applied LGPLv3 and source code formatting.

[vamsas.git] / src / uk / ac / vamsas / test / simpleclient / ArchiveStreamReader.java

diff --git a/src/uk/ac/vamsas/test/simpleclient/ArchiveStreamReader.java b/src/uk/ac/vamsas/test/simpleclient/ArchiveStreamReader.java
index d3fe14f..ff96afc 100644 (file)
--- a/src/uk/ac/vamsas/test/simpleclient/ArchiveStreamReader.java
+++ b/src/uk/ac/vamsas/test/simpleclient/ArchiveStreamReader.java
@@ -1,53 +1,77 @@
-package uk.ac.vamsas.test.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-
-
-import uk.ac.vamsas.client.simpleclient.SessionFile;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-public class ArchiveStreamReader {
-  /**
-   * tests VamsasArchiveReader archive reader on a vamsas jar file opened as a stream
-   * @param args
-   */
-  public static void main(String args[]) {
-    
-    try {
-      VamsasFile av = new VamsasFile(new File(args[0]));
-      VamsasArchiveReader var = new VamsasArchiveReader(av.getLock());
-      VAMSAS roots[]=null;
-      if (var.isValid()) {
-        InputStreamReader vdoc = new InputStreamReader(var.getVamsasDocumentStream());
-        VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
-        if (ArchiveReports.reportDocument(doc, var, true, System.out)) {
-          roots = doc.getVAMSAS();
-        }
-      } else {
-        InputStream vxmlis = var.getVamsasXmlStream();
-        
-        if (vxmlis!=null) { // Might be an old vamsas file.
-          BufferedInputStream ixml = new BufferedInputStream(var.getVamsasXmlStream());
-          InputStreamReader vxml = new InputStreamReader(ixml);
-          VAMSAS root;
-          // unmarshal seems to always close the stream (should check this)
-          if ((root = VAMSAS.unmarshal(vxml))!=null) {
-            System.out.println("Read a root.");
-            roots = new VAMSAS[1];
-            roots[0] = root;
-          }
-        }
-      }
-      if (!ArchiveReports.rootReport(roots, true, System.out))
-        System.err.print(args[0]+" is not a valid vamsas archive.");
-    } catch (Exception e) {
-      e.printStackTrace(System.err);
-    }
-  }
-}
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ *  Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ *  \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.test.simpleclient;\r
+\r
+import java.io.BufferedInputStream;\r
+import java.io.File;\r
+import java.io.InputStream;\r
+import java.io.InputStreamReader;\r
+\r
+import uk.ac.vamsas.client.simpleclient.SessionFile;\r
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;\r
+import uk.ac.vamsas.client.simpleclient.VamsasFile;\r
+import uk.ac.vamsas.objects.core.VAMSAS;\r
+import uk.ac.vamsas.objects.core.VamsasDocument;\r
+\r
+public class ArchiveStreamReader {\r
+  /**\r
+   * tests VamsasArchiveReader archive reader on a vamsas jar file opened as a\r
+   * stream\r
+   * \r
+   * @param args\r
+   */\r
+  public static void main(String args[]) {\r
+\r
+    try {\r
+      VamsasFile av = new VamsasFile(new File(args[0]));\r
+      VamsasArchiveReader var = new VamsasArchiveReader(av.getLock());\r
+      VAMSAS roots[] = null;\r
+      if (var.isValid()) {\r
+        InputStreamReader vdoc = new InputStreamReader(var\r
+            .getVamsasDocumentStream());\r
+        VamsasDocument doc = VamsasDocument.unmarshal(vdoc);\r
+        if (ArchiveReports.reportDocument(doc, var, true, System.out)) {\r
+          roots = doc.getVAMSAS();\r
+        }\r
+      } else {\r
+        InputStream vxmlis = var.getVamsasXmlStream();\r
+\r
+        if (vxmlis != null) { // Might be an old vamsas file.\r
+          BufferedInputStream ixml = new BufferedInputStream(var\r
+              .getVamsasXmlStream());\r
+          InputStreamReader vxml = new InputStreamReader(ixml);\r
+          VAMSAS root;\r
+          // unmarshal seems to always close the stream (should check this)\r
+          if ((root = VAMSAS.unmarshal(vxml)) != null) {\r
+            System.out.println("Read a root.");\r
+            roots = new VAMSAS[1];\r
+            roots[0] = root;\r
+          }\r
+        }\r
+      }\r
+      if (!ArchiveReports.rootReport(roots, true, System.out))\r
+        System.err.print(args[0] + " is not a valid vamsas archive.");\r
+    } catch (Exception e) {\r
+      e.printStackTrace(System.err);\r
+    }\r
+  }\r
+}\r