public void newView_actionPerformed(ActionEvent e)
{
+ newView(true);
+ }
+ /**
+ *
+ * @param copyAnnotation if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(boolean copyAnnotation)
+ {
+ return newView(null, copyAnnotation);
+ }
+ /**
+ *
+ * @param viewTitle title of newly created view
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle)
+ {
+ return newView(viewTitle, true);
+ }
+ /**
+ *
+ * @param viewTitle title of newly created view
+ * @param copyAnnotation if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
+ {
AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
true);
+ if (!copyAnnotation)
+ {
+ // just remove all the current annotation except for the automatic stuff
+ newap.av.alignment.deleteAllGroups();
+ for (AlignmentAnnotation alan: newap.av.alignment.getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated)
+ {
+ newap.av.alignment.deleteAnnotation(alan);
+ };
+ }
+ }
newap.av.gatherViewsHere = false;
newap.av.redoList = viewport.redoList;
int index = Desktop.getViewCount(viewport.getSequenceSetId());
- String newViewName = "View " + index;
-
+ // make sure the new view has a unique name - this is essential for Jalview 2 archives
+ boolean addFirstIndex = false;
+ if (viewTitle==null || viewTitle.trim().length()==0)
+ {
+ viewTitle = "View";
+ addFirstIndex = true;
+ } else {
+ index=1;// we count from 1 if given a specific name
+ }
+ String newViewName = viewTitle + ((addFirstIndex) ? " "+index : "");
Vector comps = (Vector) PaintRefresher.components.get(viewport
.getSequenceSetId());
Vector existingNames = new Vector();
while (existingNames.contains(newViewName))
{
- newViewName = "View " + (++index);
+ newViewName = viewTitle + " "+(++index);
}
newap.av.viewName = newViewName;
viewport.gatherViewsHere = true;
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newap;
}
public void expandViews_actionPerformed(ActionEvent e)
{
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>");
+ StringBuffer contents = new AlignmentProperties(viewport.alignment).formatAsHtml();
+ editPane.setText("<html>"+contents.toString() + "</html>");
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
webService, this);
}
+ // TODO: remove this code when 2.7 is released
+ // DEBUG - alignmentView
+ /*JMenuItem testAlView = new JMenuItem("Test AlignmentView");
+ final AlignFrame af = this;
+ testAlView.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.alignment, af.viewport.colSel, af.viewport.selectionGroup);
+ }
+
+ });
+ webService.add(testAlView);*/
+ // TODO: refactor to RestClient discoverer and merge menu entries for rest-style services with other types of analysis/calculation service
+ // SHmmr test client - still being implemented.
+ // jalview.ws.rest.RestClient.makeShmmrRestClient().attachWSMenuEntry(webService, this);
+ // DEBUG - alignmentView
}
/*
git://source.jalview.org / jalview.git / blobdiff