From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 29 Jun 2015 09:21:38 +0000 (+0100)
Subject: JAL-1759 correct conversion of Jmol Chain.chainId (int) to string +
X-Git-Tag: Release_2_10_0~562^2~13
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=b80b8920baba71a797b3c17c2be4ca0a3ba2bf25

JAL-1759 correct conversion of Jmol Chain.chainId (int) to string +
tests
---

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 2f117d3..3b6f0c2 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -144,7 +144,9 @@ public class PDBFileWithJmol extends AlignFile implements
         modelIndex++;
         for (BioPolymer bp : ((BioModel) model).bioPolymers)
         {
-          int _lastChainId = 0;
+          int lastChainId = 0; // int value of character e.g. 65 for A
+          String lastChainIdAlpha = "";
+
           int[] groups = bp.getLeadAtomIndices();
           char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
           int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
@@ -152,7 +154,7 @@ public class PDBFileWithJmol extends AlignFile implements
           do
           {
             if (groupc >= groups.length
-                    || ms.at[groups[groupc]].group.chain.chainID != _lastChainId)
+                    || ms.at[groups[groupc]].group.chain.chainID != lastChainId)
             {
               /*
                * on change of chain (or at end), construct the sequence and
@@ -181,14 +183,14 @@ public class PDBFileWithJmol extends AlignFile implements
                 String modelTitle = (String) ms
                         .getInfo(modelIndex, "title");
                 SequenceI sq = new Sequence("" + getDataName() + "|"
-                        + modelTitle + "|" + _lastChainId, newseq,
+                        + modelTitle + "|" + lastChainIdAlpha, newseq,
                         firstrnum, lastrnum);
                 PDBEntry pdbe = new PDBEntry();
                 pdbe.setFile(getDataName());
                 pdbe.setId(getDataName());
                 pdbe.setProperty(new Hashtable());
                 // pdbe.getProperty().put("CHAIN", "" + _lastChainId);
-                pdbe.setChainCode(String.valueOf(_lastChainId));
+                pdbe.setChainCode(lastChainIdAlpha);
                 sq.addPDBId(pdbe);
                 // JAL-1533
                 // Need to put the number of models for this polymer somewhere
@@ -199,9 +201,9 @@ public class PDBFileWithJmol extends AlignFile implements
                 {
                   String mt = modelTitle == null ? getDataName()
                           : modelTitle;
-                  if (_lastChainId >= ' ')
+                  if (lastChainId >= ' ')
                   {
-                    mt += _lastChainId;
+                    mt += lastChainIdAlpha;
                   }
                   AlignmentAnnotation ann = new AlignmentAnnotation(
                           "Secondary Structure", "Secondary Structure for "
@@ -226,7 +228,8 @@ public class PDBFileWithJmol extends AlignFile implements
               if (len == 0)
               {
                 firstrnum = group.getResno();
-                _lastChainId = group.chain.chainID;
+                lastChainId = group.chain.chainID;
+                lastChainIdAlpha = group.chain.getIDStr();
               }
               else
               {
diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index 0df7851..07f9bd5 100644
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -16,19 +16,27 @@ import jalview.schemes.TaylorColourScheme;
 import java.awt.Color;
 import java.util.Vector;
 
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class PDBChainTest
 {
-  PDBChain c = new PDBChain("1GAQ", "A");
+  PDBChain c;
 
-  Atom a1 = new Atom(1f, 2f, 3f);
+  final Atom a1 = new Atom(1f, 2f, 3f);
 
-  Atom a2 = new Atom(5f, 6f, 4f);
+  final Atom a2 = new Atom(5f, 6f, 4f);
 
-  Atom a3 = new Atom(2f, 5f, 6f);
+  final Atom a3 = new Atom(2f, 5f, 6f);
 
-  Atom a4 = new Atom(2f, 1f, 7f);
+  final Atom a4 = new Atom(2f, 1f, 7f);
+
+  @BeforeMethod
+  public void setUp()
+  {
+    System.out.println("setup");
+    c = new PDBChain("1GAQ", "A");
+  }
 
   @Test
   public void testGetNewlineString()
diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index a4fd286..03b60e6 100644
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -15,6 +15,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 
 import java.io.IOException;
+import java.util.List;
 
 import org.testng.annotations.Test;
 
@@ -96,6 +97,21 @@ public class PDBfileTest
     assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
     assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT"));
     assertEquals("3W5V|D", chainD.sequence.getName());
+
+    /*
+     * verify PDB-related data in parsed sequences
+     */
+    List<SequenceI> seqs = pf.getSeqs();
+    assertEquals(4, seqs.size());
+    assertEquals("3W5V|A", seqs.get(0).getName());
+    assertEquals("3W5V|B", seqs.get(1).getName());
+    assertEquals("3W5V|C", seqs.get(2).getName());
+    assertEquals("3W5V|D", seqs.get(3).getName());
+    assertEquals(1, seqs.get(0).getPDBId().size());
+    PDBEntry pdbe = seqs.get(0).getPDBId().get(0);
+    assertEquals("A", pdbe.getChainCode());
+    assertEquals("3W5V", pdbe.getId());
+    assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
   }
 
   /**
@@ -265,7 +281,7 @@ public class PDBfileTest
   private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf)
   {
     AlignmentI al = new Alignment(pf.getSeqsAsArray());
-    pf.addAnnotations((Alignment) al);
+    pf.addAnnotations(al);
     return al.getAlignmentAnnotation();
   }
   }