGroup() == null)
{
return;
}
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+
+
+ //Jalview no longer allows deletion of residues.
+ //Check here whether any residues are in selection area
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+ {
+ for (int i = 0; i < sg.sequences.size(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int j = sg.getStartRes();
+ do
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+ {
+ JOptionPane.showInternalMessageDialog(
+ Desktop.desktop, "Cannot delete residues from alignment!\n"
+ + "Try hiding columns instead.",
+ "Deletion of residues not permitted",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ j++;
+ }while(j<=sg.getEndRes());
+ }
+ }*/
+
+
addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
HistoryItem.HIDE));
- SequenceGroup sg = viewport.getSelectionGroup();
- for (int i = 0; i < sg.sequences.size(); i++)
+ for (int i = 0; i < sg.getSize(false); i++)
{
SequenceI seq = sg.getSequenceAt(i);
int index = viewport.getAlignment().findIndex(seq);
+
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize(false) == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
+
if (seq.getSequence().length() < 1)
{
- seqsdeleted = true;
viewport.getAlignment().deleteSequence(seq);
}
else
@@ -520,13 +980,10 @@ public class AlignFrame
viewport.setSelectionGroup(null);
viewport.alignment.deleteGroup(sg);
- if (seqsdeleted)
- {
- viewport.firePropertyChange("alignment", null,
+ viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
- }
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
+
if (viewport.getAlignment().getHeight() < 1)
{
@@ -538,12 +995,13 @@ public class AlignFrame
{
}
}
-
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.alignment.deleteAllGroups();
@@ -551,6 +1009,11 @@ public class AlignFrame
alignPanel.repaint();
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup();
@@ -561,25 +1024,45 @@ public class AlignFrame
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
- sg.setEndRes(viewport.alignment.getWidth());
+ sg.setEndRes(viewport.alignment.getWidth() - 1);
viewport.setSelectionGroup(sg);
PaintRefresher.Refresh(null, viewport.alignment);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
+ if(viewport.cursorMode)
+ {
+ alignPanel.seqPanel.keyboardNo1 = null;
+ alignPanel.seqPanel.keyboardNo2 = null;
+ }
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSelectionGroup(null);
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
+ alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.repaint();
PaintRefresher.Refresh(null, viewport.alignment);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
- if(sg==null)
+
+ if (sg == null)
{
selectAllSequenceMenuItem_actionPerformed(null);
+
return;
}
@@ -592,6 +1075,11 @@ public class AlignFrame
PaintRefresher.Refresh(null, viewport.alignment);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
ColumnSelection colSel = viewport.getColumnSelection();
@@ -622,10 +1110,15 @@ public class AlignFrame
}
}
- alignPanel.repaint();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
ColumnSelection colSel = viewport.getColumnSelection();
@@ -655,179 +1148,415 @@ public class AlignFrame
}
}
- alignPanel.repaint();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
addHistoryItem(new HistoryItem("Remove Gapped Columns",
viewport.alignment, HistoryItem.HIDE));
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+
viewport.getAlignment().removeGaps();
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
+
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
HistoryItem.HIDE));
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+
+
SequenceI current;
int jSize;
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ Vector seqs = null;
+
+ int start = 0;
+ int end = viewport.alignment.getWidth();
+
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSequences(true) != null
+ && viewport.getSelectionGroup().getSize(true) > 0)
{
- current = viewport.getAlignment().getSequenceAt(i);
+ seqs = viewport.getSelectionGroup().getSequences(true);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes()+1;
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequences();
+ }
+
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ current = (SequenceI) seqs.elementAt(i);
jSize = current.getLength();
- for (int j = 0; j < jSize; j++)
+ // Removing a range is much quicker than removing gaps
+ // one by one for long sequences
+ int j = start;
+ int rangeStart=-1, rangeEnd=-1;
+
+ do
{
if (jalview.util.Comparison.isGap(current.getCharAt(j)))
{
- current.deleteCharAt(j);
- j--;
- jSize--;
+ if(rangeStart==-1)
+ {
+ rangeStart = j;
+ rangeEnd = j+1;
+ }
+ else
+ {
+ rangeEnd++;
+ }
+ j++;
}
+ else
+ {
+ if(rangeStart>-1)
+ {
+ current.deleteChars(rangeStart, rangeEnd);
+ j-=rangeEnd-rangeStart;
+ jSize-=rangeEnd-rangeStart;
+ rangeStart = -1;
+ rangeEnd = -1;
+ }
+ else
+ j++;
+ }
+ }
+ while (j < end && j < jSize);
+ if(rangeStart>-1)
+ {
+ current.deleteChars(rangeStart, rangeEnd);
}
}
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
- public void padGapsMenuitem_actionPerformed(ActionEvent e)
- {
- addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
- HistoryItem.HIDE));
+ public void alignmentChanged()
+ {
+ if(viewport.padGaps)
+ viewport.getAlignment().padGaps();
- SequenceI current;
- int Width = viewport.getAlignment().getWidth() - 1;
+ if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
+ {
+ viewport.updateConsensus();
+ viewport.updateConservation();
+ }
+ resetAllColourSchemes();
+ if(alignPanel.overviewPanel!=null)
+ alignPanel.overviewPanel.updateOverviewImage();
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ viewport.alignment.adjustSequenceAnnotations();
+
+ alignPanel.repaint();
+ }
+
+ void resetAllColourSchemes()
+ {
+ ColourSchemeI cs = viewport.globalColourScheme;
+ if(cs!=null)
{
- current = viewport.getAlignment().getSequenceAt(i);
+ if (cs instanceof ClustalxColourScheme)
+ {
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+ resetClustalX(viewport.alignment.getSequences(),
+ viewport.alignment.getWidth());
+ }
- if (current.getLength() < Width)
+ cs.setConsensus(viewport.vconsensus);
+ if (cs.conservationApplied())
{
- current.insertCharAt(Width, viewport.getGapCharacter());
+ Alignment al = (Alignment) viewport.alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3,
+ al.getSequences(), 0,
+ al.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+
+ cs.setConservation(c);
}
}
- viewport.updateConservation();
- viewport.updateConsensus();
- alignPanel.repaint();
+ int s, sSize = viewport.alignment.getGroups().size();
+ for(s=0; s 0)) ||
+ (viewport.getSelectionGroup().getSize(false) < 4) &&
+ (viewport.getSelectionGroup().getSize(false) > 0)) ||
(viewport.getAlignment().getHeight() < 4))
{
JOptionPane.showInternalMessageDialog(this,
@@ -1202,57 +2094,81 @@ public class AlignFrame
return;
}
- try
- {
- PCAPanel pcaPanel = new PCAPanel(viewport, null);
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(pcaPanel);
- Desktop.addInternalFrame(frame, "Principal component analysis",
- 400, 400);
- }
- catch (java.lang.OutOfMemoryError ex)
+ new PCAPanel(viewport);
+ }
+
+
+ public void autoCalculate_actionPerformed(ActionEvent e)
+ {
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ if(viewport.autoCalculateConsensus)
{
- JOptionPane.showInternalMessageDialog(this,
- "Too many sequences selected\nfor Principal Component Analysis!!",
- "Out of memory",
- JOptionPane.WARNING_MESSAGE);
+ alignmentChanged();
}
}
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "PID", "Average distance tree using PID");
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ * @param pwType DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ */
void NewTreePanel(String type, String pwType, String title)
{
- final TreePanel tp;
+ TreePanel tp;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() > 3))
+ (viewport.getSelectionGroup().getSize(false) > 3))
{
int s = 0;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.sequences.size())
+ while (s < sg.getSize(false))
{
- if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
+ if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
sg.getEndRes())
{
JOptionPane.showMessageDialog(Desktop.desktop,
@@ -1267,9 +2183,7 @@ public class AlignFrame
}
title = title + " on region";
- tp = new TreePanel(viewport,
- viewport.getSelectionGroup().sequences, type, pwType,
- sg.getStartRes(), sg.getEndRes());
+ tp = new TreePanel(viewport, type, pwType);
}
else
{
@@ -1286,18 +2200,20 @@ public class AlignFrame
return;
}
- tp = new TreePanel(viewport,
- viewport.getAlignment().getSequences(), type, pwType,
- 0,
- viewport.alignment.getWidth());
+ tp = new TreePanel(viewport, type, pwType);
}
addTreeMenuItem(tp, title);
- viewport.setCurrentTree(tp.getTree());
Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param title DOCUMENT ME!
+ * @param order DOCUMENT ME!
+ */
public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
{
final JMenuItem item = new JMenuItem("by " + title);
@@ -1316,6 +2232,15 @@ public class AlignFrame
});
}
+ /**
+ * 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.
+ */
void addTreeMenuItem(final TreePanel treePanel, String title)
{
final JMenuItem item = new JMenuItem(title);
@@ -1356,73 +2281,25 @@ public class AlignFrame
}
;
});
- viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
- {
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (evt.getPropertyName().equals("alignment"))
- {
- treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
- treePanel.repaint();
- }
- }
- });
- }
-
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
- {
- // TODO:resolve which menu item was actually selected
- // Now, check we have enough sequences
- SequenceI[] msa = null;
-
- 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()];
-
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
- }
- 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);
- }
- }
- }
-
- if (msa != null)
- {
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
- title, msa, false, true);
- }
}
- public void ClustalRealign_actionPerformed(ActionEvent e)
+ /**
+ * Work out whether the whole set of sequences
+ * or just the selected set will be submitted for multiple alignment.
+ *
+ */
+ private SequenceI[] gatherSequencesForAlignment()
{
- // TODO:resolve which menu item was actually selected
// Now, check we have enough sequences
SequenceI[] msa = null;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() > 1))
+ (viewport.getSelectionGroup().getSize(false) > 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()];
+ msa = new SequenceI[sz = seqs.getSize(false)];
for (int i = 0; i < sz; i++)
{
@@ -1443,33 +2320,34 @@ public class AlignFrame
}
}
}
-
- if (msa != null)
- {
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
- title, msa, true, true);
- }
+ return msa;
}
- protected void jpred_actionPerformed(ActionEvent e)
+ /**
+ * 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).
+ */
+ SequenceI[] gatherSeqOrMsaForSecStrPrediction()
{
SequenceI seq = null;
SequenceI[] msa = null;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() > 0))
+ (viewport.getSelectionGroup().getSize(false) > 0))
{
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
SequenceGroup seqs = viewport.getSelectionGroup();
- if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
+ if ( (seqs.getSize(false) == 1) || !viewport.alignment.isAligned())
{
seq = (SequenceI) seqs.getSequenceAt(0);
}
else
{
int sz;
- msa = new SequenceI[sz = seqs.getSize()];
+ msa = new SequenceI[sz = seqs.getSize(false)];
for (int i = 0; i < sz; i++)
{
@@ -1495,63 +2373,26 @@ public class AlignFrame
}
}
}
-
if (msa != null)
{
- JPredClient ct = new JPredClient(title, msa);
- }
- else if (seq != null)
- {
- JPredClient ct = new JPredClient(title, seq);
- }
- else
- {
- System.err.print(
- "JALVIEW ERROR! - Unexpected JPred selection state!\n");
- }
- }
-
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
- {
- // TODO:resolve which menu item was actually selected
- // Now, check we have enough sequences
- SequenceI[] msa = null;
-
- 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()];
-
- for (int i = 0; i < sz; i++)
- {
- msa[i] = (SequenceI) seqs.getSequenceAt(i);
- }
+ return msa;
}
else
{
- Vector seqs = viewport.getAlignment().getSequences();
-
- if (seqs.size() > 1)
+ if (seq != null)
{
- msa = new SequenceI[seqs.size()];
-
- for (int i = 0; i < seqs.size(); i++)
- {
- msa[i] = (SequenceI) seqs.elementAt(i);
- }
+ return new SequenceI[]
+ {
+ seq};
}
}
-
- if (msa != null)
- {
- MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
- false, true);
- }
+ return null;
}
-
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
@@ -1573,7 +2414,7 @@ public class AlignFrame
{
jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
"File");
- viewport.setCurrentTree( ShowNewickTree(fin, choice).getTree() );
+ viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
}
catch (Exception ex)
{
@@ -1586,19 +2427,41 @@ public class AlignFrame
}
}
+
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
+ return ShowNewickTree(nf,title,600,500,4,5);
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nf DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
+ {
TreePanel tp = null;
+
try
{
nf.parse();
+
if (nf.getTree() != null)
{
tp = new TreePanel(viewport,
- viewport.getAlignment().getSequences(), nf,
- "FromFile",
- title);
- Desktop.addInternalFrame(tp, title, 600, 500);
+ "FromFile",
+ title,
+ nf);
+
+ tp.setSize(w,h);
+
+ if(x>0 && y>0)
+ tp.setLocation(x,y);
+
+
+ Desktop.addInternalFrame(tp, title, w, h);
addTreeMenuItem(tp, title);
}
}
@@ -1606,6 +2469,7 @@ public class AlignFrame
{
ex.printStackTrace();
}
+
return tp;
}
@@ -1631,4 +2495,377 @@ 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))
+ {
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
+ Vector wsmenu = new Vector();
+ if (msaws != null)
+ {
+ // Add any Multiple Sequence Alignment Services
+ final JMenu msawsmenu = new JMenu("Alignment");
+ final AlignFrame af = this;
+ 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)
+ {
+ SequenceI[] msa = gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(sh, title, msa,
+ false, true, viewport.getAlignment().getDataset(), af);
+
+ }
+
+ });
+ 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)
+ {
+ SequenceI[] msa = gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(sh, title, msa,
+ true, true, viewport.getAlignment().getDataset(), af);
+
+ }
+
+ });
+ msawsmenu.add(methodR);
+
+ }
+ }
+ wsmenu.add(msawsmenu);
+ }
+ if (secstrpr != null)
+ {
+ // Add any secondary structure prediction services
+ 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)
+ {
+ SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
+ if (msa.length == 1)
+ {
+ // Single Sequence prediction
+ new jalview.ws.JPredClient(sh,title, msa[0]);
+ }
+ else
+ {
+ if (msa.length > 1)
+ {
+ // Single Sequence prediction
+ jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
+ title, msa);
+ }
+ }
+ }
+ });
+ secstrmenu.add(method);
+ }
+ wsmenu.add(secstrmenu);
+ }
+ this.webService.removeAll();
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
+ {
+ webService.add( (JMenu) wsmenu.get(i));
+ }
+ }
+ else
+ {
+ this.webService.removeAll();
+ 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"));
+
+ 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);
+ }
+ }*/
+
+
+
+
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+ SequenceI [] selection = viewport.getSelectionAsNewSequence();
+ String [] seqstring = viewport.getViewAsString(true);
+
+ int s, sSize = selection.length;
+ SequenceI [] newSeq = new SequenceI[sSize];
+
+ int res, resSize;
+ StringBuffer protein;
+ String seq;
+ for(s=0; s