--- /dev/null
+package jalview.javascript;
+
+import jalview.appletgui.AlignFrame;
+
+/**
+ * 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);
+
+ /**
+ * 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);
+
+ /**
+ * 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.
+ @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 the make the given location the top left hand corner for given current view
+ *
+ * @param alf
+ * @param topRow
+ * @param leftHandColumn
+ */
+ public abstract void scrollViewToIn(AlignFrame alf, String topRow,
+ 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);
+
+}
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git://source.jalview.org / jalview.git / blobdiff