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Using the Jalview Applet for Input to an HTML Form
**Unfortunately Javascript - Java communication is not possible using Internet Explorer or Opera on Macs. Please use Safari or Firefox. JalviewLite has the public method getAlignment(String outputFormat, boolean suffix) which can be called using Javascript. If more than one Jalview window is open, Jalview returns the alignment in the active window. The output format can be either Fasta, PFAM, Clustal, MSF, PIR, or BLC. The boolean value refers to whether the sequence limits should be appended to the sequence, eg /35-287 Note: You must either give Jalview a name in the applet tag or use the applets index in your Javascript. Since Jalview 2.2.1, the following public methods are availble to be called via Javascript: //get list of selected sequences public String getSelectedSequences() // get alignment as format public String getAlignment(String format) // get alignment displayed in alf as format public String getAlignmentFrom(AlignFrame alf, 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 // with jalview start-end sequence suffix appended public String getAlignmentFrom(AlignFrame alf, String format, String suffix) // add the given annotation to the current alignment public void loadAnnotation(String annotation) // add the given 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) // load a new alignment public AlignFrame loadAlignment(String text, String title) // create a new view and return the alignFrame instance public AlignFrame newView() // create a new view on alf and return the alignFrame instance public AlignFrame newViewFrom(AlignFrame alf) // create a new view named name and return the alignFrame instance public AlignFrame newView(String name) // create a new view named name on alf // and return the alignFrame instance public AlignFrame newViewFrom(AlignFrame alf, String name) // 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) |