From 691798cf6a90094f4c83e79fd5c703457b1135b0 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 21 Oct 2011 13:01:02 +0100
Subject: [PATCH] (JAL-965) new api methods to allow features to be loaded
 without automatically enabling feature display.

---
 examples/jalviewLiteJs.html                  |   10 ++++++++++
 src/jalview/appletgui/AlignFrame.java        |   25 ++++++++++++++++++++-----
 src/jalview/bin/JalviewLite.java             |   23 +++++++++++++++++++++++
 src/jalview/javascript/JalviewLiteJsApi.java |   15 +++++++++++++++
 4 files changed, 68 insertions(+), 5 deletions(-)

diff --git a/examples/jalviewLiteJs.html b/examples/jalviewLiteJs.html
index e33b30d..197ef56 100644
--- 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
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -161,14 +161,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Load a features file onto the alignment
    * 
-   * @param String
-   *          DOCUMENT ME!
+   * @param file file URL, content, or other resolvable path
+   * @param type is protocol for accessing data referred to by file
    */
 
   public void parseFeaturesFile(String file, String type)
   {
+    parseFeaturesFile(file, type, true);
+  }
+  
+  /**
+   * Load a features file onto the alignment
+   * 
+   * @param file file URL, content, or other resolvable path
+   * @param type is protocol for accessing data referred to by file
+   * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
+   */
+  public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)
+  {    
     Hashtable featureLinks = new Hashtable();
     boolean featuresFile = false;
     try
@@ -188,8 +200,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
       }
-      viewport.showSequenceFeatures = true;
-      sequenceFeatures.setState(true);
+      if (autoenabledisplay)
+      {
+        viewport.showSequenceFeatures = true;
+        sequenceFeatures.setState(true);
+      }
       if (viewport.featureSettings != null)
       {
         viewport.featureSettings.refreshTable();
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 562bc92..0cba50e 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -716,6 +716,29 @@ public class JalviewLite extends Applet implements
   /*
    * (non-Javadoc)
    * 
+   * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
+   */
+  public void loadFeatures(String features, boolean autoenabledisplay)
+  {
+    loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
+   * , java.lang.String)
+   */
+  public void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
+  {
+    alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);
+  }
+
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
    */
   public String getFeatures(String format)
diff --git a/src/jalview/javascript/JalviewLiteJsApi.java b/src/jalview/javascript/JalviewLiteJsApi.java
index 103e7da..d064790 100644
--- 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
-- 
1.7.10.2