new AnnotationExporter().exportAnnotations(
alignPanel,
viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
- viewport.alignment.getGroups()
+ viewport.alignment.getGroups(),
+ ((Alignment)viewport.alignment).alignmentProperties
);
}
{
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);
}
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).alignmentProperties != null)
+ {
+ Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;
+ Enumeration en = props.keys();
+ contents.append("<br><br><table border=\"1\">");
+ while(en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ contents.append("<tr><td>"+key+"</td><td>"+props.get(key)+"</td></tr>");
+ }
+ contents.append("</table>");
+ }
+ editPane.setText(contents.toString()+"</html>");
+ JInternalFrame frame = new JInternalFrame();
+ frame.getContentPane().add(editPane);
+
+ Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
+ }
+
+
/**
* DOCUMENT ME!
*
}
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: 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.io.DBRefFetcher(
+ alignPanel.av.getSequenceSelection(),
+ alignPanel.alignFrame).fetchDBRefs(false);
+ }
+
+ });
+ }
+
/* public void vamsasStore_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-
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 {
git://source.jalview.org / jalview.git / blobdiff