JAL-1827 code and comment tidy up

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 49cb6d5..d32a10d 100644 (file)
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -130,33 +130,34 @@ public class PDBFileWithJmol extends AlignFile implements
     switch (proteinStructureSubType)
     {
     case HELIX310:
-      if (secstr[pos] == 0)
-      {
-        secstr[pos] = '3';
-      }
+      secstr[pos] = '3';
+      break;
+    case HELIX:
+    case HELIXALPHA:
+      secstr[pos] = 'H';
+      break;
+    case HELIXPI:
+      secstr[pos] = 'P';
+      break;
+    case SHEET:
+      secstr[pos] = 'E';
+      break;
+    default:
+      secstr[pos] = 0;
+    }
+
+    switch (proteinStructureSubType)
+    {
+    case HELIX310:
     case HELIXALPHA:
-      if (secstr[pos] == 0)
-      {
-        secstr[pos] = 'H';
-      }
     case HELIXPI:
-      if (secstr[pos] == 0)
-      {
-        secstr[pos] = 'P';
-      }
     case HELIX:
-      if (secstr[pos] == 0)
-      {
-        secstr[pos] = 'H';
-      }
       secstrcode[pos] = 'H';
       break;
     case SHEET:
-      secstr[pos] = 'E';
       secstrcode[pos] = 'E';
       break;
     default:
-      secstr[pos] = 0;
       secstrcode[pos] = 0;
     }
   }
@@ -365,7 +366,7 @@ public class PDBFileWithJmol extends AlignFile implements
     waitForScript(jmolModel);
 
     /*
-     * Convert one or more Jmol Model objects to Jalview objects.
+     * Convert one or more Jmol Model objects to Jalview sequences
      */
     if (jmolModel.ms.mc > 0)
     {
@@ -389,7 +390,7 @@ public class PDBFileWithJmol extends AlignFile implements
       String modelTitle = (String) ms.getInfo(modelIndex, "title");
 
       /*
-       * as chains can span BioPolymers, we first make a flattened list, 
+       * Chains can span BioPolymers, so first make a flattened list, 
        * and then work out the lengths of chains present
        */
       List<Monomer> monomers = getMonomers(ms, (BioModel) model);
@@ -452,8 +453,9 @@ public class PDBFileWithJmol extends AlignFile implements
     /*
      * construct and add the Jalview sequence
      */
-    SequenceI sq = new Sequence("" + getDataName() + "|" + modelTitle + "|"
-            + chainId, seq, firstResNum, firstResNum + length - 1);
+    String seqName = "" + getDataName() + "|" + modelTitle + "|"
+            + chainId;
+    SequenceI sq = new Sequence(seqName, seq, firstResNum, firstResNum + length - 1);
     seqs.add(sq);
 
     /*
@@ -574,6 +576,8 @@ public class PDBFileWithJmol extends AlignFile implements
   }
 
   /**
+   * Add a PDBEntry giving the source of PDB data to the sequence
+   * 
    * @param sq
    * @param chainId
    */
@@ -583,7 +587,6 @@ public class PDBFileWithJmol extends AlignFile implements
     pdbe.setFile(getDataName());
     pdbe.setId(getDataName());
     pdbe.setProperty(new Hashtable());
-    // pdbe.getProperty().put("CHAIN", "" + _lastChainId);
     pdbe.setChainCode(chainId);
     sq.addPDBId(pdbe);
   }
@@ -628,10 +631,10 @@ public class PDBFileWithJmol extends AlignFile implements
   }
 
   /**
-   * Returns a flattened list of Monomer (residue) in order, across all
+   * Returns a flattened list of Monomer (residues) in order, across all
    * BioPolymers in the model. This simplifies assembling chains which span
-   * BioPolymers. The result does not include any alternate residues reported
-   * for the same sequence position (RESNUM value).
+   * BioPolymers. The result omits any alternate residues reported for the same
+   * sequence position (RESNUM value).
    * 
    * @param ms
    * @param model
@@ -640,9 +643,10 @@ public class PDBFileWithJmol extends AlignFile implements
   protected List<Monomer> getMonomers(ModelSet ms, BioModel model)
   {
     List<Monomer> result = new ArrayList<Monomer>();
-    String lastSeqCode = "";
+    int lastResNo = Integer.MIN_VALUE;
 
-    for (BioPolymer bp : model.bioPolymers) {
+    for (BioPolymer bp : model.bioPolymers)
+    {
       for (int groupLeadAtoms : bp.getLeadAtomIndices())
       {
         Group group = ms.at[groupLeadAtoms].group;
@@ -650,18 +654,14 @@ public class PDBFileWithJmol extends AlignFile implements
         {
           /*
            * ignore alternate residue at same position
-           * example: 1ejg has residues A:LEU, B:ILE, C:ILE at RESNUM=25
+           * example: 1ejg has residues A:LEU, B:ILE at RESNUM=25
            */
-          String seqcodeString = group.getSeqcodeString();
-          if (!lastSeqCode.equals(seqcodeString))
+          int resNo = group.getResno();
+          if (lastResNo != resNo)
           {
             result.add((Monomer) group);
           }
-          else
-          {
-            System.out.println("skipping");
-          }
-          lastSeqCode = seqcodeString;
+          lastResNo = resNo;
         }
       }
     }

diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
index fd02d00..4dc7095 100644 (file)
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
@@ -33,6 +33,7 @@ import jalview.io.FileLoader;
 
 import java.util.Vector;
 
+import org.jmol.c.STR;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -206,4 +207,35 @@ public class PDBFileWithJmolTest
     assertEquals("ALC", seqs.get(0).getSequenceAsString());
     assertEquals("ALC", mcseqs.get(0).getSequenceAsString());
   }
+
+  @Test(groups = "Functional")
+  public void testSetSecondaryStructure()
+  {
+    PDBFileWithJmol testee = new PDBFileWithJmol();
+    char[] struct = new char[10];
+    char[] structCode = new char[10];
+    struct[0] = '1';
+    structCode[0] = '1';
+
+    testee.setSecondaryStructure(STR.NONE, 0, struct, structCode);
+    testee.setSecondaryStructure(STR.HELIX, 1, struct, structCode);
+    testee.setSecondaryStructure(STR.HELIX310, 2, struct, structCode);
+    testee.setSecondaryStructure(STR.HELIXALPHA, 3, struct, structCode);
+    testee.setSecondaryStructure(STR.HELIXPI, 4, struct, structCode);
+    testee.setSecondaryStructure(STR.SHEET, 5, struct, structCode);
+
+    assertEquals(0, struct[0]);
+    assertEquals('H', struct[1]);
+    assertEquals('3', struct[2]);
+    assertEquals('H', struct[3]);
+    assertEquals('P', struct[4]);
+    assertEquals('E', struct[5]);
+
+    assertEquals(0, structCode[0]);
+    assertEquals('H', structCode[1]);
+    assertEquals('H', structCode[2]);
+    assertEquals('H', structCode[3]);
+    assertEquals('H', structCode[4]);
+    assertEquals('E', structCode[5]);
+  }
 }