import java.awt.event.*;
import java.awt.print.*;
import javax.swing.*;
+import javax.swing.event.MenuEvent;
import jalview.analysis.*;
import jalview.commands.*;
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;
}
setMenusFromViewport(viewport);
-
+ buildSortByAnnotationScoresMenu();
if (viewport.wrapAlignment)
{
wrapMenuItem_actionPerformed(null);
showTranslation.setVisible( nucleotide );
conservationMenuItem.setEnabled( !nucleotide );
modifyConservation.setEnabled( !nucleotide );
-
+
//Remember AlignFrame always starts as protein
if(!nucleotide)
{
calculateMenu.remove(calculateMenu.getItemCount()-2);
}
+ setShowProductsEnabled();
}
+
+
/**
* Need to call this method when tabs are selected for multiple views,
* or when loading from Jalview2XML.java
{
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" },
+ jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
+ jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
currentFileFormat,
false);
currentFileFormat);
jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
-
+ if (currentFileFormat.indexOf(" ")>-1)
+ {
+ currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" "));
+ }
saveAlignment(fileName, currentFileFormat);
}
}
omitHidden = viewport.getViewAsString(false);
}
}
+ FormatAdapter f = new FormatAdapter();
- String output = new FormatAdapter().formatSequences(
+ String output = f.formatSequences(
format,
- viewport.alignment.getSequencesArray(),
- omitHidden);
+ (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future
+ omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
if (output == null)
{
cap.setText(new FormatAdapter().formatSequences(
e.getActionCommand(),
- viewport.alignment.getSequencesArray(),
- omitHidden));
+ viewport.alignment,
+ omitHidden, viewport.colSel));
}
/**
new AnnotationExporter().exportAnnotations(
alignPanel,
viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
- viewport.alignment.getGroups()
+ viewport.alignment.getGroups(),
+ ((Alignment)viewport.alignment).alignmentProperties
);
}
}
}
-
-
+ /**
+ *
+ * @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!
*
*/
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();
CommandI command = (CommandI) viewport.redoList.pop();
viewport.historyList.push(command);
- command.doCommand();
+ command.doCommand(getViewAlignments());
AlignViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
{
return;
}
-
+ // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
SequenceI [] seqs = viewport.getSelectionAsNewSequence();
String[] omitHidden = null;
sequences = alignment.getSequencesArray();
}
+ int alwidth=0;
if (newAlignment)
{
// 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();
{
annotationAdded=true;
if (alann[i].sequenceRef==null && !alann[i].autoCalculated) {
- alignment.addAnnotation(new AlignmentAnnotation(alann[i]));
+ AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+ newann.padAnnotation(alwidth);
+ alignment.addAnnotation(newann);
}
}
}
{
annotationAdded=true;
sequences[i].getAnnotation()[a].adjustForAlignment();
+ sequences[i].getAnnotation()[a].padAnnotation(alwidth);
alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier
alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
}
-
-
}
}
if (!newAlignment) {
+
// propagate alignment changed.
viewport.setEndSeq(alignment.getHeight());
if (annotationAdded)
{
- alignPanel.annotationPanel.adjustPanelHeight();
+ // Duplicate sequence annotation in all views.
+ AlignmentI[] alview = this.getViewAlignments();
+ for (int i = 0; i < sequences.length; i++)
+ {
+ AlignmentAnnotation sann[] = sequences[i].getAnnotation();
+ if (sann == null)
+ continue;
+ for (int avnum=0;avnum<alview.length; avnum++)
+ {
+ if (alview[avnum]!=alignment)
+ {
+ // duplicate in a view other than the one with input focus
+ int avwidth = alview[avnum].getWidth()+1;
+ // this relies on sann being preserved after we
+ // modify the sequence's annotation array for each duplication
+ for (int a=0; a<sann.length; a++)
+ {
+ AlignmentAnnotation newann = new AlignmentAnnotation(sann[a]);
+ sequences[i].addAlignmentAnnotation(newann);
+ newann.padAnnotation(avwidth);
+ alview[avnum].addAnnotation(newann); // annotation was duplicated earlier
+ alview[avnum].setAnnotationIndex(newann, a);
+ }
+ }
+ }
+ }
+ buildSortByAnnotationScoresMenu();
}
viewport.firePropertyChange("alignment", null, alignment.getSequences());
+
} else {
AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
}
+ public void alignmentProperties()
+ {
+ JEditorPane editPane = new JEditorPane("text/html","");
+ editPane.setEditable(false);
+ StringBuffer contents = new StringBuffer("<html>");
+
+ float avg = 0;
+ int min=Integer.MAX_VALUE, max=0;
+ for(int i=0; i<viewport.alignment.getHeight(); i++)
+ {
+ 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("<br>Sequences: "+ viewport.alignment.getHeight());
+ contents.append("<br>Minimum Sequence Length: "+min);
+ contents.append("<br>Maximum Sequence Length: "+max);
+ contents.append("<br>Average Length: "+(int)avg);
+
+ if (((Alignment)viewport.alignment).getProperties() != null)
+ {
+ Hashtable props = ((Alignment)viewport.alignment).getProperties();
+ Enumeration en = props.keys();
+ contents.append("<br><br><table border=\"1\">");
+ while(en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ StringBuffer val = new StringBuffer();
+ String vals = props.get(key).toString();
+ int pos=0, npos;
+ do {
+ npos = vals.indexOf("\n",pos);
+ if (npos==-1)
+ {
+ val.append(vals.substring(pos));
+ } else {
+ val.append(vals.substring(pos, npos));
+ val.append("<br>");
+ }
+ pos = npos+1;
+ } while (npos!=-1);
+ contents.append("<tr><td>"+key+"</td><td>"+val+"</td></tr>");
+ }
+ contents.append("</table>");
+ }
+ editPane.setText(contents.toString()+"</html>");
+ JInternalFrame frame = new JInternalFrame();
+ frame.getContentPane().add(new JScrollPane(editPane));
+
+ Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
+ }
+
+
/**
* DOCUMENT ME!
*
alignPanel.paintAlignment(true);
}
-
/**
* DOCUMENT ME!
*
}
});
}
+ /**
+ * Add a new sort by annotation score menu item
+ * @param sort the menu to add the option to
+ * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
+ */
+ public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
+ {
+ final JMenuItem item = new JMenuItem(scoreLabel);
+ sort.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+ });
+ }
+ /**
+ * 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.
{
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,
+ fin = new jalview.io.NewickFile(choice,
"File");
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
}
catch (Exception ex)
{
JOptionPane.showMessageDialog(Desktop.desktop,
- "Problem reading tree file",
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);
+ }
}
}
{
ex.printStackTrace();
}
-
+
return tp;
}
*/
public void BuildWebServiceMenu()
{
+ // TODO: add support for context dependent disabling of services based on alignment and current selection
+ // TODO: refactor to allow list of AbstractName/Handler bindings to be stored or retrieved from elsewhere
+ // 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))
{
}
wsmenu.add(secstrmenu);
}
- this.webService.removeAll();
+ resetWebServiceMenu();
for (int i = 0, j = wsmenu.size(); i < j; 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.
+ }
+
+
+ /**
+ * 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 uniprot records for the alignment or the currently selected sequences");
+ webService.add(rfetch);
+ rfetch.addActionListener(new ActionListener() {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new jalview.ws.DBRefFetcher(
+ alignPanel.av.getSequenceSelection(),
+ alignPanel.alignFrame).fetchDBRefs(false);
+ }
+
+ });
}
/* public void vamsasStore_actionPerformed(ActionEvent e)
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);
+ }
+ }
+ /**
+ * search selection for sequence xRef products and build the
+ * show products menu.
+ * @param selection
+ * @param dataset
+ * @return true if showProducts menu should be enabled.
+ */
+ public boolean canShowProducts(SequenceI[] selection, boolean isRegionSelection, Alignment dataset)
+ {
+ boolean showp=false;
+ try {
+ showProducts.removeAll();
+ final boolean dna = viewport.getAlignment().isNucleotide();
+ final Alignment ds = dataset;
+ String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, dataset);
+ //Object[] prods = CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), selection, dataset, true);
+ final SequenceI[] sel = selection;
+ for (int t=0; ptypes!=null && t<ptypes.length; t++)
+ {
+ showp=true;
+ final boolean isRegSel = isRegionSelection;
+ final AlignFrame af = this;
+ final String source = ptypes[t];
+ JMenuItem xtype = new JMenuItem(ptypes[t]);
+ xtype.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: new thread for this call with vis-delay
+ af.showProductsFor(sel, 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;
+ }
+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() {
+ public void run()
+ {
+ final long sttime = System.currentTimeMillis();
+ ths.setProgressBar("Searching for sequences from "+fsrc, sttime);
+ try {
+ Alignment ds = ths.getViewport().alignment.getDataset(); // update our local dataset reference
+ Alignment prods = CrossRef.findXrefSequences(fsel, fdna, fsrc, ds);
+ if (prods!=null)
+ {
+ SequenceI[] sprods = new SequenceI[prods.getHeight()];
+ for (int s=0; s<sprods.length;s++)
+ {
+ sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+ if (ds.getSequences()==null || !ds.getSequences().contains(sprods[s].getDatasetSequence()))
+ ds.addSequence(sprods[s].getDatasetSequence());
+ sprods[s].updatePDBIds();
+ }
+ Alignment al = new Alignment(sprods);
+ AlignedCodonFrame[] cf = prods.getCodonFrames();
+ for (int s=0; cf!=null && s<cf.length; s++)
+ {
+ al.addCodonFrame(cf[s]);
+ cf[s] = null;
+ }
+ al.setDataset(ds);
+ AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ String newtitle =""+((fdna) ? "Proteins " : "Nucleotides ") + " for "+((fisRegSel) ? "selected region of " : "")
+ + getTitle();
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ } else {
+ System.err.println("No Sequences generated for xRef type "+fsrc);
+ }
+ }
+ catch (Exception e)
+ {
+ jalview.bin.Cache.log.error("Exception when finding crossreferences",e);
+ }
+ catch (Error e)
+ {
+ jalview.bin.Cache.log.error("Error when finding crossreferences",e);
+ }
+ ths.setProgressBar("Finished searching for sequences from "+fsrc, sttime);
+ }
+
+ };
+ Thread frunner = new Thread(foo);
+ frunner.start();
+ }
+public boolean canShowTranslationProducts(SequenceI[] selection, AlignmentI alignment)
+{
+ // old way
+ try {
+ return (jalview.analysis.Dna.canTranslate(selection, viewport.getViewAsVisibleContigs(true)));
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.warn("canTranslate threw an exception - please report to help@jalview.org",e);
+ return false;
+ }
+}
+
+public void showProducts_actionPerformed(ActionEvent e)
+{
+ ///////////////////////////////
+ // Collect Data to be translated/transferred
+
+ SequenceI [] selection = viewport.getSequenceSelection();
+ AlignmentI al = null;
+ try {
+ al = jalview.analysis.Dna.CdnaTranslate(selection, viewport.getViewAsVisibleContigs(true),
+ viewport.getGapCharacter(), viewport.getAlignment().getDataset());
+ } catch (Exception ex) {
+ al = null;
+ jalview.bin.Cache.log.debug("Exception during translation.",ex);
+ }
+ if (al==null)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+ "Translation Failed",
+ JOptionPane.WARNING_MESSAGE);
+ } else {
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+ DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+ }
+
public void showTranslation_actionPerformed(ActionEvent e)
{
///////////////////////////////
// Collect Data to be translated/transferred
- SequenceI [] selection = viewport.getSelectionAsNewSequence();
+ 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.alignment.getWidth(), viewport.getAlignment().getDataset());
} catch (Exception ex) {
al = null;
jalview.bin.Cache.log.debug("Exception during translation.",ex);
{
// (isAnnotation)
alignPanel.adjustAnnotationHeight();
+ buildSortByAnnotationScoresMenu();
}
}
{
return viewport;
}
+
+
+ /**
+ * Open the dialog for regex description parsing.
+ */
+ protected void extractScores_actionPerformed(ActionEvent e)
+ {
+ ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
+ if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ }
}
class PrintThread