Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures

[jalview.git] / src / jalview / ext / jmol / JmolParser.java

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index ddf3b1a..2a510a2 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -28,7 +28,6 @@ import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -60,6 +59,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
+  public JmolParser(boolean immediate, String inFile,
+          DataSourceType sourceType) throws IOException
+  {
+    super(immediate, inFile, sourceType);
+  }
+
   public JmolParser(String inFile, DataSourceType sourceType)
           throws IOException
   {
@@ -183,7 +188,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
-      xferSettings();
+      if (isParseImmediately())
+      {
+        // configure parsing settings from the static singleton
+        xferSettings();
+      }
 
       makeResidueList();
       makeCaBondList();
@@ -200,7 +209,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           prot.add(chainseq);
         }
 
-        if (StructureImportSettings.isProcessSecondaryStructure())
+        // look at local setting for adding secondary tructure
+        if (predictSecondaryStructure)
         {
           createAnnotation(chainseq, chain, ms.at);
         }
@@ -355,10 +365,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
           int firstResNum)
   {
-    char[] seq = sq.getSequence();
+    int length = sq.getLength();
     boolean ssFound = false;
-    Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
-    for (int p = 0; p < seq.length; p++)
+    Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+    for (int p = 0; p < length; p++)
     {
       if (secstr[p] >= 'A' && secstr[p] <= 'z')
       {