X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=3025907fe46adc023add9e13001dddebcf85dae2;hb=049cfa5fc078e6daac6158f25cea7d9a60b48969;hp=7fe17c8d3d6c9bf9a096a98615213ec8cea3d593;hpb=775f6ea659bce2510739e5a5f8bd3f156662d6df;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 7fe17c8..3025907 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -191,11 +191,13 @@ public abstract class StructureFile extends AlignFile
       {
         // TODO: use the PDB ID of the structure if one is available, to save
         // bandwidth and avoid uploading the whole structure to the service
-        Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(
-                new Object[] {});
-        AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
-                new Class[] { FileParse.class }).invoke(annotate3d,
-                new Object[] { new FileParse(getDataName(), dataSourceType) }));
+        Object annotate3d = cl.getConstructor(new Class[] {})
+                .newInstance(new Object[] {});
+        AlignmentI al = ((AlignmentI) cl
+                .getMethod("getRNAMLFor", new Class[]
+                { FileParse.class })
+                .invoke(annotate3d, new Object[]
+                { new FileParse(getDataName(), dataSourceType) }));
         for (SequenceI sq : al.getSequences())
         {
           if (sq.getDatasetSequence() != null)
@@ -222,8 +224,8 @@ public abstract class StructureFile extends AlignFile
   }
 
   @SuppressWarnings("unchecked")
-  protected void replaceAndUpdateChains(List<SequenceI> prot,
-          AlignmentI al, String pep, boolean b)
+  protected void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
+          String pep, boolean b)
   {
     List<List<? extends Object>> replaced = AlignSeq
             .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
@@ -288,8 +290,8 @@ public abstract class StructureFile extends AlignFile
         processWithJmolParser(proteinSequences);
       } catch (Exception x)
       {
-        System.err
-                .println("Exceptions from Jmol when processing data in pdb file");
+        System.err.println(
+                "Exceptions from Jmol when processing data in pdb file");
         x.printStackTrace();
       }
     }
@@ -304,8 +306,11 @@ public abstract class StructureFile extends AlignFile
       Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       if (cl != null)
       {
-        final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class });
-        final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
+        final Constructor constructor = cl
+                .getConstructor(new Class[]
+                { FileParse.class });
+        final Object[] args = new Object[] {
+            new FileParse(getDataName(), dataSourceType) };
 
         StructureImportSettings.setShowSeqFeatures(false);
         StructureImportSettings.setVisibleChainAnnotation(false);
@@ -314,8 +319,8 @@ public abstract class StructureFile extends AlignFile
         StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
-        AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
-                "getSeqsAsArray", new Class[] {}).invoke(jmf));
+        AlignmentI al = new Alignment((SequenceI[]) cl
+                .getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
         cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
                 .invoke(jmf, al);
         for (SequenceI sq : al.getSequences())
@@ -392,8 +397,10 @@ public abstract class StructureFile extends AlignFile
 
   public static boolean isRNA(SequenceI seq)
   {
-    for (char c : seq.getSequence())
+    int length = seq.getLength();
+    for (int i = 0; i < length; i++)
     {
+      char c = seq.getCharAt(i);
       if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
       {
         return false;
@@ -406,7 +413,8 @@ public abstract class StructureFile extends AlignFile
    * make a friendly ID string.
    * 
    * @param dataName
-   * @return truncated dataName to after last '/'
+   * @return truncated dataName to after last '/' and pruned .extension if
+   *         present
    */
   protected String safeName(String dataName)
   {
@@ -415,6 +423,10 @@ public abstract class StructureFile extends AlignFile
     {
       dataName = dataName.substring(p + 1);
     }
+    if (dataName.indexOf(".") > -1)
+    {
+      dataName = dataName.substring(0, dataName.lastIndexOf("."));
+    }
     return dataName;
   }