X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=beaaf79217f4f841f35a3c3745421c0a2c2ce638;hb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;hp=b2ba256e6851d4fbeb6f269606e4f86cf8808ecb;hpb=8a5e0bc033d75200f22202146b5dc448b2b70a39;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index b2ba256..beaaf79 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
@@ -38,8 +39,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javajs.awt.Dimension;
-
 import org.jmol.api.JmolStatusListener;
 import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
@@ -61,9 +60,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  public JmolParser(String inFile, String type) throws IOException
+  public JmolParser(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public JmolParser(FileParse fp) throws IOException
@@ -351,10 +351,10 @@ 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')
       {
@@ -472,7 +472,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public String print()
+  public String print(SequenceI[] seqs, boolean jvSuffix)
   {
     return null;
   }
@@ -626,7 +626,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     return null;
   }