X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=f9d842fd087c298dd08de0207aacf9495dc4e857;hb=08044f16da407871ea84ccbfbc09e34cceb74080;hp=8cbe37d3d439824889373b77c521f5f91e749d08;hpb=65bf1cd0ea1526762e829059bf6ae0901db9731d;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 8cbe37d..f9d842f 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -48,6 +48,10 @@ public class PDBfile extends jalview.io.FileParse {
         if (inType.equals("File")) {
             dataIn = new BufferedReader(new FileReader(inFile));
         }
+        else if(inType.equals("Paste"))
+        {
+            dataIn = new BufferedReader(new StringReader(inFile));
+        }
         else {
             URL url = new URL(inFile);
             this.fileSize = 0;
@@ -79,7 +83,6 @@ public class PDBfile extends jalview.io.FileParse {
                             //   System.out.println("Adding to chain " + tmpatom.chain);
                             findChain(tmpatom.chain).atoms.addElement(tmpatom);
                         } else {
-                            //  System.out.println("Making chain " + tmpatom.chain);
                             PDBChain tmpchain = new PDBChain(tmpatom.chain);
                             chains.addElement(tmpchain);
                             tmpchain.atoms.addElement(tmpatom);
@@ -132,10 +135,11 @@ public class PDBfile extends jalview.io.FileParse {
         }
     }
 
-    public void colourBySequence(jalview.gui.SequenceRenderer sr,
-                                 jalview.gui.FeatureRenderer fr) {
+    public void colourBySequence()//jalview.gui.SequenceRenderer sr,
+                                // jalview.gui.FeatureRenderer fr)
+                                {
             for (int i = 0; i < chains.size(); i++) {
-              ((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);
+              //((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);
             }
     }