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JAL-2418 source formatting
[jalview.git] / src / jalview / io / HTMLOutput.java
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 77006db..81cdd3c 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -86,12 +86,12 @@ public abstract class HTMLOutput implements Runnable
       };
     }
     AlignmentExportData exportData = jalview.gui.AlignFrame
-            .getAlignmentForExport(FileFormat.Json,
-                    ap.getAlignViewport(), exportSettings);
+            .getAlignmentForExport(FileFormat.Json, ap.getAlignViewport(),
+                    exportSettings);
     String bioJSON = new FormatAdapter(ap, exportData.getSettings())
             .formatSequences(FileFormat.Json, exportData.getAlignment(),
-                    exportData.getOmitHidden(), exportData
-.getStartEndPostions(), ap.getAlignViewport()
+                    exportData.getOmitHidden(),
+                    exportData.getStartEndPostions(), ap.getAlignViewport()
                             .getAlignment().getHiddenColumns());
     return bioJSON;
   }
@@ -124,7 +124,7 @@ public abstract class HTMLOutput implements Runnable
         {
           sb.append(line).append(lineSeparator);
         }
-  
+
       } catch (Exception ex)
       {
         ex.printStackTrace();
@@ -134,7 +134,7 @@ public abstract class HTMLOutput implements Runnable
         {
           isReader.close();
         }
-  
+
         if (buffReader != null)
         {
           buffReader.close();
@@ -146,89 +146,55 @@ public abstract class HTMLOutput implements Runnable
 
   public static String getImageMapHTML()
   {
-    return new String(
-            "<html>\n"
-                    + "<head>\n"
-                    + "<script language=\"JavaScript\">\n"
-                    + "var ns4 = document.layers;\n"
-                    + "var ns6 = document.getElementById && !document.all;\n"
-                    + "var ie4 = document.all;\n"
-                    + "offsetX = 0;\n"
-                    + "offsetY = 20;\n"
-                    + "var toolTipSTYLE=\"\";\n"
-                    + "function initToolTips()\n"
-                    + "{\n"
-                    + "  if(ns4||ns6||ie4)\n"
-                    + "  {\n"
-                    + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
-                    + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
-                    + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
-                    + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
-                    + "    else\n"
-                    + "    {\n"
-                    + "      toolTipSTYLE.visibility = \"visible\";\n"
-                    + "      toolTipSTYLE.display = \"none\";\n"
-                    + "    }\n"
-                    + "    document.onmousemove = moveToMouseLoc;\n"
-                    + "  }\n"
-                    + "}\n"
-                    + "function toolTip(msg, fg, bg)\n"
-                    + "{\n"
-                    + "  if(toolTip.arguments.length < 1) // hide\n"
-                    + "  {\n"
-                    + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
-                    + "    else toolTipSTYLE.display = \"none\";\n"
-                    + "  }\n"
-                    + "  else // show\n"
-                    + "  {\n"
-                    + "    if(!fg) fg = \"#555555\";\n"
-                    + "    if(!bg) bg = \"#FFFFFF\";\n"
-                    + "    var content =\n"
-                    + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
-                    + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
-                    + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
-                    + "    '\" size=\"-2\">&nbsp;' + msg +\n"
-                    + "    '&nbsp;</font></td></table></td></table>';\n"
-                    + "    if(ns4)\n"
-                    + "    {\n"
-                    + "      toolTipSTYLE.document.write(content);\n"
-                    + "      toolTipSTYLE.document.close();\n"
-                    + "      toolTipSTYLE.visibility = \"visible\";\n"
-                    + "    }\n"
-                    + "    if(ns6)\n"
-                    + "    {\n"
-                    + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
-                    + "      toolTipSTYLE.display='block'\n"
-                    + "    }\n"
-                    + "    if(ie4)\n"
-                    + "    {\n"
-                    + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
-                    + "      toolTipSTYLE.display='block'\n"
-                    + "    }\n"
-                    + "  }\n"
-                    + "}\n"
-                    + "function moveToMouseLoc(e)\n"
-                    + "{\n"
-                    + "  if(ns4||ns6)\n"
-                    + "  {\n"
-                    + "    x = e.pageX;\n"
-                    + "    y = e.pageY;\n"
-                    + "  }\n"
-                    + "  else\n"
-                    + "  {\n"
-                    + "    x = event.x + document.body.scrollLeft;\n"
-                    + "    y = event.y + document.body.scrollTop;\n"
-                    + "  }\n"
-                    + "  toolTipSTYLE.left = x + offsetX;\n"
-                    + "  toolTipSTYLE.top = y + offsetY;\n"
-                    + "  return true;\n"
-                    + "}\n"
-                    + "</script>\n"
-                    + "</head>\n"
-                    + "<body>\n"
-                    + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
-                    + "<script language=\"JavaScript\"><!--\n"
-                    + "initToolTips(); //--></script>\n");
+    return new String("<html>\n" + "<head>\n"
+            + "<script language=\"JavaScript\">\n"
+            + "var ns4 = document.layers;\n"
+            + "var ns6 = document.getElementById && !document.all;\n"
+            + "var ie4 = document.all;\n" + "offsetX = 0;\n"
+            + "offsetY = 20;\n" + "var toolTipSTYLE=\"\";\n"
+            + "function initToolTips()\n" + "{\n" + "  if(ns4||ns6||ie4)\n"
+            + "  {\n"
+            + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+            + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+            + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+            + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+            + "    else\n" + "    {\n"
+            + "      toolTipSTYLE.visibility = \"visible\";\n"
+            + "      toolTipSTYLE.display = \"none\";\n" + "    }\n"
+            + "    document.onmousemove = moveToMouseLoc;\n" + "  }\n"
+            + "}\n" + "function toolTip(msg, fg, bg)\n" + "{\n"
+            + "  if(toolTip.arguments.length < 1) // hide\n" + "  {\n"
+            + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+            + "    else toolTipSTYLE.display = \"none\";\n" + "  }\n"
+            + "  else // show\n" + "  {\n"
+            + "    if(!fg) fg = \"#555555\";\n"
+            + "    if(!bg) bg = \"#FFFFFF\";\n" + "    var content =\n"
+            + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+            + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+            + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+            + "    '\" size=\"-2\">&nbsp;' + msg +\n"
+            + "    '&nbsp;</font></td></table></td></table>';\n"
+            + "    if(ns4)\n" + "    {\n"
+            + "      toolTipSTYLE.document.write(content);\n"
+            + "      toolTipSTYLE.document.close();\n"
+            + "      toolTipSTYLE.visibility = \"visible\";\n" + "    }\n"
+            + "    if(ns6)\n" + "    {\n"
+            + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+            + "      toolTipSTYLE.display='block'\n" + "    }\n"
+            + "    if(ie4)\n" + "    {\n"
+            + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
+            + "      toolTipSTYLE.display='block'\n" + "    }\n" + "  }\n"
+            + "}\n" + "function moveToMouseLoc(e)\n" + "{\n"
+            + "  if(ns4||ns6)\n" + "  {\n" + "    x = e.pageX;\n"
+            + "    y = e.pageY;\n" + "  }\n" + "  else\n" + "  {\n"
+            + "    x = event.x + document.body.scrollLeft;\n"
+            + "    y = event.y + document.body.scrollTop;\n" + "  }\n"
+            + "  toolTipSTYLE.left = x + offsetX;\n"
+            + "  toolTipSTYLE.top = y + offsetY;\n" + "  return true;\n"
+            + "}\n" + "</script>\n" + "</head>\n" + "<body>\n"
+            + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+            + "<script language=\"JavaScript\"><!--\n"
+            + "initToolTips(); //--></script>\n");
 
   }
 
@@ -246,15 +212,15 @@ public abstract class HTMLOutput implements Runnable
             "HTML files");
     jvFileChooser.setFileView(new JalviewFileView());
 
-    jvFileChooser.setDialogTitle(MessageManager
-            .getString("label.save_as_html"));
+    jvFileChooser
+            .setDialogTitle(MessageManager.getString("label.save_as_html"));
     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 
     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
     {
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
-              .getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+              jvFileChooser.getSelectedFile().getParent());
       selectedFile = jvFileChooser.getSelectedFile().getPath();
     }
     else