X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=8fece9d1ad00146b9be41c7feb6dc16fee973420;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=f7d6448cff10ca5df14536edc173d75ff119d14d;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index f7d6448..8fece9d 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -47,9 +47,11 @@ public class StockholmFileTest
   {
     testFileIOwithFormat(new File(PfamFile), "STH");
   }
+
   @Test
   public void pfamFileDataExtraction() throws Exception
-  {  AppletFormatAdapter af = new AppletFormatAdapter();
+  {
+    AppletFormatAdapter af = new AppletFormatAdapter();
     AlignmentI al = af.readFile(PfamFile, af.FILE,
             new IdentifyFile().Identify(PfamFile, af.FILE));
     int numpdb = 0;
@@ -100,7 +102,8 @@ public class StockholmFileTest
         al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
       }
       String outputfile = rf.formatSequences(ioformat, al, true);
-      System.out.println("Output file in '"+ioformat+"':\n"+outputfile+"\n<<EOF\n");
+      System.out.println("Output file in '" + ioformat + "':\n"
+              + outputfile + "\n<<EOF\n");
       // test for consistency in io
       Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
               AppletFormatAdapter.PASTE, ioformat);
@@ -155,36 +158,48 @@ public class StockholmFileTest
     // we might want to revise this in future
     int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
             : aa_original.length);
-    Map<Integer,java.util.BitSet> orig_groups=new HashMap<Integer,java.util.BitSet>(),new_groups=new HashMap<Integer,java.util.BitSet>();
+    Map<Integer, java.util.BitSet> orig_groups = new HashMap<Integer, java.util.BitSet>(), new_groups = new HashMap<Integer, java.util.BitSet>();
 
     if (aa_new != null && aa_original != null)
     {
       for (int i = 0; i < aa_original.length; i++)
       {
-        if (aa_new.length>i) {
-          assertTrue("Different alignment annotation at position "+i,
-                equalss(aa_original[i], aa_new[i]));
+        if (aa_new.length > i)
+        {
+          assertTrue("Different alignment annotation at position " + i,
+                  equalss(aa_original[i], aa_new[i]));
           // compare graphGroup or graph properties - needed to verify JAL-1299
-          assertTrue("Graph type not identical.",aa_original[i].graph==aa_new[i].graph);
-          assertTrue("Visibility not identical.", aa_original[i].visible==aa_new[i].visible);
+          assertTrue("Graph type not identical.",
+                  aa_original[i].graph == aa_new[i].graph);
+          assertTrue("Visibility not identical.",
+                  aa_original[i].visible == aa_new[i].visible);
           assertTrue(
                   "Threshold line not identical.",
                   aa_original[i].threshold == null ? aa_new[i].threshold == null
                           : aa_original[i].threshold
                                   .equals(aa_new[i].threshold));
           // graphGroup may differ, but pattern should be the same
-          Integer o_ggrp=new Integer(aa_original[i].graphGroup+2),n_ggrp=new Integer(aa_new[i].graphGroup+2);
-          BitSet orig_g=orig_groups.get(o_ggrp),new_g=new_groups.get(n_ggrp);
-          if (orig_g==null) {
-            orig_groups.put(o_ggrp,orig_g= new BitSet());
+          Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2), n_ggrp = new Integer(
+                  aa_new[i].graphGroup + 2);
+          BitSet orig_g = orig_groups.get(o_ggrp), new_g = new_groups
+                  .get(n_ggrp);
+          if (orig_g == null)
+          {
+            orig_groups.put(o_ggrp, orig_g = new BitSet());
           }
-          if (new_g==null) {
-            new_groups.put(n_ggrp, new_g=new BitSet());
+          if (new_g == null)
+          {
+            new_groups.put(n_ggrp, new_g = new BitSet());
           }
-          assertTrue("Graph Group pattern differs at annotation "+i, orig_g.equals(new_g));
-          orig_g.set(i); new_g.set(i);
-        } else {
-          System.err.println("No matching annotation row for "+aa_original[i].toString());
+          assertTrue("Graph Group pattern differs at annotation " + i,
+                  orig_g.equals(new_g));
+          orig_g.set(i);
+          new_g.set(i);
+        }
+        else
+        {
+          System.err.println("No matching annotation row for "
+                  + aa_original[i].toString());
         }
       }
     }
@@ -293,23 +308,28 @@ public class StockholmFileTest
   {
     if (annot_or.annotations.length != annot_new.annotations.length)
     {
-      System.err.println("Different lengths for annotation row elements: "+annot_or.annotations.length +"!="+ annot_new.annotations.length);
+      System.err.println("Different lengths for annotation row elements: "
+              + annot_or.annotations.length + "!="
+              + annot_new.annotations.length);
       return false;
     }
     for (int i = 0; i < annot_or.annotations.length; i++)
     {
-      Annotation an_or=annot_or.annotations[i],an_new=annot_new.annotations[i];
-      if (an_or != null
-              && an_new!= null)
+      Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
+      if (an_or != null && an_new != null)
       {
-        if (!an_or.displayCharacter.trim()
-                .equals(an_new.displayCharacter.trim())
-                || !(""+an_or.secondaryStructure).trim().equals((""+an_new.secondaryStructure).trim())
+        if (!an_or.displayCharacter.trim().equals(
+                an_new.displayCharacter.trim())
+                || !("" + an_or.secondaryStructure).trim().equals(
+                        ("" + an_new.secondaryStructure).trim())
                 || (an_or.description != an_new.description && (an_or.description == null
                         || an_new.description == null || !an_or.description
                           .equals(an_new.description))))
         {
-          System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+annot_or.annotations[i].toString()+"\nElement "+i+" in new: "+annot_new.annotations[i].toString());
+          System.err.println("Annotation Element Mismatch\nElement " + i
+                  + " in original: " + annot_or.annotations[i].toString()
+                  + "\nElement " + i + " in new: "
+                  + annot_new.annotations[i].toString());
           return false;
         }
       }
@@ -320,7 +340,16 @@ public class StockholmFileTest
       }
       else
       {
-        System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+(annot_or.annotations[i]==null ? "is null" : annot_or.annotations[i].toString())+"\nElement "+i+" in new: "+(annot_new.annotations[i] == null ? "is null" : annot_new.annotations[i].toString()));
+        System.err.println("Annotation Element Mismatch\nElement "
+                + i
+                + " in original: "
+                + (annot_or.annotations[i] == null ? "is null"
+                        : annot_or.annotations[i].toString())
+                + "\nElement "
+                + i
+                + " in new: "
+                + (annot_new.annotations[i] == null ? "is null"
+                        : annot_new.annotations[i].toString()));
         return false;
       }
     }