X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FJalviewLiteJsApi.java;h=b5811aa52d91adc4a2c2e53fc3ea8278fe59491f;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=02da9d403e1e2c6835659a92c2b4555f3b83751c;hpb=0c0991e85ba4c0536b366abe020eaf84ca6e29a4;p=jalview.git

diff --git a/src/jalview/javascript/JalviewLiteJsApi.java b/src/jalview/javascript/JalviewLiteJsApi.java
index 02da9d4..b5811aa 100644
--- a/src/jalview/javascript/JalviewLiteJsApi.java
+++ b/src/jalview/javascript/JalviewLiteJsApi.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
@@ -15,7 +35,7 @@ import jalview.appletgui.AlignFrame;
 
 /**
  * @author jimp
- *
+ * 
  */
 public interface JalviewLiteJsApi
 {
@@ -53,7 +73,8 @@ public interface JalviewLiteJsApi
    * @return String list of selected sequence IDs, each terminated by the given
    *         separator
    */
-  public abstract String getSelectedSequencesFrom(AlignFrame alf, String sep);
+  public abstract String getSelectedSequencesFrom(AlignFrame alf,
+          String sep);
 
   /**
    * 
@@ -100,7 +121,8 @@ public interface JalviewLiteJsApi
    * @param sep
    *          separator between toselect fields
    */
-  public abstract void select(String sequenceIds, String columns, String sep);
+  public abstract void select(String sequenceIds, String columns,
+          String sep);
 
   /**
    * select regions of the given alignment frame
@@ -155,35 +177,46 @@ public interface JalviewLiteJsApi
    * @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);
+  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 
+   * 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);
 
@@ -196,13 +229,14 @@ public interface JalviewLiteJsApi
    * @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
@@ -210,13 +244,16 @@ public interface JalviewLiteJsApi
    * @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
    */
@@ -224,6 +261,7 @@ public interface JalviewLiteJsApi
 
   /**
    * get alignment displayed in alf as format
+   * 
    * @param alf
    * @param format
    * @return
@@ -232,6 +270,7 @@ public interface JalviewLiteJsApi
 
   /**
    * get alignment as format with jalview start-end sequence suffix appended
+   * 
    * @param format
    * @param suffix
    * @return
@@ -239,8 +278,9 @@ public interface JalviewLiteJsApi
   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
@@ -251,19 +291,51 @@ public interface JalviewLiteJsApi
 
   /**
    * 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);
+  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
    */
@@ -271,6 +343,7 @@ public interface JalviewLiteJsApi
 
   /**
    * get the sequence features in alf in the given format (Jalview or GFF)
+   * 
    * @param alf
    * @param format
    * @return
@@ -279,12 +352,14 @@ public interface JalviewLiteJsApi
 
   /**
    * 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
    */
@@ -292,12 +367,14 @@ public interface JalviewLiteJsApi
 
   /**
    * 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
    */
@@ -305,6 +382,7 @@ public interface JalviewLiteJsApi
 
   /**
    * create a new view on alf and return the alignFrame instance
+   * 
    * @param alf
    * @return
    */
@@ -312,6 +390,7 @@ public interface JalviewLiteJsApi
 
   /**
    * create a new view named name on alf
+   * 
    * @param alf
    * @param name
    * @return
@@ -330,32 +409,56 @@ public interface JalviewLiteJsApi
 
   /**
    * 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);
+  public abstract void setStructureListener(String listener,
+          String modelSet);
 
   /**
    * remove any callback using the given listener function and associated with
@@ -400,7 +503,8 @@ public interface JalviewLiteJsApi
           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
@@ -410,6 +514,24 @@ public interface JalviewLiteJsApi
           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()
@@ -449,8 +571,8 @@ public interface JalviewLiteJsApi
    * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
    *      boolean)
    */
-  public abstract void setFeatureGroupStateOn(AlignFrame alf,
-          String groups, boolean state);
+  public abstract void setFeatureGroupStateOn(AlignFrame alf, String groups,
+          boolean state);
 
   public abstract void setFeatureGroupState(String groups, boolean state);
 
@@ -471,10 +593,11 @@ public interface JalviewLiteJsApi
 
   /**
    * 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
+}