Dont use myGraphics

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index f97216b..f9d842f 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -18,8 +18,6 @@
 */\r
 package MCview;\r
 \r
-import jalview.datamodel.*;\r
-\r
 import java.io.*;\r
 \r
 import java.net.*;\r
@@ -50,6 +48,10 @@ public class PDBfile extends jalview.io.FileParse {
         if (inType.equals("File")) {\r
             dataIn = new BufferedReader(new FileReader(inFile));\r
         }\r
+        else if(inType.equals("Paste"))\r
+        {\r
+            dataIn = new BufferedReader(new StringReader(inFile));\r
+        }\r
         else {\r
             URL url = new URL(inFile);\r
             this.fileSize = 0;\r
@@ -81,7 +83,6 @@ public class PDBfile extends jalview.io.FileParse {
                             //   System.out.println("Adding to chain " + tmpatom.chain);\r
                             findChain(tmpatom.chain).atoms.addElement(tmpatom);\r
                         } else {\r
-                            //  System.out.println("Making chain " + tmpatom.chain);\r
                             PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
                             chains.addElement(tmpchain);\r
                             tmpchain.atoms.addElement(tmpatom);\r
@@ -97,11 +98,6 @@ public class PDBfile extends jalview.io.FileParse {
 \r
         makeResidueList();\r
         makeCaBondList();\r
-\r
-        //    for (int i=0; i < chains.size() ; i++) {\r
-        //  String pog = ((PDBChain)chains.elementAt(i)).print();\r
-        //  System.out.println(pog);\r
-        // }\r
     }\r
 \r
     public void makeResidueList() {\r
@@ -139,12 +135,12 @@ public class PDBfile extends jalview.io.FileParse {
         }\r
     }\r
 \r
-    public void colourBySequence(Sequence seq) {\r
-        //SMJS TODO\r
-        //    int max = seq.maxchain;\r
-        //    if (seq.maxchain != -1) {\r
-        //      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);\r
-        //    }\r
+    public void colourBySequence()//jalview.gui.SequenceRenderer sr,\r
+                                // jalview.gui.FeatureRenderer fr)\r
+                                {\r
+            for (int i = 0; i < chains.size(); i++) {\r
+              //((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);\r
+            }\r
     }\r
 \r
     public void setChainColours() {\r