X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=9c23a0af68dd02273967ac7632163da45ae57925;hb=aa213924876640ba82e866da5a750d9cdaa816d2;hp=52e7408f61710eb29d4bf6c278bbc6a080830243;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 52e7408..9c23a0a 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -492,6 +492,8 @@ public class JalviewLite extends Applet implements
       boolean seqlimits = suffix.equalsIgnoreCase("true");
       if (alf.viewport.getSelectionGroup() != null)
       {
+        // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data
+        // TODO consider using getSequenceSelection instead here
         String reply = new AppletFormatAdapter().formatSequences(format,
                 new Alignment(alf.viewport.getSelectionAsNewSequence()),
                 seqlimits);
@@ -716,6 +718,29 @@ 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 boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
+  {
+    return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);
+  }
+
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
    */
   public String getFeatures(String format)
@@ -1798,8 +1823,7 @@ public class JalviewLite extends Applet implements
 
         if (protocol == jalview.io.AppletFormatAdapter.PASTE)
         {
-          newAlignFrame.setTitle("Sequences from "
-                  + applet.getDocumentBase());
+          newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());
         }
 
         newAlignFrame.statusBar.setText("Successfully loaded file " + file);
@@ -1840,7 +1864,46 @@ public class JalviewLite extends Applet implements
           }
         }
 
-        String param = applet.getParameter("features");
+
+        /*
+         * Try to load T-Coffee score file
+         */
+        String sScoreFile = applet.getParameter("scoreFile");
+        if( sScoreFile != null && !"".equals(sScoreFile) ) {
+            try {
+              if (debug) {
+                System.err.println("Attempting to load T-COFFEE score file from the scoreFile parameter");
+              }
+              if (!newAlignFrame.loadScoreFile(sScoreFile)) {
+                System.err.println("Failed to parse T-COFFEE parameter as a valid score file ('"+sScoreFile+"')");
+              }
+            }catch( Exception e ) {
+            	System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());
+            }
+        }
+       
+
+        // ///////////////////////////
+        // modify display of features
+        // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed
+        //
+        // hide specific groups
+        // 
+        String param = applet.getParameter("hidefeaturegroups");
+        if (param != null)
+        {
+          newAlignFrame.setFeatureGroupState(separatorListToArray(param), false);        
+//          applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+        }
+        // show specific groups
+        param = applet.getParameter("showfeaturegroups");
+        if (param != null)
+        {
+          newAlignFrame.setFeatureGroupState(separatorListToArray(param), true);        
+//          applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+        }
+        // and now load features
+        param = applet.getParameter("features");
         if (param != null)
         {
           param = setProtocolState(param);
@@ -2059,21 +2122,6 @@ public class JalviewLite extends Applet implements
                   protocols);
 
         }
-        // ///////////////////////////
-        // modify display of features
-        //
-        // hide specific groups
-        param = applet.getParameter("hidefeaturegroups");
-        if (param != null)
-        {
-          applet.setFeatureGroupStateOn(newAlignFrame, param, false);
-        }
-        // show specific groups
-        param = applet.getParameter("showfeaturegroups");
-        if (param != null)
-        {
-          applet.setFeatureGroupStateOn(newAlignFrame, param, true);
-        }
       }
       else
       {