X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimUtils.java;h=1b0285cf5d9352cd350b76fe430d636cdb0c49ec;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=ad5e350ee4529e171307f1ad40b7ba451eebc62c;hpb=e42524a147f92c836a0a336dde394394976216d2;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
index ad5e350..1b0285c 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
@@ -76,8 +76,8 @@ public abstract class ChimUtils
     {
       if (decimal > 0)
       {
-        subModelNumber = Integer.parseInt(inputLine.substring(decimal
-                + hash + 2, space));
+        subModelNumber = Integer
+                .parseInt(inputLine.substring(decimal + hash + 2, space));
         space = decimal + hash + 1;
       }
       modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
@@ -120,8 +120,8 @@ public abstract class ChimUtils
     {
       if (decimal > 0)
       {
-        subModelNumber = Integer.parseInt(inputLine.substring(decimal
-                + hash + 2, space));
+        subModelNumber = Integer
+                .parseInt(inputLine.substring(decimal + hash + 2, space));
         space = decimal + hash + 1;
       }
       modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
@@ -622,8 +622,8 @@ public abstract class ChimUtils
         {
           try
           {
-            chimeraModel = chimeraManager.getChimeraModel(
-                    Integer.valueOf(model), 0);
+            chimeraModel = chimeraManager
+                    .getChimeraModel(Integer.valueOf(model), 0);
           } catch (NumberFormatException ex)
           {
             // ignore
@@ -699,8 +699,8 @@ public abstract class ChimUtils
       if (modelIDNoResChain[0] != null)
       {
         String modelID = modelIDNoResChain[0];
-        List<ChimeraModel> models = chimeraManager.getChimeraModels(
-                modelID, ModelType.PDB_MODEL);
+        List<ChimeraModel> models = chimeraManager.getChimeraModels(modelID,
+                ModelType.PDB_MODEL);
         if (models.size() == 1)
         { // usual case with only one model
           chimeraModel = models.get(0);
@@ -729,8 +729,8 @@ public abstract class ChimUtils
           // TODO: [Optional] What is this doing?
           try
           {
-            chimeraModel = chimeraManager.getChimeraModel(
-                    Integer.valueOf(modelID), 0);
+            chimeraModel = chimeraManager
+                    .getChimeraModel(Integer.valueOf(modelID), 0);
           } catch (NumberFormatException ex)
           {
             // ignore
@@ -769,8 +769,8 @@ public abstract class ChimUtils
         }
         else if (chimeraModel.getChainCount() == 1)
         {
-          chimeraResidue = chimeraModel.getResidue(chimeraModel
-                  .getChainNames().iterator().next(), residue);
+          chimeraResidue = chimeraModel.getResidue(
+                  chimeraModel.getChainNames().iterator().next(), residue);
         }
         // System.out.println("ChimeraResidue = " + chimeraResidue);
       }
@@ -946,7 +946,8 @@ public abstract class ChimUtils
     aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
     aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
     aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
-    aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+    aaNames.put("PHE",
+            "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
     aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
     aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
     aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");