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[jalview.git] / src / jalview / io / HTMLOutput.java
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index e53f14c..3d2a148 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -28,11 +28,15 @@ import jalview.gui.*;
 public class HTMLOutput
 {
   AlignViewport av;
+
   SequenceRenderer sr;
+
   FeatureRenderer fr;
+
   Color color;
 
-  public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1)
+  public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
+          FeatureRenderer fr1)
   {
     this.av = ap.av;
     this.sr = sr;
@@ -40,12 +44,10 @@ public class HTMLOutput
     fr = new FeatureRenderer(ap);
     fr.transferSettings(fr1);
 
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"), new String[]
-        {"html"},
-        new String[]
-        {"HTML files"}, "HTML files");
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "html" }, new String[]
+    { "HTML files" }, "HTML files");
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save as HTML");
@@ -56,19 +58,19 @@ public class HTMLOutput
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
 
       try
       {
         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-            choice));
+                choice));
         out.println("<HTML>");
         out.println("<style type=\"text/css\">");
         out.println("<!--");
-        out.print("td {font-family: \"" + av.getFont().getFamily() +
-                  "\", \"" + av.getFont().getName() + "\", mono; " +
-                  "font-size: " + av.getFont().getSize() + "px; ");
+        out.print("td {font-family: \"" + av.getFont().getFamily()
+                + "\", \"" + av.getFont().getName() + "\", mono; "
+                + "font-size: " + av.getFont().getSize() + "px; ");
 
         if (av.getFont().getStyle() == Font.BOLD)
         {
@@ -98,8 +100,7 @@ public class HTMLOutput
         out.println("\n</body>\n</html>");
         out.close();
         jalview.util.BrowserLauncher.openURL("file:///" + choice);
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -109,10 +110,10 @@ public class HTMLOutput
   void drawUnwrappedAlignment(PrintWriter out)
   {
     out.println("<table border=\"1\"><tr><td>\n");
-    out.println(
-        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+    out
+            .println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 
-    //////////////
+    // ////////////
     SequenceI seq;
     AlignmentI alignment = av.getAlignment();
 
@@ -126,8 +127,8 @@ public class HTMLOutput
       out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
     }
 
-    out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
-                "<br>|</td>");
+    out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
+            + "<br>|</td>");
     out.println("</tr>");
 
     for (i = 0; i < alignment.getHeight(); i++)
@@ -136,8 +137,7 @@ public class HTMLOutput
 
       String id = seq.getDisplayId(av.getShowJVSuffix());
 
-      out.println("<tr><td nowrap>" + id +
-                  "&nbsp;&nbsp;</td>");
+      out.println("<tr><td nowrap>" + id + "&nbsp;&nbsp;</td>");
 
       for (int res = 0; res < seq.getLength(); res++)
       {
@@ -154,9 +154,9 @@ public class HTMLOutput
 
         if (color.getRGB() < -1)
         {
-          out.println("<td bgcolor=\"#" +
-                      jalview.util.Format.getHexString(color) + "\">" +
-                      seq.getCharAt(res) + "</td>");
+          out.println("<td bgcolor=\"#"
+                  + jalview.util.Format.getHexString(color) + "\">"
+                  + seq.getCharAt(res) + "</td>");
         }
         else
         {
@@ -167,15 +167,15 @@ public class HTMLOutput
       out.println("</tr>");
     }
 
-    //////////////
+    // ////////////
     out.println("</table>");
     out.println("</td></tr></table>");
   }
 
   void drawWrappedAlignment(PrintWriter out)
   {
-    ////////////////////////////////////
-    /// How many sequences and residues can we fit on a printable page?
+    // //////////////////////////////////
+    // / How many sequences and residues can we fit on a printable page?
     AlignmentI al = av.getAlignment();
     SequenceI seq;
     String r;
@@ -183,11 +183,11 @@ public class HTMLOutput
     String b;
 
     out.println("<table border=\"1\"><tr><td>\n");
-    out.println(
-        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+    out
+            .println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
 
-    for (int startRes = 0; startRes < al.getWidth();
-         startRes += av.getWrappedWidth())
+    for (int startRes = 0; startRes < al.getWidth(); startRes += av
+            .getWrappedWidth())
     {
       int endRes = startRes + av.getWrappedWidth();
 
@@ -228,8 +228,7 @@ public class HTMLOutput
 
         String id = seq.getDisplayId(av.getShowJVSuffix());
 
-        out.println("<td nowrap>" + id +
-                    "&nbsp;&nbsp;</td>");
+        out.println("<td nowrap>" + id + "&nbsp;&nbsp;</td>");
 
         if (av.getScaleLeftWrapped())
         {
@@ -239,8 +238,7 @@ public class HTMLOutput
           }
           else
           {
-            out.println("<td nowrap>" + startPos +
-                        "&nbsp;&nbsp;</td>");
+            out.println("<td nowrap>" + startPos + "&nbsp;&nbsp;</td>");
           }
         }
 
@@ -259,9 +257,9 @@ public class HTMLOutput
 
           if (color.getRGB() < -1)
           {
-            out.println("<td bgcolor=\"#" +
-                        jalview.util.Format.getHexString(color) + "\">" +
-                        seq.getCharAt(res) + "</td>");
+            out.println("<td bgcolor=\"#"
+                    + jalview.util.Format.getHexString(color) + "\">"
+                    + seq.getCharAt(res) + "</td>");
           }
           else
           {
@@ -270,18 +268,17 @@ public class HTMLOutput
 
         }
 
-        if (av.getScaleRightWrapped() &&
-            endRes < startRes + av.getWrappedWidth())
+        if (av.getScaleRightWrapped()
+                && endRes < startRes + av.getWrappedWidth())
         {
-          out.println("<td colspan=\"" +
-                      (startRes + av.getWrappedWidth() - endRes) + "\">"
-                      + "&nbsp;&nbsp;</td>");
+          out.println("<td colspan=\""
+                  + (startRes + av.getWrappedWidth() - endRes) + "\">"
+                  + "&nbsp;&nbsp;</td>");
         }
 
         if (av.getScaleRightWrapped() && startPos < endPos)
         {
-          out.println("<td nowrap>&nbsp;" + endPos +
-                      "&nbsp;&nbsp;</td>");
+          out.println("<td nowrap>&nbsp;" + endPos + "&nbsp;&nbsp;</td>");
         }
 
         out.println("</tr>");
@@ -300,90 +297,88 @@ public class HTMLOutput
   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");
+            "<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");
 
   }
 }