+ String loadPDBFile(String file, String pdbId)\r
+ {\r
+ System.out.println("load file "+file);\r
+ try\r
+ {\r
+ JarInputStream jin = null;\r
+\r
+ if (file.startsWith("http://"))\r
+ {\r
+ jin = new JarInputStream(new URL(file).openStream());\r
+ }\r
+ else\r
+ {\r
+ jin = new JarInputStream(new FileInputStream(file));\r
+ }\r
+\r
+ JarEntry entry = null;\r
+ do\r
+ {\r
+ entry = jin.getNextJarEntry();\r
+ }\r
+ while (!entry.getName().equals(pdbId));\r
+\r
+ BufferedReader in = new BufferedReader(new InputStreamReader(jin));\r
+ File outFile = File.createTempFile("jalview_pdb", ".txt");\r
+ outFile.deleteOnExit();\r
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+ String data;\r
+\r
+ while ( (data = in.readLine()) != null)\r
+ {\r
+ out.println(data);\r
+ }\r
+ out.close();\r
+ return outFile.getAbsolutePath();\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+\r
+ AlignFrame LoadFromObject(JalviewModel object, String file)\r