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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