+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ public String getAlignmentFrom(AlignFrame alf, String format)
+ {
+ return getAlignmentFrom(alf, format, "true");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
+ * java.lang.String)
+ */
+ public String getAlignment(String format, String suffix)
+ {
+ return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
+ */
+ public String getAlignmentFrom(AlignFrame alf, String format,
+ String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ alf.viewport.getAlignment(), seqlimits);
+ return reply;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
+ */
+ public void loadAnnotation(String annotation)
+ {
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ {
+ if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
+ .getAlignment(), annotation, AppletFormatAdapter.PASTE))
+ {
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
+ */
+ public void loadFeatures(String features, boolean autoenabledisplay)
+ {
+ loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,
+ boolean autoenabledisplay)
+ {
+ return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
+ autoenabledisplay);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
+ */
+ public String getFeatures(String format)
+ {
+ return getFeaturesFrom(getDefaultTargetFrame(), format);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ public String getFeaturesFrom(AlignFrame alf, String format)
+ {
+ return alf.outputFeatures(false, format);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
+ */
+ public String getAnnotation()
+ {
+ return getAnnotationFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
+ * )
+ */
+ public String getAnnotationFrom(AlignFrame alf)
+ {
+ return alf.outputAnnotations(false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newView()
+ */
+ public AlignFrame newView()
+ {
+ return newViewFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
+ */
+ public AlignFrame newView(String name)
+ {
+ return newViewFrom(getDefaultTargetFrame(), name);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
+ */
+ public AlignFrame newViewFrom(AlignFrame alf)
+ {
+ return alf.newView(null);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ public AlignFrame newViewFrom(AlignFrame alf, String name)
+ {
+ return alf.newView(name);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
+ * java.lang.String)
+ */
+ public AlignFrame loadAlignment(String text, String title)
+ {
+ Alignment al = null;
+
+ String format = new IdentifyFile().Identify(text,
+ AppletFormatAdapter.PASTE);
+ try
+ {
+ al = new AppletFormatAdapter().readFile(text,
+ AppletFormatAdapter.PASTE, format);
+ if (al.getHeight() > 0)
+ {
+ return new AlignFrame(al, this, title, false);
+ }
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
+ */
+ public void setMouseoverListener(String listener)
+ {
+ setMouseoverListener(currentAlignFrame, listener);
+ }
+
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ public void setMouseoverListener(AlignFrame af, String listener)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
+ return;
+ }
+ }
+ jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
+ this, af, listener);
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .addStructureViewerListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a mouseover listener for "
+ + ((af == null) ? "All frames" : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
+ */
+ public void setSelectionListener(String listener)
+ {
+ setSelectionListener(null, listener);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ public void setSelectionListener(AlignFrame af, String listener)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ return;
+ }
+ }
+ jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
+ this, af, listener);
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .addSelectionListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a selection listener for "
+ + ((af == null) ? "All frames" : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
+ * java.lang.String)
+ */
+ public void setStructureListener(String listener, String modelSet)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ return;
+ }
+ }
+ jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
+ this, listener, separatorListToArray(modelSet));
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .addStructureViewerListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a javascript structure viewer listener '"
+ + listener + "'");
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ public void removeJavascriptListener(AlignFrame af, String listener)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ listener = null;
+ }
+ }
+ boolean rprt = false;
+ for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
+ {
+ Object lstn = javascriptListeners.elementAt(ms);
+ JsCallBack lstner = (JsCallBack) lstn;
+ if ((af == null || lstner.getAlignFrame() == af)
+ && (listener == null || lstner.getListenerFunction().equals(
+ listener)))
+ {
+ javascriptListeners.removeElement(lstner);
+ msSize--;
+ if (lstner instanceof SelectionListener)
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeSelectionListener((SelectionListener) lstner);
+ }
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeStructureViewerListener(lstner, null);
+ }
+ rprt = debug;
+ if (debug)
+ {
+ System.err.println("Removed listener '" + listener + "'");
+ }
+ }
+ else
+ {
+ ms++;
+ }
+ }
+ if (rprt)
+ {
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ public void stop()