From 6ed26af2e3297ee68cbc3aba1d17215dfbc376bf Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 21 Jan 2014 12:00:54 +0000 Subject: [PATCH 1/1] JAL-957 javascript api documentation page --- examples-jbake/content/jalviewLiteJs.html | 257 +++++++++++++++++++++++++++++ 1 file changed, 257 insertions(+) create mode 100644 examples-jbake/content/jalviewLiteJs.html diff --git a/examples-jbake/content/jalviewLiteJs.html b/examples-jbake/content/jalviewLiteJs.html new file mode 100644 index 0000000..c14a7fe --- /dev/null +++ b/examples-jbake/content/jalviewLiteJs.html @@ -0,0 +1,257 @@ +title=Javascript API +type=page +status=published +level=0 +~~~~~~ + + +

The jalviewLite applet's application programming interface (API) includes two components. A JalviewLite Javascript Library and the public methods on the JalviewLite applet. +

+

Notes

+ + +

JalviewLite's Javascript API

 +

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
+
+
+ -- 1.7.10.2