--- /dev/null
+package jalview.bin;
+
+import jalview.gui.AlignFrame;
+
+/**
+ * JAL-3369 JalviewJS API BH 2019.07.17
+ *
+ * @author hansonr
+ *
+ */
+public interface JalviewJSApi
+{
+
+ void showOverview();
+
+ /**
+ * process commandline arguments after the JavaScript application has started
+ *
+ * @param args
+ * @return
+ */
+ Object parseArguments(String[] args);
+
+
+ /**
+ * Open a new Tree panel on the desktop statically. Params are standard (not
+ * set by Groovy). No dialog is opened.
+ *
+ * @param af
+ * may be null
+ * @param treeType
+ * @param modelName
+ * @return null, or the string "label.you_need_at_least_n_sequences" if number
+ * of sequences selected is inappropriate
+ */
+ public Object openTreePanel(AlignFrame af, String treeType,
+ String modelName);
+
+ /**
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
+ *
+ * @param af
+ * may be null
+ * @param modelName
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
+ */
+ public Object openPcaPanel(AlignFrame af, String modelName);
+
+ /**
+ * The following public methods may be called externally, eg via javascript in
+ * an HTML page.
+ *
+ * <br>
+ * <em>TODO: introduce abstract interface for
+ * jalview.appletgui.AlignFrame</em><br>
+ *
+ * Most function arguments are strings, which contain serialised versions of
+ * lists. Lists of things are separated by a separator character - either the
+ * default or a user supplied one. Ranges and positions on an alignment or
+ * sequence can be specified as a list, where an item containing a single
+ * number is a single position, and an item like 1-2 specifies columns 1 and 2
+ * as a range.
+ */
+
+ // /**
+ // * @author jimp
+ // *
+ // */
+ // public interface JalviewLiteJsApi
+ // {
+
+ /**
+ * @return String list of selected sequence IDs, each terminated by the
+ * 'boolean not' character (""+0x00AC); or (¬);
+ */
+
+ public abstract String getSelectedSequences();
+
+ /**
+ * @param sep
+ * separator string or null for default
+ * @return String list of selected sequence IDs, each terminated by given
+ * separator string
+ */
+
+ public abstract String getSelectedSequences(String sep);
+
+ /**
+ * @param alf
+ * AlignFrame containing selection
+ * @return String list of selected sequence IDs, each terminated by current
+ * default separator sequence
+ *
+ */
+ public abstract String getSelectedSequencesFrom(AlignFrame alf);
+
+ /**
+ * get list of selected sequence IDs separated by given separator
+ *
+ * @param alf
+ * window containing selection
+ * @param sep
+ * separator string to use - default is 'boolean not'
+ * @return String list of selected sequence IDs, each terminated by the given
+ * separator
+ */
+ public abstract String getSelectedSequencesFrom(AlignFrame alf,
+ String sep);
+
+ /**
+ *
+ * @param sequenceId
+ * id of sequence to highlight
+ * @param position
+ * integer position [ tobe implemented or range ] on sequence
+ * @param alignedPosition
+ * true/false/empty string - indicate if position is an alignment
+ * column or unaligned sequence position
+ */
+
+ public abstract void highlight(String sequenceId, String position,
+ String alignedPosition);
+
+ /**
+ *
+ * @param sequenceId
+ * id of sequence to highlight
+ * @param position
+ * integer position [ tobe implemented or range ] on sequence
+ * @param alignedPosition
+ * false, blank or something else - indicate if position is an
+ * alignment column or unaligned sequence position
+ */
+ public abstract void highlightIn(AlignFrame alf, String sequenceId,
+ String position, String alignedPosition);
+
+ /**
+ * select regions of the currrent alignment frame
+ *
+ * @param sequenceIds
+ * String separated list of sequence ids or empty string
+ * @param columns
+ * String separated list { column range or column, ..} or empty
+ * string
+ */
+
+ public abstract void select(String sequenceIds, String columns);
+
+ /**
+ * select regions of the currrent alignment frame
+ *
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+
+ public abstract void select(String sequenceIds, String columns,
+ String sep);
+
+ /**
+ * select regions of the given alignment frame
+ *
+ * @param alf
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+ public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ String columns);
+
+ /**
+ * select regions of the given alignment frame
+ *
+ * @param alf
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+ public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ String columns, String sep);
+
+ /**
+ * get sequences selected in current AlignFrame and return their alignment in
+ * format 'format' either with or without suffix
+ *
+ * @param alf
+ * - where selection is
+ * @param format
+ * - format of alignment file
+ * @param suffix
+ * - "true" to append /start-end string to each sequence ID
+ * @return selected sequences as flat file or empty string if there was no
+ * current selection
+ */
+
+ public abstract String getSelectedSequencesAsAlignment(String format,
+ String suffix);
+
+ /**
+ * get sequences selected in alf and return their alignment in format 'format'
+ * either with or without suffix
+ *
+ * @param alf
+ * - where selection is
+ * @param format
+ * - format of alignment file
+ * @param suffix
+ * - "true" to append /start-end string to each sequence ID
+ * @return selected sequences as flat file or empty string if there was no
+ * current selection
+ */
+ public abstract String getSelectedSequencesAsAlignmentFrom(
+ AlignFrame alf,
+ String format, String suffix);
+
+ /**
+ * get a separator separated list of sequence IDs reflecting the order of the
+ * current alignment
+ *
+ * @return
+ */
+
+ public abstract String getAlignmentOrder();
+
+ /**
+ * get a separator separated list of sequence IDs reflecting the order of the
+ * alignment in alf
+ *
+ * @param alf
+ * @return
+ */
+ public abstract String getAlignmentOrderFrom(AlignFrame alf);
+
+ /**
+ * get a sep separated list of sequence IDs reflecting the order of the
+ * alignment in alf
+ *
+ * @param alf
+ * @param sep
+ * - separator to use
+ * @return
+ */
+ public abstract String getAlignmentOrderFrom(AlignFrame alf,
+ String sep);
+
+ /**
+ * re-order the current alignment using the given list of sequence IDs
+ *
+ * @param order
+ * - sep separated list
+ * @param undoName
+ * - string to use when referring to ordering action in undo buffer
+ * @return 'true' if alignment was actually reordered. empty string if
+ * alignment did not contain sequences.
+ */
+
+ public abstract String orderBy(String order, String undoName);
+
+ /**
+ * re-order the current alignment using the given list of sequence IDs
+ * separated by sep
+ *
+ * @param order
+ * - sep separated list
+ * @param undoName
+ * - string to use when referring to ordering action in undo buffer
+ * @param sep
+ * @return 'true' if alignment was actually reordered. empty string if
+ * alignment did not contain sequences.
+ */
+
+ public abstract String orderBy(String order, String undoName,
+ String sep);
+
+ /**
+ * re-order the given alignment using the given list of sequence IDs separated
+ * by sep
+ *
+ * @param alf
+ * @param order
+ * - sep separated list
+ * @param undoName
+ * - string to use when referring to ordering action in undo buffer
+ * @param sep
+ * @return 'true' if alignment was actually reordered. empty string if
+ * alignment did not contain sequences.
+ */
+ public abstract String orderAlignmentBy(AlignFrame alf, String order,
+ String undoName, String sep);
+
+ /**
+ * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
+ * PFAM - see jalview.io.AppletFormatAdapter for full list);
+ *
+ * @param format
+ * @return
+ */
+
+ public abstract String getAlignment(String format);
+
+ /**
+ * get alignment displayed in alf as format
+ *
+ * @param alf
+ * @param format
+ * @return
+ */
+ public abstract String getAlignmentFrom(AlignFrame alf, String format);
+
+ /**
+ * get alignment as format with jalview start-end sequence suffix appended
+ *
+ * @param format
+ * @param suffix
+ * @return
+ */
+
+ public abstract String getAlignment(String format, String suffix);
+
+ /**
+ * get alignment displayed in alf as format with or without the jalview
+ * start-end sequence suffix appended
+ *
+ * @param alf
+ * @param format
+ * @param suffix
+ * @return
+ */
+ public abstract String getAlignmentFrom(AlignFrame alf, String format,
+ String suffix);
+
+ /**
+ * add the given features or annotation to the current alignment
+ *
+ * @param annotation
+ */
+
+ public abstract void loadAnnotation(String annotation);
+
+ /**
+ * add the given features or annotation to the given alignment view
+ *
+ * @param alf
+ * @param annotation
+ */
+ public abstract void loadAnnotationFrom(AlignFrame alf,
+ String annotation);
+
+ /**
+ * parse the given string as a jalview feature or GFF annotation file and
+ * optionally enable feature display on the current AlignFrame
+ *
+ * @param features
+ * - gff or features file
+ * @param autoenabledisplay
+ * - when true, feature display will be enabled if any features can
+ * be parsed from the string.
+ */
+
+ public abstract void loadFeatures(String features,
+ boolean autoenabledisplay);
+
+ /**
+ * parse the given string as a jalview feature or GFF annotation file and
+ * optionally enable feature display on the given AlignFrame.
+ *
+ * @param alf
+ * @param features
+ * - gff or features file
+ * @param autoenabledisplay
+ * - when true, feature display will be enabled if any features can
+ * be parsed from the string.
+ * @return true if data parsed as features
+ */
+ public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
+ boolean autoenabledisplay);
+
+ /**
+ * get the sequence features in the given format (Jalview or GFF);
+ *
+ * @param format
+ * @return
+ */
+
+ public abstract String getFeatures(String format);
+
+ /**
+ * get the sequence features in alf in the given format (Jalview or GFF);
+ *
+ * @param alf
+ * @param format
+ * @return
+ */
+ public abstract String getFeaturesFrom(AlignFrame alf, String format);
+
+ /**
+ * get current alignment's annotation as an annotation file
+ *
+ * @return
+ */
+
+ public abstract String getAnnotation();
+
+ /**
+ * get alignment view alf's annotation as an annotation file
+ *
+ * @param alf
+ * @return
+ */
+ public abstract String getAnnotationFrom(AlignFrame alf);
+
+ // BH incompatibility here -- JalviewLite created an AlignFrame; Jalview
+ // creates an AlignmentPanel
+ // /**
+ // * create a new view and return the AlignFrame instance
+ // *
+ // * @return
+ // */
+ //
+ // public abstract AlignFrame newView();
+ //
+ // /**
+ // * create a new view named name and return the AlignFrame instance
+ // *
+ // * @param name
+ // * @return
+ // */
+ //
+ // public abstract AlignFrame newView(String name);
+ //
+ // /**
+ // * create a new view on alf and return the AlignFrame instance
+ // *
+ // * @param alf
+ // * @return
+ // */
+ // public abstract AlignFrame newViewFrom(AlignFrame alf);
+ //
+ // /**
+ // * create a new view named name on alf
+ // *
+ // * @param alf
+ // * @param name
+ // * @return
+ // */
+ // public abstract AlignFrame newViewFrom(AlignFrame alf, String name);
+
+ /**
+ *
+ * @param text
+ * alignment file as a string
+ * @param title
+ * window title
+ * @return null or new alignment frame
+ */
+
+ public abstract AlignFrame loadAlignment(String text, String title);
+
+ /**
+ * register a javascript function to handle any alignment mouseover events
+ *
+ * @param listener
+ * name of javascript function (called with arguments
+ * [jalview.appletgui.AlignFrame,String(sequence id);,String(column
+ * in alignment);, String(position in sequence);]
+ */
+
+ public abstract void setMouseoverListener(String listener);
+
+ /**
+ * register a javascript function to handle mouseover events
+ *
+ * @param af
+ * (null or specific AlignFrame for which events are to be listened
+ * for);
+ * @param listener
+ * name of javascript function
+ */
+ public abstract void setMouseoverListener(AlignFrame af,
+ String listener);
+
+ /**
+ * register a javascript function to handle any alignment selection events.
+ * Events are generated when the user completes a selection event, or when the
+ * user deselects all selected regions.
+ *
+ * @param listener
+ * name of javascript function (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 (i.e.
+ * single number or hyphenated range); that were selected);]
+ */
+
+ public abstract void setSelectionListener(String listener);
+
+ public abstract void setSelectionListener(AlignFrame af,
+ String listener);
+
+ /**
+ * register a javascript function to handle events normally routed to a Jmol
+ * structure viewer.
+ *
+ * @param listener
+ * - javascript function (arguments are variable, see
+ * jalview.javascript.MouseOverStructureListener for full details);
+ * @param modelSet
+ * - separator separated list of PDB file URIs that this viewer is
+ * handling. These files must be in the same order they appear in
+ * Jmol (e.g. first one is frame 1, second is frame 2, etc);.
+ * @see jalview.javascript.MouseOverStructureListener
+ */
+
+ public abstract 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);
+ *
+ * @param af
+ * (may be null);
+ * @param listener
+ * (may be null);
+ */
+ public abstract void removeJavascriptListener(AlignFrame af,
+ String listener);
+
+ /**
+ * send a mouseover message to all the alignment windows associated with the
+ * given residue in the pdbfile
+ *
+ * @param pdbResNum
+ * @param chain
+ * @param pdbfile
+ */
+
+ public abstract void mouseOverStructure(String pdbResNum, String chain,
+ String pdbfile);
+
+ /**
+ * bind a pdb file to a sequence in the given AlignFrame.
+ *
+ * @param alFrame
+ * - null or specific AlignFrame. This specifies the dataset that
+ * will be searched for a seuqence called sequenceId
+ * @param sequenceId
+ * - sequenceId within the dataset.
+ * @param pdbEntryString
+ * - the short name for the PDB file
+ * @param pdbFile
+ * - pdb file - either a URL or a valid PDB file.
+ * @return true if binding was as success TODO: consider making an exception
+ * structure for indicating when PDB parsing or sequenceId location
+ * fails.
+ */
+ public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ String pdbEntryString, String pdbFile);
+
+ /**
+ * adjust horizontal/vertical scroll to make the given location the top left
+ * hand corner for the given view
+ *
+ * @param alf
+ * @param topRow
+ * @param leftHandColumn
+ */
+ public abstract void scrollViewToIn(AlignFrame alf, String topRow,
+ String leftHandColumn);
+
+ /**
+ * adjust vertical scroll to make the given row the top one for given view
+ *
+ * @param alf
+ * @param topRow
+ */
+ public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
+
+ /**
+ * adjust horizontal scroll to make the given column the left one in the given
+ * view
+ *
+ * @param alf
+ * @param leftHandColumn
+ */
+ public abstract void scrollViewToColumnIn(AlignFrame alf,
+ String leftHandColumn);
+
+ /**
+ *
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups();
+ */
+
+ public abstract String getFeatureGroups();
+
+ /**
+ * @param alf
+ * AlignFrame to get feature groups on
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups();
+ */
+ public abstract String getFeatureGroupsOn(AlignFrame alf);
+
+ /**
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
+ */
+
+ public abstract String getFeatureGroupsOfState(boolean visible);
+
+ /**
+ * @param alf
+ * align frame to get groups of state visible
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
+ */
+ public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
+ boolean visible);
+
+ /**
+ * @param groups
+ * tab separated list of group names
+ * @param state
+ * true or false
+ * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
+ * boolean);
+ */
+ public abstract void setFeatureGroupStateOn(AlignFrame alf,
+ String groups,
+ boolean state);
+
+
+ public abstract void setFeatureGroupState(String groups, boolean state);
+
+ /**
+ * List separator string
+ *
+ * @return the separator
+ */
+
+ public abstract String getSeparator();
+
+ /**
+ * List separator string
+ *
+ * @param separator
+ * the separator to set. empty string will reset separator to default
+ */
+
+ public abstract void setSeparator(String separator);
+
+ /**
+ * Retrieve fragments of a large packet of data made available by JalviewLite.
+ *
+ * @param messageclass
+ * @param viewId
+ * @return next chunk of message
+ */
+
+ public abstract String getJsMessage(String messageclass, String viewId);
+
+ /// in http://www.jalview.org/examples/jalviewLiteJs.html but missing here
+
+ // 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);
+
+
+ public String arrayToSeparatorList(String[] array);
+
+ // get a string array from a list
+
+ public String[] separatorListToArray(String list);
+
+ // debug flag - controls output to standard out
+ public static boolean debug = false;
+
+}
git://source.jalview.org / jalview.git / commitdiff