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

diff --git a/examples/jalviewLiteJs.html b/examples/jalviewLiteJs.html
index e33b30d..197ef56 100644 (file)
--- a/examples/jalviewLiteJs.html
+++ b/examples/jalviewLiteJs.html
@@ -215,11 +215,21 @@ public String getAlignmentFrom(AlignFrame alf, String format)
 public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
 
 // add the given features or annotation to the current alignment
+// if features are loaded, feature display is automatically enabled
 public void loadAnnotation(String annotation)
 
 // add the given features or annotation to the given alignment view
+// if features are loaded, feature display is automatically enabled
 public void loadAnnotationFrom(AlignFrame alf, String annotation)
 
+// parse the given string as a jalview or GFF features file and optionally enable feature display on the current alignment
+// (v2.7.1)
+public abstract void loadFeatures(String features, boolean autoenabledisplay)
+
+// parse the given string as a jalview or GFF features file and optionally enable feature display on the given alignment
+// (v2.7.1)
+public abstract void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
+
 // get the sequence features in the given format (Jalview or GFF)
 public String getFeatures(String format)
 

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 759075a..5790bc3 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -161,14 +161,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }\r
 \r
   /**\r
-   * DOCUMENT ME!\r
+   * Load a features file onto the alignment\r
    * \r
-   * @param String\r
-   *          DOCUMENT ME!\r
+   * @param file file URL, content, or other resolvable path\r
+   * @param type is protocol for accessing data referred to by file\r
    */\r
 \r
   public void parseFeaturesFile(String file, String type)\r
   {\r
+    parseFeaturesFile(file, type, true);\r
+  }\r
+  \r
+  /**\r
+   * Load a features file onto the alignment\r
+   * \r
+   * @param file file URL, content, or other resolvable path\r
+   * @param type is protocol for accessing data referred to by file\r
+   * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded\r
+   */\r
+  public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)\r
+  {    \r
     Hashtable featureLinks = new Hashtable();\r
     boolean featuresFile = false;\r
     try\r
@@ -188,8 +200,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {\r
         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;\r
       }\r
-      viewport.showSequenceFeatures = true;\r
-      sequenceFeatures.setState(true);\r
+      if (autoenabledisplay)\r
+      {\r
+        viewport.showSequenceFeatures = true;\r
+        sequenceFeatures.setState(true);\r
+      }\r
       if (viewport.featureSettings != null)\r
       {\r
         viewport.featureSettings.refreshTable();\r

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 562bc92..0cba50e 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -716,6 +716,29 @@ public class JalviewLite extends Applet implements
   /*\r
    * (non-Javadoc)\r
    * \r
+   * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)\r
+   */\r
+  public void loadFeatures(String features, boolean autoenabledisplay)\r
+  {\r
+    loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);\r
+  }\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
+   * @see\r
+   * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame\r
+   * , java.lang.String)\r
+   */\r
+  public void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)\r
+  {\r
+    alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);\r
+  }\r
+\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)\r
    */\r
   public String getFeatures(String format)\r

diff --git a/src/jalview/javascript/JalviewLiteJsApi.java b/src/jalview/javascript/JalviewLiteJsApi.java
index 103e7da..d064790 100644 (file)
--- a/src/jalview/javascript/JalviewLiteJsApi.java
+++ b/src/jalview/javascript/JalviewLiteJsApi.java
@@ -280,6 +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