The jalviewLite applet's application programming interface (API) includes two components. A JalviewLite Javascript Library and the public methods on the JalviewLite applet. -
-The following public methods on the jalviewLite applet are available to be called from javascript:
-//get list of IDs of selected sequences -public String getSelectedSequences() - -// list of IDs of selected sequences terminated by sep or, if sep is null, '¬' (¬) -public String getSelectedSequences(sep) - -// get list of selected sequences from specific alignFrame. (2.7) -public String getSelectedSequencesFrom(AlignFrame alf) -public String getSelectedSequencesFrom(AlignFrame alf, String sep) - -// highlight a position in a specific sequence or a column in an alignment containing it -// provide ID sequence to highlight, integer (range highlighting will be supported in future versions) -// and flag indicating if position is an alignment column or given according to sequence numbering (2.7) -public void highlight(String sequenceId, String position, String alignedPosition) -public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition) - - -// select regions of the currrent alignment frame using a list of sequence ids and a list of -// column numbers and ranges (with minus sign indicating start-end) (separated by default separator) (2.7) -public void select(String sequenceIds, String columns) -public void select(String sequenceIds, String columns, String sep) -public void selectIn(AlignFrame alf, String sequenceIds, String columns) -public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep) - - -// get selected sequences as alignment as format with or without start-end suffix -public String getSelectedSequencesAsAlignment(String format, boolean suffix) - -// get selected sequences as alignment from given view as format with or without start-end suffix -public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix) - -// get a separator separated list of sequence IDs reflecting the order of the current alignment (2.7) -public String getAlignmentOrder(); -public String getAlignmentOrderFrom(AlignFrame alf); -public String getAlignmentOrderFrom(AlignFrame alf, String sep); - -// re-order the current alignment using the given list of sequence IDs separated by sep -// undoName - is string to use when referring to ordering action in undo buffer -// returns 'true' if alignment was actually reordered. empty string if alignment did not contain sequences. -// (v2.7) -public String orderBy(String order, String undoName) -public String orderBy(String order, String undoName, String sep) -String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep) - - -// get alignment as format -public String getAlignment(String format) - -// get alignment as format with jalview -// start-end sequence suffix appended -public String getAlignment(String format, String suffix) - -// get alignment displayed in alf as format -public String getAlignmentFrom(AlignFrame alf, String format) - -// get alignment displayed in alf as format -// with jalview start-end sequence suffix appended -public String getAlignmentFrom(AlignFrame alf, String format, String suffix) - -// add the given features or annotation to the current alignment -// if features are loaded, feature display is automatically enabled -public void loadAnnotation(String annotation) - -// add the given features or annotation to the given alignment view -// if features are loaded, feature display is automatically enabled -public void loadAnnotationFrom(AlignFrame alf, String annotation) - -// parse the given string as a jalview or GFF features file and optionally enable feature display on the current alignment -// (v2.8) -public abstract void loadFeatures(String features, boolean autoenabledisplay) - -// parse the given string as a jalview or GFF features file and optionally enable feature display on the given alignment -// (v2.8) -public abstract void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay) - -// get the sequence features in the given format (Jalview or GFF) -public String getFeatures(String format) - -// get the sequence features in alf in the given format (Jalview or GFF) -public String getFeaturesFrom(AlignFrame alf, String format) - -// get current alignment's annotation as an annotation file -public String getAnnotation() - -// get alignment view alf's annotation as an annotation file -public String getAnnotationFrom(AlignFrame alf) - -// create a new view and return the alignFrame instance -public AlignFrame newView() - -// create a new view named name and return the alignFrame instance -public AlignFrame newView(String name) - -// create a new view on alf and return the alignFrame instance -public AlignFrame newViewFrom(AlignFrame alf) - -// create a new view named name on alf -// and return the alignFrame instance -public AlignFrame newViewFrom(AlignFrame alf, String name) - -// load a new alignment -// remember to store the AlignFrame object reference -// if you want to manipulate the new alignment view. -public AlignFrame loadAlignment(String text, String title) - - -// register a javascript function to handle any alignment mouseover events -// listener is name of javascript function which will be called -// with arguments [jalview.appletgui.AlignFrame,String(sequence id), -// String(column in alignment), String(position in sequence)] -// (v2.7) -public void setMouseoverListener(String listener) - -// register a javascript function to handle mouseover events for specific alignframe -// (v2.7) -public void setMouseoverListener(AlignFrame af, String listener) - -// register a javascript function to handle alignment selection events. -// Events are generated when the user completes a selection event, or when -// the user deselects all selected regions. -// listener is name of javascript function that will be called with arguments -// [jalview.appletgui.AlignFrame, String(sequence set id), -// String(separator separated list of sequences which were selected), -// String(separator separated list of column ranges)] -// (v2.7) -public void setSelectionListener(String listener) - -// register a selection listener for a specific alignment frame -// (v2.7) -public void setSelectionListener(AlignFrame af, String listener) - -// register a javascript function to handle events normally routed -// to a Jmol structure viewer. -// listener is a javascript function called with several different types -// of arguments, dependent on the type of structure callback event. -// See jalview.javascript.MouseOverStructureListener for full details or -// the embedded Jmol example. -// modelSet - is a separator separated list of PDB file URIs that this viewer is handling (where position in list equals model number in Jmol). -// (v2.7) -public void setStructureListener(String listener, String modelSet) - -// remove any callback using the given listener function and associated with -// the given alignFrame (or null for all callbacks) (v2.7) -public void removeJavascriptListener(AlignFrame af, String listener) - -// send a mouseover message to all the alignment windows associated with the -// given residue in the pdbfile (v2.7) -public void mouseOverStructure(String pdbResNum, String chain, String pdbfile) - -// bind a pdb file to a sequence in the given alignFrame - this will be searched -// for sequences matching sequenceId. The PDB file in pdbFile is either the contents -// of a PDB file or a URI that can be used to retrieve the file, and the pdbEntryString -// is the user friendly name (or PDBID) shown in jalview's user interface. -// returns true if binding was as success (v2.7) -public boolean addPdbFile(AlignFrame alFrame, - String sequenceId, String pdbEntryString, String pdbFile) - -// adjust horizontal/vertical scroll in alf to the make -// the given location the top left hand corner for given current view (v2.7) -public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn) - -// adjust horizontal scroll in alf to the make -// the given location the left hand corner for given current view (v2.7) -public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn) - -// adjust horizontal/vertical scroll in alf to the make -// the given location the top row for given current view (v2.7) -public void scrollViewToRowIn(AlignFrame alf, String topRow) - - -// return separator separated list of feature groups -// on the current alignment -public String getFeatureGroups() - -// return separator separated list of feature groups on alf -public String getFeatureGroupsOn(AlignFrame alf) - -// return separator separated list of feature groups -// either visible or hidden -public String getFeatureGroupsOfState(boolean state) - -// return separator separated list of feature groups -// either visible or hidden on alf -public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state) - -// set the separator separated list of feature groups as -// visible or hidden on the current alignment -public void setFeatureGroupState(String groupList, boolean state) - -// set the separator separated list of feature groups -// as visible or hidden on alf -public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state) - -// helper functions - -// Asynchronously retrieve next chunk of a large packet of data made available -// for a JalviewLite event handler, or the empty string if no more data is available. -// messageclass and viewId are keys used to retrieve a specific message related -// to an event. -// Use this in a javascript timer or GUI update thread to retrieve data without -// blocking the JalviewLite applet. DO NOT USE IN THE CALLBACK THAT HANDLED THE EVENT -// (v2.7) -public String getJsMessage(String messageclass, String viewId) - - -// convert list to a separator separated array -public String arrayToSeparatorList(String[] list) - -// get a string array from a list -public String[] separatorListToArray(String list) - -// get the current separator -public String getSeparator() - -// set the current separator -public void setSeparator(String) - -//// JalviewLite global state methods and fields - -// return the build date as a string -public static String getBuildDate() - -// return the JalviewLite version as a string -public static String getVersion() - -// debug flag - controls output to standard out -public static boolean debug - -- \ No newline at end of file