*/
package jalview.javascript;
-import jalview.api.AlignFrameI;
+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.AlignFrameI</em><br>
+ * <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.
/**
* @param alf
- * AlignFrameI containing selection
+ * alignframe containing selection
* @return String list of selected sequence IDs, each terminated by current
* default separator sequence
*
*/
- public abstract String getSelectedSequencesFrom(AlignFrameI alf);
+ public abstract String getSelectedSequencesFrom(AlignFrame alf);
/**
* get list of selected sequence IDs separated by given separator
* @return String list of selected sequence IDs, each terminated by the given
* separator
*/
- public abstract String getSelectedSequencesFrom(AlignFrameI alf,
+ public abstract String getSelectedSequencesFrom(AlignFrame alf,
String sep);
/**
* false, blank or something else - indicate if position is an
* alignment column or unaligned sequence position
*/
- public abstract void highlightIn(AlignFrameI alf, String sequenceId,
+ public abstract void highlightIn(AlignFrame alf, String sequenceId,
String position, String alignedPosition);
/**
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrameI alf, String sequenceIds,
+ public abstract void selectIn(AlignFrame alf, String sequenceIds,
String columns);
/**
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrameI alf, String sequenceIds,
+ public abstract void selectIn(AlignFrame alf, String sequenceIds,
String columns, String sep);
/**
- * get sequences selected in current AlignFrameI and return their alignment in
+ * get sequences selected in current alignFrame and return their alignment in
* format 'format' either with or without suffix
*
* @param alf
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
- public abstract String getSelectedSequencesAsAlignmentFrom(
- AlignFrameI alf,
+ public abstract String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix);
/**
* @param alf
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrameI alf);
+ public abstract String getAlignmentOrderFrom(AlignFrame alf);
/**
* get a sep separated list of sequence IDs reflecting the order of the
* - separator to use
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrameI alf, String sep);
+ public abstract String getAlignmentOrderFrom(AlignFrame alf, String sep);
/**
* re-order the current alignment using the given list of sequence IDs
* @return 'true' if alignment was actually reordered. empty string if
* alignment did not contain sequences.
*/
- public abstract String orderAlignmentBy(AlignFrameI alf, String order,
+ public abstract String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep);
/**
* @param format
* @return
*/
- public abstract String getAlignmentFrom(AlignFrameI alf, String format);
+ public abstract String getAlignmentFrom(AlignFrame alf, String format);
/**
* get alignment as format with jalview start-end sequence suffix appended
* @param suffix
* @return
*/
- public abstract String getAlignmentFrom(AlignFrameI alf, String format,
+ public abstract String getAlignmentFrom(AlignFrame alf, String format,
String suffix);
/**
* @param alf
* @param annotation
*/
- public abstract void loadAnnotationFrom(AlignFrameI alf,
+ 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 AlignFrameI
+ * optionally enable feature display on the current alignFrame
*
* @param features
* - gff or features file
/**
* parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the given AlignFrameI.
+ * optionally enable feature display on the given alignFrame.
*
* @param alf
* @param features
* be parsed from the string.
* @return true if data parsed as features
*/
- public abstract boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay);
/**
* @param format
* @return
*/
- public abstract String getFeaturesFrom(AlignFrameI alf, String format);
+ public abstract String getFeaturesFrom(AlignFrame alf, String format);
/**
* get current alignment's annotation as an annotation file
* @param alf
* @return
*/
- public abstract String getAnnotationFrom(AlignFrameI alf);
+ public abstract String getAnnotationFrom(AlignFrame alf);
/**
- * create a new view and return the AlignFrameI instance
+ * create a new view and return the alignFrame instance
*
* @return
*/
- public abstract AlignFrameI newView();
+ public abstract AlignFrame newView();
/**
- * create a new view named name and return the AlignFrameI instance
+ * create a new view named name and return the alignFrame instance
*
* @param name
* @return
*/
- public abstract AlignFrameI newView(String name);
+ public abstract AlignFrame newView(String name);
/**
- * create a new view on alf and return the AlignFrameI instance
+ * create a new view on alf and return the alignFrame instance
*
* @param alf
* @return
*/
- public abstract AlignFrameI newViewFrom(AlignFrameI alf);
+ public abstract AlignFrame newViewFrom(AlignFrame alf);
/**
* create a new view named name on alf
* @param name
* @return
*/
- public abstract AlignFrameI newViewFrom(AlignFrameI alf, String name);
+ public abstract AlignFrame newViewFrom(AlignFrame alf, String name);
/**
*
* window title
* @return null or new alignment frame
*/
- public abstract AlignFrameI loadAlignment(String text, String title);
+ 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.AlignFrameI,String(sequence id),String(column
- * in alignment), String(position in sequence)]
+ * [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 AlignFrameI for which events are to be listened
+ * (null or specific alignframe for which events are to be listened
* for)
* @param listener
* name of javascript function
*/
- public abstract void setMouseoverListener(AlignFrameI af,
- String listener);
+ public abstract void setMouseoverListener(AlignFrame af, String listener);
/**
* register a javascript function to handle any alignment selection events.
*
* @param listener
* name of javascript function (called with arguments
- * [jalview.appletgui.AlignFrameI, String(sequence set id),
+ * [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(AlignFrameI af,
- String listener);
+ public abstract void setSelectionListener(AlignFrame af, String listener);
/**
* register a javascript function to handle events normally routed to a Jmol
/**
* remove any callback using the given listener function and associated with
- * the given AlignFrameI (or null for all callbacks)
+ * the given alignFrame (or null for all callbacks)
*
* @param af
* (may be null)
* @param listener
* (may be null)
*/
- public abstract void removeJavascriptListener(AlignFrameI af,
+ public abstract void removeJavascriptListener(AlignFrame af,
String listener);
/**
String pdbfile);
/**
- * bind a pdb file to a sequence in the given AlignFrameI.
+ * bind a pdb file to a sequence in the given alignFrame.
*
* @param alFrame
- * - null or specific AlignFrameI. This specifies the dataset that
+ * - null or specific alignFrame. This specifies the dataset that
* will be searched for a seuqence called sequenceId
* @param sequenceId
* - sequenceId within the dataset.
* structure for indicating when PDB parsing or sequenceId location
* fails.
*/
- public abstract boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+ public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile);
/**
* @param topRow
* @param leftHandColumn
*/
- public abstract void scrollViewToIn(AlignFrameI alf, String topRow,
+ public abstract void scrollViewToIn(AlignFrame alf, String topRow,
String leftHandColumn);
/**
* @param alf
* @param topRow
*/
- public abstract void scrollViewToRowIn(AlignFrameI alf, String topRow);
+ public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
/**
* adjust horizontal scroll to make the given column the left one in the given
* @param alf
* @param leftHandColumn
*/
- public abstract void scrollViewToColumnIn(AlignFrameI alf,
+ public abstract void scrollViewToColumnIn(AlignFrame alf,
String leftHandColumn);
/**
*
* @return
- * @see jalview.appletgui.AlignFrameI#getFeatureGroups()
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
*/
public abstract String getFeatureGroups();
/**
* @param alf
- * AlignFrameI to get feature groups on
+ * alignframe to get feature groups on
* @return
- * @see jalview.appletgui.AlignFrameI#getFeatureGroups()
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
*/
- public abstract String getFeatureGroupsOn(AlignFrameI alf);
+ public abstract String getFeatureGroupsOn(AlignFrame alf);
/**
* @param visible
* @return
- * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean)
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
*/
public abstract String getFeatureGroupsOfState(boolean visible);
* align frame to get groups of state visible
* @param visible
* @return
- * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean)
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
*/
- public abstract String getFeatureGroupsOfStateOn(AlignFrameI alf,
+ public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
boolean visible);
/**
* tab separated list of group names
* @param state
* true or false
- * @see jalview.appletgui.AlignFrameI#setFeatureGroupState(java.lang.String[],
+ * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
* boolean)
*/
- public abstract void setFeatureGroupStateOn(AlignFrameI alf,
- String groups,
+ public abstract void setFeatureGroupStateOn(AlignFrame alf, String groups,
boolean state);
public abstract void setFeatureGroupState(String groups, boolean state);