X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=15cbf01120e7eebd8a857cb6558fadf4f81a519d;hb=942de34caf73a7d61104783c8d278c32eaf6b65d;hp=ee2f7fd05fffa603850360c869b2bebbc09217c0;hpb=6f499ac9fb1c218b04b64e7343f365b664b0bf20;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ee2f7fd..15cbf01 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -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.*;
@@ -58,11 +59,17 @@ public class AlignFrame
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.
@@ -112,8 +119,6 @@ public class AlignFrame
void init()
{
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
-
if (viewport.conservation == null)
{
BLOSUM62Colour.setEnabled(false);
@@ -137,12 +142,13 @@ 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);
@@ -156,7 +162,12 @@ public class AlignFrame
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;
@@ -498,14 +509,17 @@ public class AlignFrame
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
@@ -519,6 +533,7 @@ 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);
@@ -580,10 +595,18 @@ public class AlignFrame
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
*/
@@ -668,7 +691,7 @@ public class AlignFrame
public void save_actionPerformed(ActionEvent e)
{
if(fileName==null
- || currentFileFormat==null
+ || (currentFileFormat==null || jalview.io.AppletFormatAdapter.isValidFormat(currentFileFormat, true))
|| fileName.startsWith("http")
)
{
@@ -689,10 +712,8 @@ public class AlignFrame
{
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);
@@ -722,7 +743,10 @@ public class AlignFrame
currentFileFormat);
jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
-
+ if (currentFileFormat.indexOf(" ")>-1)
+ {
+ currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" "));
+ }
saveAlignment(fileName, currentFileFormat);
}
}
@@ -749,8 +773,18 @@ public class AlignFrame
}
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)
@@ -766,11 +800,11 @@ public class AlignFrame
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)
{
@@ -841,8 +875,8 @@ public class AlignFrame
cap.setText(new FormatAdapter().formatSequences(
e.getActionCommand(),
- viewport.alignment.getSequencesArray(),
- omitHidden));
+ viewport.alignment,
+ omitHidden, viewport.colSel));
}
/**
@@ -912,7 +946,8 @@ public class AlignFrame
new AnnotationExporter().exportAnnotations(
alignPanel,
viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
- viewport.alignment.getGroups()
+ viewport.alignment.getGroups(),
+ ((Alignment)viewport.alignment).alignmentProperties
);
}
@@ -1048,8 +1083,28 @@ 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!
*
@@ -1057,9 +1112,11 @@ public class AlignFrame
*/
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();
@@ -1087,7 +1144,7 @@ public class AlignFrame
CommandI command = (CommandI) viewport.redoList.pop();
viewport.historyList.push(command);
- command.doCommand();
+ command.doCommand(getViewAlignments());
AlignViewport originalSource = getOriginatingSource(command);
updateEditMenuBar();
@@ -1310,7 +1367,7 @@ 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;
@@ -1402,9 +1459,9 @@ public class AlignFrame
}
/**
- * 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)
{
@@ -1474,10 +1531,11 @@ public class AlignFrame
sequences = alignment.getSequencesArray();
}
+ int alwidth=0;
if (newAlignment)
{
-
+
if (Desktop.jalviewClipboard != null)
{
// dataset is inherited
@@ -1488,12 +1546,14 @@ public class AlignFrame
// 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();
@@ -1501,10 +1561,10 @@ public class AlignFrame
// an existing alignment
Vector newDs = (importDs) ? new Vector() : null; // used to create
// minimum dataset set
-
+
for (int i = 0; i < sequences.length; i++)
{
- if (importDs)
+ if (importDs)
{
newDs.addElement(null);
}
@@ -1514,7 +1574,7 @@ public class AlignFrame
{
if (!newDs.contains(ds))
{
- newDs.setElementAt(ds, i);
+ newDs.setElementAt(ds, i);
ds = new Sequence(ds);
// update with new dataset sequence
sequences[i].setDatasetSequence(ds);
@@ -1545,7 +1605,9 @@ public class AlignFrame
{
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);
}
}
}
@@ -1572,21 +1634,48 @@ public class AlignFrame
{
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>>This is a fix for the moment, until a better solution is found!!<<<
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
-
+
// TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
if (!externalPaste) {
if (title.startsWith("Copied sequences"))
@@ -2101,6 +2190,12 @@ public class AlignFrame
alignPanel.paintAlignment(true);
}
+ public void centreColumnLabels_actionPerformed(ActionEvent e)
+ {
+ viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+ alignPanel.paintAlignment(true);
+ }
+
/**
@@ -2261,6 +2356,65 @@ 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; imax)
+ max = size;
+ if(sizeSequences: "+ viewport.alignment.getHeight());
+ contents.append("
Minimum Sequence Length: "+min);
+ contents.append("
Maximum Sequence Length: "+max);
+ contents.append("
Average Length: "+(int)avg);
+
+ if (((Alignment)viewport.alignment).getProperties() != null)
+ {
+ Hashtable props = ((Alignment)viewport.alignment).getProperties();
+ Enumeration en = props.keys();
+ contents.append("
");
+ 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("
");
+ }
+ pos = npos+1;
+ } while (npos!=-1);
+ contents.append(""+key+" | "+val+" |
");
+ }
+ contents.append("
");
+ }
+ editPane.setText(contents.toString()+"");
+ JInternalFrame frame = new JInternalFrame();
+ frame.getContentPane().add(new JScrollPane(editPane));
+
+ Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
+ }
+
+
/**
* DOCUMENT ME!
*
@@ -2735,7 +2889,7 @@ public class AlignFrame
{
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);
@@ -2767,7 +2921,6 @@ public class AlignFrame
alignPanel.paintAlignment(true);
}
-
/**
* DOCUMENT ME!
*
@@ -2985,6 +3138,73 @@ public class AlignFrame
}
});
}
+ /**
+ * 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());//,viewport.getSelectionGroup());
+ 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 && i0);
+ scoreSorts.clear();
+
+ _annotationScoreVectorHash =
+ viewport.alignment.getAlignmentAnnotation().hashCode();
+ }
+ }
/**
* Maintain the Order by->Displayed Tree menu.
@@ -3050,7 +3270,7 @@ public class AlignFrame
* 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;
@@ -3088,12 +3308,14 @@ public class AlignFrame
}
/**
- * 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;
@@ -3136,21 +3358,28 @@ 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,
+ 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);
+ }
}
}
@@ -3215,7 +3444,7 @@ public class AlignFrame
{
ex.printStackTrace();
}
-
+
return tp;
}
@@ -3226,11 +3455,18 @@ public class AlignFrame
*/
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)
@@ -3241,42 +3477,9 @@ public class AlignFrame
{
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);
}
@@ -3288,33 +3491,26 @@ public class AlignFrame
{
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);
}
- 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));
@@ -3322,12 +3518,34 @@ public class AlignFrame
}
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)
@@ -3348,22 +3566,177 @@ public class AlignFrame
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 && t0)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ }
}
class PrintThread