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- 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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- Make a new View and Get and Set
- Group Display List
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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)
+Click here to view decorated page
-// 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)
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-// get alignment as format
-public String getAlignment(String format)
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-// get alignment as format with jalview
-// start-end sequence suffix appended
-public String getAlignment(String format, String suffix)
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-// get alignment displayed in alf as format
-public String getAlignmentFrom(AlignFrame alf, String format)
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-// get alignment displayed in alf as format
-// with jalview start-end sequence suffix appended
-public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
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-// add the given features or annotation to the current alignment
-public void loadAnnotation(String annotation)
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-// add the given features or annotation to the given alignment view
-public void loadAnnotationFrom(AlignFrame alf, String annotation)
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-// get the sequence features in the given format (Jalview or GFF)
-public String getFeatures(String format)
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-// get the sequence features in alf in the given format (Jalview or GFF)
-public String getFeaturesFrom(AlignFrame alf, String format)
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-// get current alignment's annotation as an annotation file
-public String getAnnotation()
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-// get alignment view alf's annotation as an annotation file
-public String getAnnotationFrom(AlignFrame alf)
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-// create a new view and return the alignFrame instance
-public AlignFrame newView()
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-// create a new view named name and return the alignFrame instance
-public AlignFrame newView(String name)
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-// create a new view on alf and return the alignFrame instance
-public AlignFrame newViewFrom(AlignFrame alf)
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-// create a new view named name on alf
-// and return the alignFrame instance
-public AlignFrame newViewFrom(AlignFrame alf, String name)
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-// load a new alignment
-public AlignFrame loadAlignment(String text, String title)
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-// return separator separated list of feature groups
-// on the current alignment
-public String getFeatureGroups()
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-// return separator separated list of feature groups on alf
-public String getFeatureGroupsOn(AlignFrame alf)
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-// return separator separated list of feature groups
-// either visible or hidden
-public String getFeatureGroupsOfState(boolean state)
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-// return separator separated list of feature groups
-// either visible or hidden on alf
-public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state)
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-// set the separator separated list of feature groups as
-// visible or hidden on the current alignment
-public void setFeatureGroupState(String groupList, boolean state)
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-// set the separator separated list of feature groups
-// as visible or hidden on alf
-public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state)
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-// helper functions
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-// convert list to a separator separated array
-public String arrayToSeparatorList(String[] list)
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-// get a string array from a list
-public String[] separatorListToArray(String list)
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-// get the current separator
-public String getSeparator()
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-// set the current separator
-public void setSeparator(String)
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-//// JalviewLite global state methods and fields
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-// return the build date as a string
-public static String getBuildDate()
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-// return the JalviewLite version as a string
-public static String getVersion()
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-// debug flag - controls output to standard out
-public static boolean debug
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