*/\r
package jalview.bin;\r
\r
+import jalview.api.StructureSelectionManagerProvider;\r
import jalview.appletgui.AlignFrame;\r
+import jalview.appletgui.AlignViewport;\r
import jalview.appletgui.EmbmenuFrame;\r
import jalview.appletgui.FeatureSettings;\r
import jalview.datamodel.Alignment;\r
import jalview.io.IdentifyFile;\r
import jalview.io.JnetAnnotationMaker;\r
import jalview.javascript.JSFunctionExec;\r
+import jalview.javascript.JalviewLiteJsApi;\r
import jalview.javascript.JsCallBack;\r
import jalview.structure.SelectionListener;\r
import jalview.structure.StructureSelectionManager;\r
* Jalview Applet. Runs in Java 1.18 runtime\r
* \r
* @author $author$\r
- * @version $Revision$\r
+ * @version $Revision: 1.92 $\r
*/\r
-public class JalviewLite extends Applet\r
+public class JalviewLite extends Applet implements StructureSelectionManagerProvider, JalviewLiteJsApi\r
{\r
\r
// /////////////////////////////////////////\r
// The following public methods maybe called\r
// externally, eg via javascript in HTML page\r
- /**\r
- * @return String list of selected sequence IDs, each terminated by the\r
- * 'boolean not' character (""+0x00AC) or (¬)\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()\r
*/\r
public String getSelectedSequences()\r
{\r
return getSelectedSequencesFrom(getDefaultTargetFrame());\r
}\r
\r
- /**\r
- * @param sep\r
- * separator string or null for default\r
- * @return String list of selected sequence IDs, each terminated by given\r
- * separator string\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)\r
*/\r
public String getSelectedSequences(String sep)\r
{\r
return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);\r
}\r
\r
- /**\r
- * @param alf\r
- * alignframe containing selection\r
- * @return String list of selected sequence IDs, each terminated by current\r
- * default separator sequence\r
- * \r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui.AlignFrame)\r
*/\r
public String getSelectedSequencesFrom(AlignFrame alf)\r
{\r
return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);\r
}\r
\r
- /**\r
- * get list of selected sequence IDs separated by given separator\r
- * \r
- * @param alf\r
- * window containing selection\r
- * @param sep\r
- * separator string to use - default is 'boolean not'\r
- * @return String list of selected sequence IDs, each terminated by the given\r
- * separator\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui.AlignFrame, java.lang.String)\r
*/\r
public String getSelectedSequencesFrom(AlignFrame alf, String sep)\r
{\r
return result.toString();\r
}\r
\r
- /**\r
- * \r
- * @param sequenceId\r
- * id of sequence to highlight\r
- * @param position\r
- * integer position [ tobe implemented or range ] on sequence\r
- * @param alignedPosition\r
- * true/false/empty string - indicate if position is an alignment\r
- * column or unaligned sequence position\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String, java.lang.String, java.lang.String)\r
*/\r
public void highlight(String sequenceId, String position,\r
String alignedPosition)\r
alignedPosition);\r
}\r
\r
- /**\r
- * \r
- * @param sequenceId\r
- * id of sequence to highlight\r
- * @param position\r
- * integer position [ tobe implemented or range ] on sequence\r
- * @param alignedPosition\r
- * false, blank or something else - indicate if position is an\r
- * alignment column or unaligned sequence position\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame, java.lang.String, java.lang.String, java.lang.String)\r
*/\r
public void highlightIn(AlignFrame alf, String sequenceId,\r
String position, String alignedPosition)\r
&& (alignedPosition.trim().length() == 0 || alignedPosition\r
.toLowerCase().indexOf("false") > -1))\r
{\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.mouseOverVamsasSequence(sq, sq.findIndex(apos), null);\r
}\r
else\r
{\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.mouseOverVamsasSequence(sq, apos, null);\r
}\r
\r
}\r
}\r
\r
- /**\r
- * select regions of the currrent alignment frame\r
- * \r
- * @param sequenceIds\r
- * String separated list of sequence ids or empty string\r
- * @param columns\r
- * String separated list { column range or column, ..} or empty\r
- * string\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, java.lang.String)\r
*/\r
public void select(String sequenceIds, String columns)\r
{\r
selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);\r
}\r
\r
- /**\r
- * select regions of the currrent alignment frame\r
- * \r
- * @param toselect\r
- * String separated list { column range, seq1...seqn sequence ids }\r
- * @param sep\r
- * separator between toselect fields\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, java.lang.String, java.lang.String)\r
*/\r
public void select(String sequenceIds, String columns, String sep)\r
{\r
selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);\r
}\r
\r
- /**\r
- * select regions of the given alignment frame\r
- * \r
- * @param alf\r
- * @param toselect\r
- * String separated list { column range, seq1...seqn sequence ids }\r
- * @param sep\r
- * separator between toselect fields\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, java.lang.String, java.lang.String)\r
*/\r
public void selectIn(AlignFrame alf, String sequenceIds, String columns)\r
{\r
selectIn(alf, sequenceIds, columns, separator);\r
}\r
\r
- /**\r
- * select regions of the given alignment frame\r
- * \r
- * @param alf\r
- * @param toselect\r
- * String separated list { column range, seq1...seqn sequence ids }\r
- * @param sep\r
- * separator between toselect fields\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, java.lang.String, java.lang.String, java.lang.String)\r
*/\r
public void selectIn(AlignFrame alf, String sequenceIds, String columns,\r
String sep)\r
}\r
}\r
\r
- /**\r
- * get sequences selected in current alignFrame and return their alignment in\r
- * format 'format' either with or without suffix\r
- * \r
- * @param alf\r
- * - where selection is\r
- * @param format\r
- * - format of alignment file\r
- * @param suffix\r
- * - "true" to append /start-end string to each sequence ID\r
- * @return selected sequences as flat file or empty string if there was no\r
- * current selection\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.String, java.lang.String)\r
*/\r
public String getSelectedSequencesAsAlignment(String format, String suffix)\r
{\r
format, suffix);\r
}\r
\r
- /**\r
- * get sequences selected in alf and return their alignment in format 'format'\r
- * either with or without suffix\r
- * \r
- * @param alf\r
- * - where selection is\r
- * @param format\r
- * - format of alignment file\r
- * @param suffix\r
- * - "true" to append /start-end string to each sequence ID\r
- * @return selected sequences as flat file or empty string if there was no\r
- * current selection\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview.appletgui.AlignFrame, java.lang.String, java.lang.String)\r
*/\r
public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,\r
String format, String suffix)\r
return "";\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()\r
+ */\r
public String getAlignmentOrder()\r
{\r
return getAlignmentOrderFrom(getDefaultTargetFrame());\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame)\r
+ */\r
public String getAlignmentOrderFrom(AlignFrame alf)\r
{\r
return getAlignmentOrderFrom(alf, separator);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
public String getAlignmentOrderFrom(AlignFrame alf, String sep)\r
{\r
AlignmentI alorder = alf.getAlignViewport().getAlignment();\r
return arrayToSeparatorList(order);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, java.lang.String)\r
+ */\r
public String orderBy(String order, String undoName)\r
{\r
return orderBy(order, undoName, separator);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, 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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame, 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
return alf.sortBy(aorder, undoName) ? "true" : "";\r
}\r
\r
+ /* (non-Javadoc)\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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
public String getAlignmentFrom(AlignFrame alf, String format)\r
{\r
return getAlignmentFrom(alf, format, "true");\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String, java.lang.String)\r
+ */\r
public String getAlignment(String format, String suffix)\r
{\r
return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, java.lang.String, java.lang.String)\r
+ */\r
public String getAlignmentFrom(AlignFrame alf, String format,\r
String suffix)\r
{\r
}\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)\r
+ */\r
public void loadAnnotation(String annotation)\r
{\r
loadAnnotationFrom(getDefaultTargetFrame(), annotation);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
public void loadAnnotationFrom(AlignFrame alf, String annotation)\r
{\r
if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()\r
}\r
}\r
\r
+ /* (non-Javadoc)\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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
public String getFeaturesFrom(AlignFrame alf, String format)\r
{\r
return alf.outputFeatures(false, format);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()\r
+ */\r
public String getAnnotation()\r
{\r
return getAnnotationFrom(getDefaultTargetFrame());\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame)\r
+ */\r
public String getAnnotationFrom(AlignFrame alf)\r
{\r
return alf.outputAnnotations(false);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#newView()\r
+ */\r
public AlignFrame newView()\r
{\r
return newViewFrom(getDefaultTargetFrame());\r
}\r
\r
+ /* (non-Javadoc)\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
+ /* (non-Javadoc)\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
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
public AlignFrame newViewFrom(AlignFrame alf, String name)\r
{\r
return alf.newView(name);\r
}\r
\r
- /**\r
- * \r
- * @param text\r
- * alignment file as a string\r
- * @param title\r
- * window title\r
- * @return null or new alignment frame\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String, java.lang.String)\r
*/\r
public AlignFrame loadAlignment(String text, String title)\r
{\r
return null;\r
}\r
\r
+ /* (non-Javadoc)\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 javascriptListeners = new Vector();\r
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
public void setMouseoverListener(AlignFrame af, String listener)\r
{\r
if (listener != null)\r
jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(\r
this, af, listener);\r
javascriptListeners.addElement(mol);\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.addStructureViewerListener(mol);\r
if (debug)\r
{\r
}\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)\r
+ */\r
public void setSelectionListener(String listener)\r
{\r
setSelectionListener(null, listener);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame, java.lang.String)\r
+ */\r
public void setSelectionListener(AlignFrame af, String listener)\r
{\r
if (listener != null)\r
jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(\r
this, af, listener);\r
javascriptListeners.addElement(mol);\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.addSelectionListener(mol);\r
if (debug)\r
{\r
}\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, java.lang.String)\r
+ */\r
public void setStructureListener(String listener, String modelSet)\r
{\r
if (listener != null)\r
jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(\r
this, listener, separatorListToArray(modelSet));\r
javascriptListeners.addElement(mol);\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.addStructureViewerListener(mol);\r
if (debug)\r
{\r
}\r
}\r
\r
- /**\r
- * remove any callback using the given listener function and associated with\r
- * the given alignFrame (or null for all callbacks)\r
- * \r
- * @param af\r
- * (may be null)\r
- * @param listener\r
- * (may be null)\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui.AlignFrame, java.lang.String)\r
*/\r
public void removeJavascriptListener(AlignFrame af, String listener)\r
{\r
msSize--;\r
if (lstner instanceof SelectionListener)\r
{\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.removeSelectionListener((SelectionListener) lstner);\r
}\r
else\r
{\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.removeStructureViewerListener(lstner, null);\r
}\r
rprt = debug;\r
\r
public void stop()\r
{\r
+ System.err.println("Applet "+getName()+" stop().");\r
+ tidyUp();\r
+ }\r
+ public void destroy()\r
+ {\r
+ System.err.println("Applet "+getName()+" destroy().");\r
+ tidyUp();\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
- Object mol = javascriptListeners.elementAt(0);\r
+ jalview.javascript.JSFunctionExec mol = javascriptListeners.elementAt(0);\r
javascriptListeners.removeElement(mol);\r
if (mol instanceof SelectionListener)\r
{\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.removeSelectionListener((SelectionListener) mol);\r
}\r
else\r
{\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.removeStructureViewerListener(mol, null);\r
}\r
+ mol.jvlite=null;\r
}\r
}\r
- jsFunctionExec.stopQueue();\r
+ if (jsFunctionExec!=null) {\r
+ jsFunctionExec.stopQueue();\r
+ jsFunctionExec.jvlite=null;\r
+ }\r
+ initialAlignFrame=null;\r
+ jsFunctionExec = null;\r
+ javascriptListeners=null;\r
+ StructureSelectionManager.release(this);\r
}\r
private jalview.javascript.JSFunctionExec jsFunctionExec;\r
- /**\r
- * send a mouseover message to all the alignment windows associated with the\r
- * given residue in the pdbfile\r
- * \r
- * @param pdbResNum\r
- * @param chain\r
- * @param pdbfile\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String, java.lang.String, java.lang.String)\r
*/\r
public void mouseOverStructure(String pdbResNum, String chain,\r
String pdbfile)\r
{\r
try\r
{\r
- StructureSelectionManager.getStructureSelectionManager()\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
.mouseOverStructure(new Integer(pdbResNum).intValue(), chain,\r
pdbfile);\r
if (debug)\r
+ pdbResNum + "'");\r
}\r
}\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame, java.lang.String, java.lang.String)\r
+ */\r
+ public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn)\r
+ {\r
+ try {\r
+ alf.scrollTo(new Integer(topRow).intValue(), new Integer(leftHandColumn).intValue());\r
+ \r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Couldn't parse integer arguments (topRow='"+topRow+"' and leftHandColumn='"+leftHandColumn+"'");\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
\r
// //////////////////////////////////////////////\r
// //////////////////////////////////////////////\r
{\r
if (frame instanceof AlignFrame)\r
{\r
+ AlignViewport vp = ((AlignFrame) frame).viewport;\r
((AlignFrame) frame).closeMenuItem_actionPerformed();\r
- if (((AlignFrame) frame).viewport.applet.currentAlignFrame == frame)\r
+ if (vp.applet.currentAlignFrame == frame)\r
{\r
- ((AlignFrame) frame).viewport.applet.currentAlignFrame = null;\r
+ vp.applet.currentAlignFrame = null;\r
}\r
+ vp.applet=null;\r
+ vp=null;\r
+ \r
}\r
lastFrameX -= 40;\r
lastFrameY -= 40;\r
applet.remove(launcher);\r
applet.repaint();\r
}\r
+ callInitCallback();\r
}\r
\r
/**\r
return "" + separator;\r
}\r
\r
- /**\r
- * @return\r
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()\r
*/\r
public String getFeatureGroups()\r
{\r
return lst;\r
}\r
\r
- /**\r
- * @param alf\r
- * alignframe to get feature groups on\r
- * @return\r
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame)\r
*/\r
public String getFeatureGroupsOn(AlignFrame alf)\r
{\r
return lst;\r
}\r
\r
- /**\r
- * @param visible\r
- * @return\r
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)\r
*/\r
public String getFeatureGroupsOfState(boolean visible)\r
{\r
.getFeatureGroupsOfState(visible));\r
}\r
\r
- /**\r
- * @param alf\r
- * align frame to get groups of state visible\r
- * @param visible\r
- * @return\r
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui.AlignFrame, boolean)\r
*/\r
public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)\r
{\r
return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));\r
}\r
\r
- /**\r
- * @param groups\r
- * tab separated list of group names\r
- * @param state\r
- * true or false\r
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],\r
- * boolean)\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.AlignFrame, java.lang.String, boolean)\r
*/\r
public void setFeatureGroupStateOn(AlignFrame alf, String groups,\r
boolean state)\r
alf.setFeatureGroupState(separatorListToArray(groups), st);\r
}\r
\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String, boolean)\r
+ */\r
public void setFeatureGroupState(String groups, boolean state)\r
{\r
setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);\r
}\r
\r
- /**\r
- * List separator string\r
- * \r
- * @return the separator\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getSeparator()\r
*/\r
public String getSeparator()\r
{\r
return separator;\r
}\r
\r
- /**\r
- * List separator string\r
- * \r
- * @param separator\r
- * the separator to set. empty string will reset separator to default\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)\r
*/\r
public void setSeparator(String separator)\r
{\r
return false;\r
}\r
\r
- /**\r
- * bind a pdb file to a sequence in the given alignFrame.\r
- * \r
- * @param alFrame\r
- * - null or specific alignFrame. This specifies the dataset that\r
- * will be searched for a seuqence called sequenceId\r
- * @param sequenceId\r
- * - sequenceId within the dataset.\r
- * @param pdbEntryString\r
- * - the short name for the PDB file\r
- * @param pdbFile\r
- * - pdb file - either a URL or a valid PDB file.\r
- * @return true if binding was as success TODO: consider making an exception\r
- * structure for indicating when PDB parsing or sequenceId location\r
- * fails.\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame, java.lang.String, java.lang.String, java.lang.String)\r
*/\r
public boolean addPdbFile(AlignFrame alFrame, String sequenceId,\r
String pdbEntryString, String pdbFile)\r
\r
public void start()\r
{\r
- callInitCallback();\r
+// callInitCallback();\r
}\r
private Hashtable<String,long[]> jshashes=new Hashtable<String,long[]>();\r
private Hashtable<String,Hashtable<String,String[]>> jsmessages=new Hashtable<String,Hashtable<String,String[]>>();\r
for (int i=0;i<colcommands.length;i++) { l[i] = colcommands[i].hashCode();}\r
jshashes.put(messageclass+"|"+viewId,l);\r
}\r
+ /* (non-Javadoc)\r
+ * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String, java.lang.String)\r
+ */\r
public String getJsMessage(String messageclass, String viewId)\r
{\r
Hashtable<String,String[]> msgset = jsmessages.get(messageclass);\r
git://source.jalview.org / jalview.git / blobdiff