new getVisibleContigs method mirrors the getVisibleContigs method in AlignmentView

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 36eecb8..99a0a2b 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -18,13 +18,10 @@
 */\r
 package MCview;\r
 \r
-import jalview.io.AppletFormatAdapter;\r
 import jalview.datamodel.*;\r
 \r
 import java.io.*;\r
 \r
-import java.net.*;\r
-\r
 import java.util.*;\r
 import java.awt.Color;\r
 \r
@@ -103,6 +100,10 @@ public class PDBfile extends jalview.io.AlignFile {
        makeResidueList();\r
        makeCaBondList();\r
 \r
+       if(id==null)\r
+       {\r
+         id = inFile.getName();\r
+       }\r
        for (int i = 0; i < chains.size(); i++)\r
        {\r
          SequenceI seq = ( (PDBChain) chains.elementAt(i)).\r
@@ -114,7 +115,8 @@ public class PDBfile extends jalview.io.AlignFile {
 \r
          PDBEntry entry = new PDBEntry();\r
          entry.setId(id);\r
-         entry.setFile(inFile.getAbsolutePath());\r
+         if(inFile!=null)\r
+           entry.setFile(inFile.getAbsolutePath());\r
 \r
          seq.setDatasetSequence(dataset);\r
          dataset.addPDBId(entry);\r