+ r = new Integer(cl).intValue();\r
+ r--;\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ if (cl.toLowerCase().equals("sequence"))\r
+ {\r
+ // we are in the dataset sequence's coordinate frame.\r
+ inseqpos = true;\r
+ }\r
+ else\r
+ {\r
+ System.err\r
+ .println("ERROR: Couldn't parse integer from point selection element of column selection string '"\r
+ + cl + "'");\r
+ return;\r
+ }\r
+ }\r
+ if (r >= 0 && r <= alw)\r
+ {\r
+ if (!seset)\r
+ {\r
+ start = r;\r
+ end = r;\r
+ seset = true;\r
+ }\r
+ else\r
+ {\r
+ // comment to prevent range extension\r
+ if (start > r)\r
+ {\r
+ start = r;\r
+ }\r
+ if (end < r)\r
+ {\r
+ end = r;\r
+ }\r
+ }\r
+ csel.addElement(r);\r
+ if (debug)\r
+ {\r
+ System.err.println("Point selection '" + cl\r
+ + "' deparsed as [" + r + "]");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ System.err.println("ERROR: Invalid Point selection '" + cl\r
+ + "' deparsed as [" + r + "]");\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (seqsfound)\r
+ {\r
+ // we only propagate the selection when it was the null selection, or the\r
+ // given sequences were found in the alignment.\r
+ if (inseqpos && sel.getSize() > 0)\r
+ {\r
+ // assume first sequence provides reference frame ?\r
+ SequenceI rs = sel.getSequenceAt(0);\r
+ start = rs.findIndex(start);\r
+ end = rs.findIndex(end);\r
+ if (csel != null)\r
+ {\r
+ Vector cs = csel.getSelected();\r
+ csel.clear();\r
+ for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)\r
+ {\r
+ csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))\r
+ .intValue()));\r
+ }\r
+ }\r
+ }\r
+ sel.setStartRes(start);\r
+ sel.setEndRes(end);\r
+ EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ alf.select(sel, csel);\r
+ }\r
+ });\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.\r
+ * String, java.lang.String)\r
+ */\r
+ public String getSelectedSequencesAsAlignment(String format, String suffix)\r
+ {\r
+ return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),\r
+ format, suffix);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview\r
+ * .appletgui.AlignFrame, java.lang.String, java.lang.String)\r
+ */\r
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,\r
+ String format, String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+ if (alf.viewport.getSelectionGroup() != null)\r
+ {\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ new Alignment(alf.viewport.getSelectionAsNewSequence()),\r
+ seqlimits);\r
+ return reply;\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+ }\r
+ return "";\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()\r
+ */\r
+ public String getAlignmentOrder()\r
+ {\r
+ return getAlignmentOrderFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame\r
+ * )\r
+ */\r
+ public String getAlignmentOrderFrom(AlignFrame alf)\r
+ {\r
+ return getAlignmentOrderFrom(alf, separator);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)\r
+ {\r
+ AlignmentI alorder = alf.getAlignViewport().getAlignment();\r
+ String[] order = new String[alorder.getHeight()];\r
+ for (int i = 0; i < order.length; i++)\r
+ {\r
+ order[i] = alorder.getSequenceAt(i).getName();\r
+ }\r
+ return arrayToSeparatorList(order);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public String orderBy(String order, String undoName)\r
+ {\r
+ return orderBy(order, undoName, separator);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public String orderBy(String order, String undoName, String sep)\r
+ {\r
+ return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String, java.lang.String)\r
+ */\r
+ public String orderAlignmentBy(AlignFrame alf, String order,\r
+ String undoName, String sep)\r
+ {\r
+ String[] ids = separatorListToArray(order, sep);\r
+ SequenceI[] sqs = null;\r
+ if (ids != null && ids.length > 0)\r
+ {\r
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(\r
+ alf.viewport.getAlignment().getSequencesArray());\r
+ int s = 0;\r
+ sqs = new SequenceI[ids.length];\r
+ for (int i = 0; i < ids.length; i++)\r
+ {\r
+ if (ids[i].trim().length() == 0)\r
+ {\r
+ continue;\r
+ }\r
+ SequenceI sq = matcher.findIdMatch(ids[i]);\r
+ if (sq != null)\r
+ {\r
+ sqs[s++] = sq;\r
+ }\r
+ }\r
+ if (s > 0)\r
+ {\r
+ SequenceI[] sqq = new SequenceI[s];\r
+ System.arraycopy(sqs, 0, sqq, 0, s);\r
+ sqs = sqq;\r
+ }\r
+ else\r
+ {\r
+ sqs = null;\r
+ }\r
+ }\r
+ if (sqs == null)\r
+ {\r
+ return "";\r
+ }\r
+ ;\r
+ final AlignmentOrder aorder = new AlignmentOrder(sqs);\r
+\r
+ if (undoName != null && undoName.trim().length() == 0)\r
+ {\r
+ undoName = null;\r
+ }\r
+ final String _undoName = undoName;\r
+ // TODO: deal with synchronization here: cannot raise any events until after\r
+ // this has returned.\r
+ return alf.sortBy(aorder, _undoName) ? "true" : "";\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)\r
+ */\r
+ public String getAlignment(String format)\r
+ {\r
+ return getAlignmentFrom(getDefaultTargetFrame(), format, "true");\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String)\r
+ */\r
+ public String getAlignmentFrom(AlignFrame alf, String format)\r
+ {\r
+ return getAlignmentFrom(alf, format, "true");\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public String getAlignment(String format, String suffix)\r
+ {\r
+ return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public String getAlignmentFrom(AlignFrame alf, String format,\r
+ String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ alf.viewport.getAlignment(), seqlimits);\r
+ return reply;\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)\r
+ */\r
+ public void loadAnnotation(String annotation)\r
+ {\r
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)\r
+ {\r
+ if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()\r
+ .getAlignment(), annotation, AppletFormatAdapter.PASTE))\r
+ {\r
+ alf.alignPanel.fontChanged();\r
+ alf.alignPanel.setScrollValues(0, 0);\r
+ }\r
+ else\r
+ {\r
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)\r
+ */\r
+ public String getFeatures(String format)\r
+ {\r
+ return getFeaturesFrom(getDefaultTargetFrame(), format);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String)\r
+ */\r
+ public String getFeaturesFrom(AlignFrame alf, String format)\r
+ {\r
+ return alf.outputFeatures(false, format);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()\r
+ */\r
+ public String getAnnotation()\r
+ {\r
+ return getAnnotationFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame\r
+ * )\r
+ */\r
+ public String getAnnotationFrom(AlignFrame alf)\r
+ {\r
+ return alf.outputAnnotations(false);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newView()\r
+ */\r
+ public AlignFrame newView()\r
+ {\r
+ return newViewFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)\r
+ */\r
+ public AlignFrame newView(String name)\r
+ {\r
+ return newViewFrom(getDefaultTargetFrame(), name);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)\r
+ */\r
+ public AlignFrame newViewFrom(AlignFrame alf)\r
+ {\r
+ return alf.newView(null);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String)\r
+ */\r
+ public AlignFrame newViewFrom(AlignFrame alf, String name)\r
+ {\r
+ return alf.newView(name);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public AlignFrame loadAlignment(String text, String title)\r
+ {\r
+ Alignment al = null;\r
+\r
+ String format = new IdentifyFile().Identify(text,\r
+ AppletFormatAdapter.PASTE);\r
+ try\r
+ {\r
+ al = new AppletFormatAdapter().readFile(text,\r
+ AppletFormatAdapter.PASTE, format);\r
+ if (al.getHeight() > 0)\r
+ {\r
+ return new AlignFrame(al, this, title, false);\r
+ }\r
+ } catch (java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)\r
+ */\r
+ public void setMouseoverListener(String listener)\r
+ {\r
+ setMouseoverListener(currentAlignFrame, listener);\r
+ }\r
+\r
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void setMouseoverListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for mouseover listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(\r
+ this, af, listener);\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addStructureViewerListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a mouseover listener for "\r
+ + ((af == null) ? "All frames" : "Just views for "\r
+ + af.getAlignViewport().getSequenceSetId()));\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)\r
+ */\r
+ public void setSelectionListener(String listener)\r
+ {\r
+ setSelectionListener(null, listener);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void setSelectionListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(\r
+ this, af, listener);\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addSelectionListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a selection listener for "\r
+ + ((af == null) ? "All frames" : "Just views for "\r
+ + af.getAlignViewport().getSequenceSetId()));\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public void setStructureListener(String listener, String modelSet)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(\r
+ this, listener, separatorListToArray(modelSet));\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addStructureViewerListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a javascript structure viewer listener '"\r
+ + listener + "'");\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui\r
+ * .AlignFrame, java.lang.String)\r
+ */\r
+ public void removeJavascriptListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ listener = null;\r
+ }\r
+ }\r
+ boolean rprt = false;\r
+ for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)\r
+ {\r
+ Object lstn = javascriptListeners.elementAt(ms);\r
+ JsCallBack lstner = (JsCallBack) lstn;\r
+ if ((af == null || lstner.getAlignFrame() == af)\r
+ && (listener == null || lstner.getListenerFunction().equals(\r
+ listener)))\r
+ {\r
+ javascriptListeners.removeElement(lstner);\r
+ msSize--;\r
+ if (lstner instanceof SelectionListener)\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeSelectionListener((SelectionListener) lstner);\r
+ }\r
+ else\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeStructureViewerListener(lstner, null);\r
+ }\r
+ rprt = debug;\r
+ if (debug)\r
+ {\r
+ System.err.println("Removed listener '" + listener + "'");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ ms++;\r
+ }\r
+ }\r
+ if (rprt)\r
+ {\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ public void stop()\r
+ {\r
+ System.err.println("Applet " + getName() + " stop().");\r
+ tidyUp();\r
+ }\r
+\r
+ public void destroy()\r
+ {\r
+ System.err.println("Applet " + getName() + " destroy().");\r
+ tidyUp();\r
+ }\r
+\r
+ private void tidyUp()\r
+ {\r
+ removeAll();\r
+ if (currentAlignFrame != null && currentAlignFrame.viewport != null\r
+ && currentAlignFrame.viewport.applet != null)\r
+ {\r
+ AlignViewport av = currentAlignFrame.viewport;\r
+ currentAlignFrame.closeMenuItem_actionPerformed();\r
+ av.applet = null;\r
+ currentAlignFrame = null;\r
+ }\r
+ if (javascriptListeners != null)\r
+ {\r
+ while (javascriptListeners.size() > 0)\r
+ {\r
+ jalview.javascript.JSFunctionExec mol = javascriptListeners\r
+ .elementAt(0);\r
+ javascriptListeners.removeElement(mol);\r
+ if (mol instanceof SelectionListener)\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeSelectionListener((SelectionListener) mol);\r
+ }\r
+ else\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeStructureViewerListener(mol, null);\r
+ }\r
+ mol.jvlite = null;\r
+ }\r
+ }\r
+ if (jsFunctionExec != null)\r
+ {\r
+ jsFunctionExec.stopQueue();\r
+ jsFunctionExec.jvlite = null;\r
+ }\r
+ initialAlignFrame = null;\r
+ jsFunctionExec = null;\r
+ javascriptListeners = null;\r
+ StructureSelectionManager.release(this);\r
+ }\r
+\r
+ private jalview.javascript.JSFunctionExec jsFunctionExec;\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public void mouseOverStructure(final String pdbResNum,\r
+ final String chain, final String pdbfile)\r
+ {\r
+ final StructureSelectionManagerProvider me = this;\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(me)\r
+ .mouseOverStructure(new Integer(pdbResNum).intValue(),\r
+ chain, pdbfile);\r
+ if (debug)\r
+ {\r
+ System.err.println("mouseOver for '" + pdbResNum\r
+ + "' in chain '" + chain + "' in structure '" + pdbfile\r
+ + "'");\r