drawableSequence removed

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index ce98a06..1aa5cac 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 package MCview;\r
 \r
-import jalview.gui.*;\r
+import jalview.datamodel.*;\r
 import java.io.*;\r
 import java.net.*;\r
 import java.util.*;\r
@@ -12,6 +12,15 @@ public class PDBfile extends jalview.io.FileParse {
 \r
   Vector lineArray = new Vector();\r
 \r
+  public PDBfile(String [] lines)\r
+  {\r
+    for(int i=0; i<lines.length; i++)\r
+      lineArray.add(lines[i]);\r
+\r
+    noLines = lineArray.size();\r
+    parse();\r
+  }\r
+\r
   public PDBfile(String inFile, String inType) throws IOException {\r
 \r
     super(inFile,inType);\r
@@ -42,8 +51,6 @@ public class PDBfile extends jalview.io.FileParse {
 \r
   public void parse() {\r
 \r
-    System.out.println("Parsing");\r
-\r
     for (int i = 0; i < lineArray.size(); i++) {\r
       StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());\r
       if (str.hasMoreTokens()) {\r
@@ -53,10 +60,10 @@ public class PDBfile extends jalview.io.FileParse {
           try {\r
             myAtom tmpatom = new myAtom(str);\r
             if (findChain(tmpatom.chain) != null) {\r
-              System.out.println("Adding to chain " + tmpatom.chain);\r
+           //   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
+            //  System.out.println("Making chain " + tmpatom.chain);\r
               PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
               chains.addElement(tmpchain);\r
               tmpchain.atoms.addElement(tmpatom);\r
@@ -110,7 +117,7 @@ public class PDBfile extends jalview.io.FileParse {
     }\r
   }\r
 \r
-  public void colourBySequence(DrawableSequence seq) {\r
+  public void colourBySequence(Sequence seq) {\r
 //SMJS TODO\r
 //    int max = seq.maxchain;\r
 //    if (seq.maxchain != -1) {\r