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.
addKeyListener();
}
-
+ /**
+ * Change the filename and format for the alignment, and
+ * enable the 'reload' button functionality.
+ * @param file valid filename
+ * @param format format of file
+ */
public void setFileName(String file, String format)
{
fileName = file;
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
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);
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
*/
public void save_actionPerformed(ActionEvent e)
{
if(fileName==null
- || currentFileFormat==null
+ || (currentFileFormat==null || jalview.io.AppletFormatAdapter.isValidFormat(currentFileFormat, true))
|| fileName.startsWith("http")
)
{
{
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);
}
}
}
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)
omitHidden = viewport.getViewAsString(false);
}
}
-
- String output = new FormatAdapter().formatSequences(
+ FormatAdapter f = new FormatAdapter();
+ 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));
}
/**
}
/**
- * DOCUMENT ME!
+ * Paste contents of Jalview clipboard
*
- * @param newAlignment DOCUMENT ME!
+ * @param newAlignment true to paste to a new alignment, otherwise add to this.
*/
void paste(boolean newAlignment)
{
alignPanel.paintAlignment(true);
}
+ public void centreColumnLabels_actionPerformed(ActionEvent e)
+ {
+ viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+ alignPanel.paintAlignment(true);
+ }
+
/**
{
SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(),
- viewport.getAlignment().getSequenceAt(0));
+ viewport.getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.alignment));
alignPanel.paintAlignment(true);
public void actionPerformed(ActionEvent e)
{
SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
+ AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());//,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
alignPanel.paintAlignment(true);
}
* 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;
}
/**
- * Decides what is submitted to a secondary structure prediction service,
- * the currently selected sequence, or the currently selected alignment
+ * 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;
{
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: 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;
if (msaws != null)
{
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);
-
- }
-
- });
- 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);
-
- }
+ jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh);
+ impl.attachWSMenuEntry(msawsmenu, this);
+
}
wsmenu.add(msawsmenu);
}
{
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);
+ jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh);
+ impl.attachWSMenuEntry(secstrmenu, this);
}
wsmenu.add(secstrmenu);
}
+ 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++)
{
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 actionPerformed(ActionEvent e)
{
- new jalview.io.DBRefFetcher(
+ new jalview.ws.DBRefFetcher(
alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame).fetchDBRefs(false);
}
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)
{
///////////////////////////////
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);
}
/**
- * 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)
{
}
}
- // 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
{
String protocol = "File";
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,
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
viewport.getAlignment(),
0, false);
- alignPanel.adjustAnnotationHeight();
- alignPanel.paintAlignment(true);
- }
- else
+ 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)
{
new FileLoader().LoadFile(viewport, file, protocol, format);
+ } else {
+ alignPanel.paintAlignment(true);
+ }
}
}
- }
- else
+ if (isAnnotation)
{
- // (isAnnotation)
+
alignPanel.adjustAnnotationHeight();
buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true);
}
-
}
catch (Exception ex)
{
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)
+ if (pp.getScoresFromDescription("col", "score column ", "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", true)>0)
{
buildSortByAnnotationScoresMenu();
}
git://source.jalview.org / jalview.git / blobdiff