package jalview.bin;
import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignFrameI;
import jalview.api.AlignViewportI;
import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.javascript.JalviewLiteJsApi;
import jalview.javascript.JsCallBack;
import jalview.javascript.MouseOverStructureListener;
+import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.applet.Applet;
import java.awt.Button;
* @author $author$
* @version $Revision: 1.92 $
*/
+@SuppressWarnings("serial")
public class JalviewLite extends Applet
implements StructureSelectionManagerProvider, JalviewLiteJsApi,
JalviewApp
return StructureSelectionManager.getStructureSelectionManager(this);
}
+ @Override
+ public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
+ {
+ return this;
+ }
+
// /////////////////////////////////////////
// The following public methods may be called
// externally, eg via javascript in HTML page
* .AlignFrame)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrame alf)
+ public String getSelectedSequencesFrom(AlignFrameI alf)
{
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
}
* .AlignFrame, java.lang.String)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
sep = separator; // "+0x00AC;
}
- if (alf.viewport.getSelectionGroup() != null)
+ if (((AlignFrame) alf).viewport.getSelectionGroup() != null)
{
- SequenceI[] seqs = alf.viewport.getSelectionGroup()
- .getSequencesInOrder(alf.viewport.getAlignment());
+ SequenceI[] seqs = ((AlignFrame) alf).viewport.getSelectionGroup()
+ .getSequencesInOrder(
+ ((AlignFrame) alf).viewport.getAlignment());
for (int i = 0; i < seqs.length; i++)
{
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
- public void highlightIn(final AlignFrame alf, final String sequenceId,
+ public void highlightIn(final AlignFrameI alf, final String sequenceId,
final String position, final String alignedPosition)
{
// TODO: could try to highlight in all alignments if alf==null
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment().getSequencesArray());
final SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
{
* java.lang.String, java.lang.String)
*/
@Override
- public void selectIn(AlignFrame alf, String sequenceIds, String columns)
+ public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
{
selectIn(alf, sequenceIds, columns, separator);
}
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
- public void selectIn(final AlignFrame alf, String sequenceIds,
+ public void selectIn(final AlignFrameI alf, String sequenceIds,
String columns, String sep)
{
if (sep == null || sep.length() == 0)
String[] cols = JalviewAppLoader.separatorListToArray(columns, sep);
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
- AlignmentI al = alf.viewport.getAlignment();
+ AlignmentI al = ((AlignFrame) alf).viewport.getAlignment();
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
boolean seqsfound = true;
if (ids != null && ids.length > 0)
@Override
public void run()
{
- alf.select(sel, csel,
- alf.getAlignViewport().getAlignment().getHiddenColumns());
+ ((AlignFrame) alf).select(sel, csel, ((AlignFrame) alf)
+ .getAlignViewport().getAlignment().getHiddenColumns());
}
});
}
* .appletgui.AlignFrame, java.lang.String, java.lang.String)
*/
@Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
String format, String suffix)
{
try
{
FileFormatI theFormat = FileFormats.getInstance().forName(format);
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
- if (alf.viewport.getSelectionGroup() != null)
+ if (((AlignFrame) alf).viewport.getSelectionGroup() != null)
{
// JBPNote: getSelectionAsNewSequence behaviour has changed - this
// method now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
String reply = new AppletFormatAdapter().formatSequences(theFormat,
- new Alignment(alf.viewport.getSelectionAsNewSequence()),
+ new Alignment(((AlignFrame) alf).viewport
+ .getSelectionAsNewSequence()),
seqlimits);
return reply;
}
* )
*/
@Override
- public String getAlignmentOrderFrom(AlignFrame alf)
+ public String getAlignmentOrderFrom(AlignFrameI alf)
{
return getAlignmentOrderFrom(alf, separator);
}
* , java.lang.String)
*/
@Override
- public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
{
- AlignmentI alorder = alf.getAlignViewport().getAlignment();
+ AlignmentI alorder = ((AlignFrame) alf).getAlignViewport()
+ .getAlignment();
String[] order = new String[alorder.getHeight()];
for (int i = 0; i < order.length; i++)
{
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
- public String orderAlignmentBy(AlignFrame alf, String order,
+ public String orderAlignmentBy(AlignFrameI alf, String order,
String undoName, String sep)
{
String[] ids = JalviewAppLoader.separatorListToArray(order, sep);
if (ids != null && ids.length > 0)
{
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.viewport.getAlignment().getSequencesArray());
+ ((AlignFrame) alf).viewport.getAlignment()
+ .getSequencesArray());
int s = 0;
sqs = new SequenceI[ids.length];
for (int i = 0; i < ids.length; i++)
final String _undoName = undoName;
// TODO: deal with synchronization here: cannot raise any events until after
// this has returned.
- return alf.sortBy(aorder, _undoName) ? TRUE : "";
+ return ((AlignFrame) alf).sortBy(aorder, _undoName) ? TRUE : "";
}
/*
* java.lang.String)
*/
@Override
- public String getAlignmentFrom(AlignFrame alf, String format)
+ public String getAlignmentFrom(AlignFrameI alf, String format)
{
return getAlignmentFrom(alf, format, TRUE);
}
* java.lang.String, java.lang.String)
*/
@Override
- public String getAlignmentFrom(AlignFrame alf, String format,
+ public String getAlignmentFrom(AlignFrameI alf, String format,
String suffix)
{
try
FileFormatI theFormat = FileFormats.getInstance().forName(format);
String reply = new AppletFormatAdapter().formatSequences(theFormat,
- alf.viewport.getAlignment(), seqlimits);
+ ((AlignFrame) alf).viewport.getAlignment(), seqlimits);
return reply;
} catch (IllegalArgumentException ex)
{
* , java.lang.String)
*/
@Override
- public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ public void loadAnnotationFrom(AlignFrameI alf, String annotation)
{
- if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
+ if (new AnnotationFile().annotateAlignmentView(
+ ((AlignFrame) alf).getAlignViewport(),
annotation, DataSourceType.PASTE))
{
- alf.alignPanel.fontChanged();
- alf.alignPanel.setScrollValues(0, 0);
+ ((AlignFrame) alf).alignPanel.fontChanged();
+ ((AlignFrame) alf).alignPanel.setScrollValues(0, 0);
}
else
{
- alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
+ ((AlignFrame) alf).parseFeaturesFile(annotation,
+ DataSourceType.PASTE);
}
}
* , java.lang.String)
*/
@Override
- public boolean loadFeaturesFrom(AlignFrame alf, String features,
+ public boolean loadFeaturesFrom(AlignFrameI alf, String features,
boolean autoenabledisplay)
{
- return alf.parseFeaturesFile(features, DataSourceType.PASTE,
+ return ((AlignFrame) alf).parseFeaturesFile(features,
+ DataSourceType.PASTE,
autoenabledisplay);
}
* java.lang.String)
*/
@Override
- public String getFeaturesFrom(AlignFrame alf, String format)
+ public String getFeaturesFrom(AlignFrameI alf, String format)
{
- return alf.outputFeatures(false, format);
+ return ((AlignFrame) alf).outputFeatures(false, format);
}
/*
* )
*/
@Override
- public String getAnnotationFrom(AlignFrame alf)
+ public String getAnnotationFrom(AlignFrameI alf)
{
- return alf.outputAnnotations(false);
+ return ((AlignFrame) alf).outputAnnotations(false);
}
/*
* @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
*/
@Override
- public AlignFrame newViewFrom(AlignFrame alf)
+ public AlignFrame newViewFrom(AlignFrameI alf)
{
- return alf.newView(null);
+ return ((AlignFrame) alf).newView(null);
}
/*
* java.lang.String)
*/
@Override
- public AlignFrame newViewFrom(AlignFrame alf, String name)
+ public AlignFrame newViewFrom(AlignFrameI alf, String name)
{
- return alf.newView(name);
+ return ((AlignFrame) alf).newView(name);
}
/*
* , java.lang.String)
*/
@Override
- public void setMouseoverListener(AlignFrame af, String listener)
+ public void setMouseoverListener(AlignFrameI af, String listener)
{
if (listener != null)
{
}
}
jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
- this, af, listener);
+ this, (AlignFrame) af, listener, debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
System.err.println("Added a mouseover listener for "
+ ((af == null) ? "All frames"
: "Just views for "
- + af.getAlignViewport().getSequenceSetId()));
+ + ((AlignFrame) af).getAlignViewport()
+ .getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
* , java.lang.String)
*/
@Override
- public void setSelectionListener(AlignFrame af, String listener)
+ public void setSelectionListener(AlignFrameI af, String listener)
{
if (listener != null)
{
}
}
jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
- this, af, listener);
+ this, (AlignFrame) af, listener, debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addSelectionListener(mol);
System.err.println("Added a selection listener for "
+ ((af == null) ? "All frames"
: "Just views for "
- + af.getAlignViewport().getSequenceSetId()));
+ + ((AlignFrame) af).getAlignViewport()
+ .getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
}
MouseOverStructureListener mol = new MouseOverStructureListener(this,
- listener, separatorListToArray(modelSet));
+ listener, separatorListToArray(modelSet), debug);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
.addStructureViewerListener(mol);
* .AlignFrame, java.lang.String)
*/
@Override
- public void removeJavascriptListener(AlignFrame af, String listener)
+ public void removeJavascriptListener(AlignFrameI af, String listener)
{
if (listener != null)
{
}
if (jsFunctionExec != null)
{
- jsFunctionExec.stopQueue();
- jsFunctionExec.jvlite = null;
+ jsFunctionExec.tidyUp();
+ jsFunctionExec = null;
}
initialAlignFrame = null;
- jsFunctionExec = null;
javascriptListeners = null;
StructureSelectionManager.release(this);
}
* java.lang.String, java.lang.String)
*/
@Override
- public void scrollViewToIn(final AlignFrame alf, final String topRow,
+ public void scrollViewToIn(final AlignFrameI alf, final String topRow,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollTo(new Integer(topRow).intValue(),
+ ((AlignFrame) alf).scrollTo(new Integer(topRow).intValue(),
new Integer(leftHandColumn).intValue());
} catch (Exception ex)
* .AlignFrame, java.lang.String)
*/
@Override
- public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
+ public void scrollViewToRowIn(final AlignFrameI alf, final String topRow)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollToRow(new Integer(topRow).intValue());
+ ((AlignFrame) alf).scrollToRow(new Integer(topRow).intValue());
} catch (Exception ex)
{
* .AlignFrame, java.lang.String)
*/
@Override
- public void scrollViewToColumnIn(final AlignFrame alf,
+ public void scrollViewToColumnIn(final AlignFrameI alf,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+ ((AlignFrame) alf)
+ .scrollToColumn(new Integer(leftHandColumn).intValue());
} catch (Exception ex)
{
boolean embedded = false;
- private boolean checkForJmol = true;
+ boolean checkForJmol = true;
- private boolean checkedForJmol = false; // ensure we don't check for jmol
+ boolean checkedForJmol = false; // ensure we don't check for jmol
// every time the app is re-inited
try
{
// do onInit with the JS executor thread
- new JSFunctionExec(this).executeJavascriptFunction(true,
+ new JSFunctionExec(this, debug).executeJavascriptFunction(true,
initjscallback, null,
"Calling oninit callback '" + initjscallback + "'.");
} catch (Exception e)
/**
* set to enable the URL based javascript execution mechanism
*/
- public boolean jsfallbackEnabled = false;
+ private boolean jsfallbackEnabled = false;
/**
* parse the string into a list
* @param list
* @return elements separated by separator
*/
+ @Override
public String[] separatorListToArray(String list)
{
return JalviewAppLoader.separatorListToArray(list, separator);
* @param list
* @return concatenated string
*/
+ @Override
public String arrayToSeparatorList(String[] list)
{
- return arrayToSeparatorList(list, separator);
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @param separator
- * @return concatenated string
- */
- public static String arrayToSeparatorList(String[] list, String separator)
- {
- // TODO use StringUtils version
- StringBuffer v = new StringBuffer();
- if (list != null && list.length > 0)
- {
- for (int i = 0, iSize = list.length; i < iSize; i++)
- {
- if (list[i] != null)
- {
- if (i > 0)
- {
- v.append(separator);
- }
- v.append(list[i]);
- }
- }
- if (debug)
- {
- System.err
- .println("Returning '" + separator + "' separated List:\n");
- System.err.println(v);
- }
- return v.toString();
- }
- if (debug)
- {
- System.err.println(
- "Returning empty '" + separator + "' separated List\n");
- }
- return "" + separator;
+ return JalviewAppLoader.arrayToSeparatorList(list, separator);
}
/*
* )
*/
@Override
- public String getFeatureGroupsOn(AlignFrame alf)
+ public String getFeatureGroupsOn(AlignFrameI alf)
{
- String lst = arrayToSeparatorList(alf.getFeatureGroups());
+ String lst = arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroups());
return lst;
}
* .AlignFrame, boolean)
*/
@Override
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
{
- return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ return arrayToSeparatorList(
+ ((AlignFrame) alf).getFeatureGroupsOfState(visible));
}
/*
* AlignFrame, java.lang.String, boolean)
*/
@Override
- public void setFeatureGroupStateOn(final AlignFrame alf,
+ public void setFeatureGroupStateOn(final AlignFrameI alf,
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
@Override
public void run()
{
- alf.setFeatureGroupState(separatorListToArray(groups), st);
+ ((AlignFrame) alf)
+ .setFeatureGroupState(separatorListToArray(groups), st);
}
});
}
* java.lang.String, java.lang.String, java.lang.String)
*/
@Override
- public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile)
{
- return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
+ return ((AlignFrame) alFrame).addPdbFile(sequenceId, pdbEntryString,
+ pdbFile);
}
@Override
// callInitCallback();
}
- private Hashtable<String, long[]> jshashes = new Hashtable<>();
+ private Hashtable<String, int[]> jshashes = new Hashtable<>();
private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
- public void setJsMessageSet(String messageclass, String viewId,
- String[] colcommands)
- {
- Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
- if (msgset == null)
- {
- msgset = new Hashtable<>();
- jsmessages.put(messageclass, msgset);
- }
- msgset.put(viewId, colcommands);
- long[] l = new long[colcommands.length];
- for (int i = 0; i < colcommands.length; i++)
- {
- l[i] = colcommands[i].hashCode();
- }
- jshashes.put(messageclass + "|" + viewId, l);
- }
- /*
- * (non-Javadoc)
- *
- * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
- * java.lang.String)
- */
@Override
- public String getJsMessage(String messageclass, String viewId)
+ public Hashtable<String, int[]> getJSHashes()
{
- Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
- if (msgset != null)
- {
- String[] msgs = msgset.get(viewId);
- if (msgs != null)
- {
- for (int i = 0; i < msgs.length; i++)
- {
- if (msgs[i] != null)
- {
- String m = msgs[i];
- msgs[i] = null;
- return m;
- }
- }
- }
- }
- return "";
+ return jshashes;
}
- public boolean isJsMessageSetChanged(String string, String string2,
- String[] colcommands)
+ @Override
+ public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
{
- long[] l = jshashes.get(string + "|" + string2);
- if (l == null && colcommands != null)
- {
- return true;
- }
- for (int i = 0; i < colcommands.length; i++)
- {
- if (l[i] != colcommands[i].hashCode())
- {
- return true;
- }
- }
- return false;
+ return jsmessages;
}
- private Vector jsExecQueue = new Vector();
+ private Vector<Runnable> jsExecQueue = new Vector<>();
- public Vector getJsExecQueue()
+ @Override
+ public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
{
+ jsFunctionExec = exec;
return jsExecQueue;
}
- public void setExecutor(JSFunctionExec jsFunctionExec2)
- {
- jsFunctionExec = jsFunctionExec2;
- }
+ // public void setExecutor(JSFunctionExec jsFunctionExec2)
+ // {
+ // jsFunctionExec = jsFunctionExec2;
+ // }
/**
* return the given colour value parameter or the given default if parameter
loaderFrame.loadTree(tree, treeFile);
}
- /**
- * bind structures in a viewer to any matching sequences in an alignFrame (use
- * sequenceIds to limit scope of search to specific sequences)
- *
- * @param alFrame
- * @param viewer
- * @param sequenceIds
- * @return TODO: consider making an exception structure for indicating when
- * binding fails public SequenceStructureBinding
- * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
- * sequenceIds) {
- *
- * if (sequenceIds != null && sequenceIds.length() > 0) { return
- * alFrame.addStructureViewInstance(viewer,
- * separatorListToArray(sequenceIds)); } else { return
- * alFrame.addStructureViewInstance(viewer, null); } // return null; }
- */
+ @Override
+ public boolean isJsfallbackEnabled()
+ {
+ return jsfallbackEnabled;
+ }
+
+ @Override
+ public JSObject getJSObject()
+ {
+ return JSObject.getWindow(this);
+ }
+
+ @Override
+ public void updateColoursFromMouseOver(Object source,
+ MouseOverStructureListener listener)
+ {
+ }
+
+ @Override
+ public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame)
+ {
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = (AlignFrame) alignFrame;
+ if (source != null)
+ {
+ if (source instanceof jalview.appletgui.AlignViewport
+ && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
+ {
+ // should be valid if it just generated an event!
+ src = ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
+
+ }
+ }
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
+ int strt = 0, end = (src == null) ? -1
+ : src.alignPanel.av.getAlignment().getWidth();
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ seqs = new String[seqsel.getSize()];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = seqsel.getSequenceAt(i).getName();
+ }
+ if (strt < seqsel.getStartRes())
+ {
+ strt = seqsel.getStartRes();
+ }
+ if (end == -1 || end > seqsel.getEndRes())
+ {
+ end = seqsel.getEndRes();
+ }
+ }
+ if (colsel != null && !colsel.isEmpty())
+ {
+ if (end == -1)
+ {
+ end = colsel.getMax() + 1;
+ }
+ cols = new String[colsel.getSelected().size()];
+ for (int i = 0; i < cols.length; i++)
+ {
+ cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ }
+ }
+ else
+ {
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ // send a valid range, otherwise we send the empty selection
+ cols = new String[2];
+ cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ }
+ }
+ return new Object[]
+ { src, setid, arrayToSeparatorList(seqs), arrayToSeparatorList(cols) };
+ }
+
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ return JSFunctionExec.getJsMessage(messageclass, viewId, this);
+ }
+
+ @Override
+ public Object getFrameForSource(VamsasSource source)
+ {
+ if (source != null)
+ {
+ if (source instanceof jalview.appletgui.AlignViewport
+ && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
+ {
+ // should be valid if it just generated an event!
+ return ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
+
+ }
+ // TODO: ensure that if '_af' is specified along with a handler
+ // function, then only events from that alignFrame are sent to that
+ // function
+ }
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+ {
+ return new jalview.appletgui.FeatureRenderer((AlignmentViewport) vp);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ boolean suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ String format, boolean suffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ // /**
+ // * bind structures in a viewer to any matching sequences in an alignFrame
+ // (use
+ // * sequenceIds to limit scope of search to specific sequences)
+ // *
+ // * @param alFrame
+ // * @param viewer
+ // * @param sequenceIds
+ // * @return TODO: consider making an exception structure for indicating when
+ // * binding fails public SequenceStructureBinding
+ // * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
+ // * sequenceIds) {
+ // *
+ // * if (sequenceIds != null && sequenceIds.length() > 0) { return
+ // * alFrame.addStructureViewInstance(viewer,
+ // * separatorListToArray(sequenceIds)); } else { return
+ // * alFrame.addStructureViewInstance(viewer, null); } // return null; }
+ // */
}
git://source.jalview.org / jalview.git / blobdiff