+ Using the JalviewLite API to fill out forms using data from JalviewLite
Click the Javascript buttons below to interact with the Applet
instance on the page.
- View the source in your browser to see how it has been done.
- The applet's public API methods are listed below
- the following example.
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+ Since Jalview 2.5, the public methods listed - below are available to be called via Javascript. -Unfortunately Javascript - Java communication is not possible - using Internet Explorer or Opera on Macs. Please use Safari or - Firefox. -If more than one Jalview window is open, Jalview returns the - alignment in the active window, unless you provide an AlignFrame - object reference. -The alignment output format can be either Fasta, PFAM, Clustal, - MSF, PIR, or BLC. -When referring to the Jalview applet in javascript, you must - either give Jalview a name in the applet tag or use the applets index. - -//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 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 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 -public void loadAnnotation(String annotation) - -// add the given features or annotation to the given alignment view -public void loadAnnotationFrom(AlignFrame alf, String annotation) - -// 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 -public AlignFrame loadAlignment(String text, String title) - -// 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 - -// 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 - - |
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