From e87f3076c7826c6bb2bc54583406f7e719df77ed Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 5 Sep 2017 12:52:50 +0100
Subject: [PATCH] JAL-2225 unused collateForPdb removed

---
 src/jalview/gui/AlignViewport.java      |   52 -------------------------------
 test/jalview/gui/AlignViewportTest.java |   51 ------------------------------
 2 files changed, 103 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index c22a37d..14b7af0 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -606,58 +606,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(Desktop.instance);
   }
 
-  /**
-   * 
-   * @param pdbEntries
-   * @return an array of SequenceI arrays, one for each PDBEntry, listing which
-   *         sequences in the alignment hold a reference to it
-   */
-  public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
-  {
-    List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
-    for (PDBEntry pdb : pdbEntries)
-    {
-      List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
-      for (SequenceI sq : alignment.getSequences())
-      {
-        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
-                .getAllPDBEntries();
-        if (pdbRefEntries == null)
-        {
-          continue;
-        }
-        for (PDBEntry pdbRefEntry : pdbRefEntries)
-        {
-          if (pdbRefEntry.getId().equals(pdb.getId()))
-          {
-            if (pdbRefEntry.getChainCode() != null
-                    && pdb.getChainCode() != null)
-            {
-              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
-                      pdb.getChainCode()) && !choosenSeqs.contains(sq))
-              {
-                choosenSeqs.add(sq);
-                continue;
-              }
-            }
-            else
-            {
-              if (!choosenSeqs.contains(sq))
-              {
-                choosenSeqs.add(sq);
-                continue;
-              }
-            }
-
-          }
-        }
-      }
-      seqvectors
-              .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
-    }
-    return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
-  }
-
   @Override
   public boolean isNormaliseSequenceLogo()
   {
diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 812fd8f..5ed0cac 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -96,57 +96,6 @@ public class AlignViewportTest
     testee = new AlignViewport(al);
   }
 
-  @Test(groups = { "Functional" })
-  public void testCollateForPdb()
-  {
-    // JBP: What behaviour is this supposed to test ?
-    /*
-     * Set up sequence pdb ids
-     */
-    PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb");
-    PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb");
-    PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb");
-
-    /*
-     * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD
-     */
-    al.getSequenceAt(0).getDatasetSequence()
-            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
-    al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
-    al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
-    /*
-     * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
-     * the results
-     */
-    al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb"));
-    /*
-     * Seq3 refers to 3abc - this does not match 3ABC (as the code stands)
-     */
-    al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb"));
-
-    /*
-     * run method under test
-     */
-    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
-        pdb3 });
-
-    // seq1 and seq3 refer to PDBEntry[0]
-    assertEquals(2, seqs[0].length);
-    assertSame(al.getSequenceAt(0), seqs[0][0]);
-    assertSame(al.getSequenceAt(2), seqs[0][1]);
-
-    // seq2 refers to PDBEntry[1]
-    assertEquals(1, seqs[1].length);
-    assertSame(al.getSequenceAt(1), seqs[1][0]);
-
-    // no sequence refers to PDBEntry[2]
-    assertEquals(0, seqs[2].length);
-  }
-
   /**
    * Test that a mapping is not deregistered when a second view is closed but
    * the first still holds a reference to the mapping
-- 
1.7.10.2