(JAL-965) new api methods to allow features to be loaded without automatically enabli...

[jalview.git] / src / jalview / javascript / JalviewLiteJsApi.java

diff --git a/src/jalview/javascript/JalviewLiteJsApi.java b/src/jalview/javascript/JalviewLiteJsApi.java
index a7255b0..d064790 100644 (file)
--- a/src/jalview/javascript/JalviewLiteJsApi.java
+++ b/src/jalview/javascript/JalviewLiteJsApi.java
@@ -1,3 +1,20 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ *******************************************************************************/
 package jalview.javascript;
 
 import jalview.appletgui.AlignFrame;
@@ -263,6 +280,21 @@ public interface JalviewLiteJsApi
   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.
+   */
+  public abstract void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay);
+
+  /**
    * get the sequence features in the given format (Jalview or GFF)
    * @param format
    * @return
@@ -400,7 +432,7 @@ 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
@@ -408,6 +440,20 @@ public interface JalviewLiteJsApi
    */
   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);
 
   /**
    *