+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.javascript;
import jalview.appletgui.AlignFrame;
/**
* @author jimp
- *
+ *
*/
public interface JalviewLiteJsApi
{
AlignFrame alf, String format, String suffix);
/**
- * get a separator separated list of sequence IDs reflecting the order of the current alignment
+ * 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
- *
+ * 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
+ * get a sep separated list of sequence IDs reflecting the order of the
+ * alignment in alf
*
* @param alf
- * @param sep - separator to use
+ * @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.
+ *
+ * @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);
* @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.
+ * @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
+ * re-order the given alignment using the given list of sequence IDs separated
+ * by sep
*
* @param alf
* @param order
* @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.
+ * @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)
+ * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
+ * PFAM - see jalview.io.AppletFormatAdapter for full list)
+ *
* @param format
* @return
*/
/**
* get alignment displayed in alf as format
+ *
* @param alf
* @param format
* @return
/**
* 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
+ * get alignment displayed in alf as format with or without the jalview
+ * start-end sequence suffix appended
+ *
* @param alf
* @param format
* @param 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
*/
/**
* get the sequence features in alf in the given format (Jalview or GFF)
+ *
* @param alf
* @param format
* @return
/**
* 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
*/
/**
* 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
*/
/**
* create a new view on alf and return the alignFrame instance
+ *
* @param alf
* @return
*/
/**
* create a new view named name on alf
+ *
* @param alf
* @param name
* @return
/**
* 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)]
+ *
+ * @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
+ *
+ * @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)]
+ * 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
+ * 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);
String pdbEntryString, String pdbFile);
/**
- * adjust horizontal/vertical scroll to the make the given location the top left hand corner for given current view
+ * adjust horizontal/vertical scroll to make the given location the top left
+ * hand corner for the given view
*
* @param alf
* @param 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()
/**
* 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);
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff