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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 82b75a1..50f7471 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -19,15 +19,20 @@ public class HTMLOutput
   {\r
     this.av = av;\r
     sr = new SequenceRenderer(av);\r
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+    JalviewFileChooser chooser = new JalviewFileChooser(\r
+      jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
+      new String[]{"html"},\r
+      new String[]{"HTML files"},\r
+      "HTML files");\r
+\r
     chooser.setFileView(new JalviewFileView());\r
     chooser.setDialogTitle("Save as HTML");\r
     chooser.setToolTipText("Save");\r
     int value = chooser.showSaveDialog(null);\r
-    if(value == JFileChooser.APPROVE_OPTION)\r
+    if(value == JalviewFileChooser.APPROVE_OPTION)\r
     {\r
       String choice =  chooser.getSelectedFile().getPath();\r
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice);\r
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
       try{\r
         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));\r
         out.println("<HTML>");\r
@@ -90,7 +95,11 @@ public class HTMLOutput
     {\r
       seq = alignment.getSequenceAt(i);\r
       groups = alignment.findAllGroups( seq );\r
-      out.println("<tr><td nowrap>"+seq.getDisplayId()+"&nbsp;&nbsp;</td>");\r
+      if(av.getShowFullId())\r
+        out.println("<tr><td nowrap>"+seq.getDisplayId()+"&nbsp;&nbsp;</td>");\r
+      else\r
+        out.println("<tr><td nowrap>"+seq.getName()+"&nbsp;&nbsp;</td>");\r
+\r
 \r
 \r
       for (int res = 0; res < seq.getLength(); res++)\r
@@ -112,16 +121,9 @@ public class HTMLOutput
 \r
         if(color.getRGB()<-1)\r
         {\r
-          r = Integer.toHexString(color.getRed());\r
-          if(r.length()<2)\r
-            r = "0"+r;\r
-          g = Integer.toHexString(color.getGreen());\r
-          if(g.length()<2)\r
-            g = "0"+g;\r
-          b = Integer.toHexString(color.getBlue());\r
-          if(b.length()<2)\r
-            b = "0"+b;\r
-          out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
+          out.println("<td bgcolor=\"#"\r
+                      + jalview.util.Format.getHexString(color)\r
+                      + "\">"+seq.getCharAt(res)+"</td>");\r
         }\r
         else\r
           out.println("<td>"+seq.getCharAt(res)+"</td>");\r
@@ -172,7 +174,10 @@ public class HTMLOutput
          out.println("<tr>");\r
          seq = al.getSequenceAt(s);\r
          groups = al.findAllGroups( seq );\r
-         out.println("<td nowrap>"+seq.getDisplayId()+"&nbsp;&nbsp;</td>");\r
+         if(av.getShowFullId())\r
+           out.println("<td nowrap>"+seq.getDisplayId()+"&nbsp;&nbsp;</td>");\r
+         else\r
+           out.println("<td nowrap>"+seq.getName()+"&nbsp;&nbsp;</td>");\r
 \r
          for (int res = startRes; res < endRes; res++)\r
               {\r