formatting

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 9c23a0a..5f75c18 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -492,7 +492,8 @@ public class JalviewLite extends Applet implements
       boolean seqlimits = suffix.equalsIgnoreCase("true");\r
       if (alf.viewport.getSelectionGroup() != null)\r
       {\r
-        // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data\r
+        // JBPNote: getSelectionAsNewSequence behaviour has changed - this\r
+        // method now returns a full copy of sequence data\r
         // TODO consider using getSequenceSelection instead here\r
         String reply = new AppletFormatAdapter().formatSequences(format,\r
                 new Alignment(alf.viewport.getSelectionAsNewSequence()),\r
@@ -732,12 +733,13 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame\r
    * , java.lang.String)\r
    */\r
-  public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)\r
+  public boolean loadFeaturesFrom(AlignFrame alf, String features,\r
+          boolean autoenabledisplay)\r
   {\r
-    return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);\r
+    return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,\r
+            autoenabledisplay);\r
   }\r
 \r
-\r
   /*\r
    * (non-Javadoc)\r
    * \r
@@ -1823,7 +1825,8 @@ public class JalviewLite extends Applet implements
 \r
         if (protocol == jalview.io.AppletFormatAdapter.PASTE)\r
         {\r
-          newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());\r
+          newAlignFrame.setTitle("Sequences from "\r
+                  + applet.getDocumentBase());\r
         }\r
 \r
         newAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
@@ -1864,43 +1867,53 @@ public class JalviewLite extends Applet implements
           }\r
         }\r
 \r
-\r
         /*\r
          * Try to load T-Coffee score file\r
          */\r
         String sScoreFile = applet.getParameter("scoreFile");\r
-        if( sScoreFile != null && !"".equals(sScoreFile) ) {\r
-            try {\r
-              if (debug) {\r
-                System.err.println("Attempting to load T-COFFEE score file from the scoreFile parameter");\r
-              }\r
-              if (!newAlignFrame.loadScoreFile(sScoreFile)) {\r
-                System.err.println("Failed to parse T-COFFEE parameter as a valid score file ('"+sScoreFile+"')");\r
-              }\r
-            }catch( Exception e ) {\r
-               System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());\r
+        if (sScoreFile != null && !"".equals(sScoreFile))\r
+        {\r
+          try\r
+          {\r
+            if (debug)\r
+            {\r
+              System.err\r
+                      .println("Attempting to load T-COFFEE score file from the scoreFile parameter");\r
+            }\r
+            if (!newAlignFrame.loadScoreFile(sScoreFile))\r
+            {\r
+              System.err\r
+                      .println("Failed to parse T-COFFEE parameter as a valid score file ('"\r
+                              + sScoreFile + "')");\r
             }\r
+          } catch (Exception e)\r
+          {\r
+            System.err.printf("Cannot read score file: '%s'. Cause: %s \n",\r
+                    sScoreFile, e.getMessage());\r
+          }\r
         }\r
-       \r
 \r
         // ///////////////////////////\r
         // modify display of features\r
-        // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed\r
+        // we do this before any features have been loaded, ensuring any hidden\r
+        // groups are hidden when features first displayed\r
         //\r
         // hide specific groups\r
-        // \r
+        //\r
         String param = applet.getParameter("hidefeaturegroups");\r
         if (param != null)\r
         {\r
-          newAlignFrame.setFeatureGroupState(separatorListToArray(param), false);        \r
-//          applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
+          newAlignFrame.setFeatureGroupState(separatorListToArray(param),\r
+                  false);\r
+          // applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
         }\r
         // show specific groups\r
         param = applet.getParameter("showfeaturegroups");\r
         if (param != null)\r
         {\r
-          newAlignFrame.setFeatureGroupState(separatorListToArray(param), true);        \r
-//          applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
+          newAlignFrame.setFeatureGroupState(separatorListToArray(param),\r
+                  true);\r
+          // applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
         }\r
         // and now load features\r
         param = applet.getParameter("features");\r