From e2c039f9c1d5f08af9bebbab26cd0ae4dbcb7ace Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 19 Aug 2016 11:57:00 +0100
Subject: [PATCH] JAL-2154 fix looping structure so for a particular pass
 (either 2-pass: retrieve cross-ref+save/recover from
 project or one pass: retrieve cross-ref and compare string)
 we do all cross-refs or dbfetches in a pass.

---
 test/jalview/io/CrossRef2xmlTests.java |   62 ++++++++++++++++++--------------
 1 file changed, 36 insertions(+), 26 deletions(-)

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index b330b2d..cc26d7e 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -127,11 +127,11 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                 : new CrossRef(seqs, dataset)
                         .findXrefSourcesForSequences(dna);
 
+        pass2 = 0;
+        do // second cross ref and recover crossref loop
+        {
         for (String db : ptypes)
         {
-          pass2 = 0;
-          do // second cross ref and recover crossref loop
-          {
             // counter for splitframe views retrieved via crossref
             int p = 0;
             // build next key so we an retrieve all views
@@ -192,21 +192,22 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                       : new CrossRef(xrseqs, dataset)
                               .findXrefSourcesForSequences(avp
                                       .getAlignViewport().isNucleotide());
-              for (String xrefdb : xrptypes)
+              pass3 = 0;
+              do // 3rd cross ref and recover crossref loop
               {
-                pass3 = 0;
-                do // 3rd cross ref and recover crossref loop
+                for (String xrefdb : xrptypes)
                 {
                   List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
                   int q = 0;
                   String nextnextxref = "{" + p + "}" + nextxref + " -> "
                           + xrefdb + "{" + q + "}";
 
-                  AlignFrame nextaf = Desktop.getAlignFrameFor(avp
-                          .getAlignViewport());
                   if (pass3 == 0)
                   {
 
+                    AlignFrame nextaf = Desktop.getAlignFrameFor(avp
+                            .getAlignViewport());
+
                     cra = new CrossRefAction(nextaf, xrseqs, avp
                             .getAlignViewport().isNucleotide(), xrefdb);
                     cra.run();
@@ -263,11 +264,20 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                             nextavp);
                     keyseq.add(nextnextxref);
                   }
-                } while (pass3++ < 2 && pass2 < 1);
-              }
+                } // end of loop around showing all xrefdb for crossrf2
+                // fetchdb->crossref1->crossref-2->verify for xrefs we
+                // either loop twice when pass2=0, or just once when pass2=1
+                // (recovered project from previous crossref)
+              } while (pass3++ < 2 && pass2 < 1);
             }
-          } while (pass2++ < 2 && pass1 < 1);
         }
+          // fetchdb-->crossref1
+          // for each xref we try to retrieve xref, store and verify when
+          // pass1=0, or just retrieve and verify when pass1=1
+        } while (pass2++ < 2 && pass1 < 1);
+        // fetchdb
+        // for each ref we
+        // loop twice: first, do the retrieve, second recover from saved project
       } while (++pass1 < 2);
     }
   }
@@ -299,22 +309,22 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     if (savedProjects != null)
     {
       if (savedProjects.get(xrefpath) == null)
-    {
-      // write a project file for this view. On the second pass, this will be
-      // recovered and cross-references verified
-      try
-      {
-        File prfile = File.createTempFile("crossRefTest", ".jvp");
-        AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
-        new Jalview2XML(false).saveAlignment(af, prfile.toString(),
-                af.getTitle());
-        System.out.println("Written view from '" + xrefpath + "' as '"
-                + prfile.getAbsolutePath() + "'");
-        savedProjects.put(xrefpath, prfile);
-      } catch (IOException q)
       {
-        Assert.fail("Unexpected IO Exception", q);
-      }
+        // write a project file for this view. On the second pass, this will be
+        // recovered and cross-references verified
+        try
+        {
+          File prfile = File.createTempFile("crossRefTest", ".jvp");
+          AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
+          new Jalview2XML(false).saveAlignment(af, prfile.toString(),
+                  af.getTitle());
+          System.out.println("Written view from '" + xrefpath + "' as '"
+                  + prfile.getAbsolutePath() + "'");
+          savedProjects.put(xrefpath, prfile);
+        } catch (IOException q)
+        {
+          Assert.fail("Unexpected IO Exception", q);
+        }
       }
       else
       {
-- 
1.7.10.2