X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fuk%2Fac%2Fvamsas%2Ftest%2Fsimpleclient%2FArchiveReader.java;h=a00be7274fcd646bb7d319ea1530f250dd898d1b;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=68e6ff4c536b1588aae45dcab0a3d47b83c89db4;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/test/simpleclient/ArchiveReader.java b/src/uk/ac/vamsas/test/simpleclient/ArchiveReader.java
index 68e6ff4..a00be72 100644
--- a/src/uk/ac/vamsas/test/simpleclient/ArchiveReader.java
+++ b/src/uk/ac/vamsas/test/simpleclient/ArchiveReader.java
@@ -1,51 +1,74 @@
-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.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-public class ArchiveReader {
-  /**
-   * tests VamsasArchiveReader archive reader on a vamsas jar file
-   * @param args
-   */
-  public static void main(String args[]) {
-    
-    try {
-      File av = new File(args[0]);
-      VamsasArchiveReader var = new VamsasArchiveReader(av);
-      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);
-    }
-  }
-}
+/*
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
+ */
+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.VamsasArchiveReader;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
+
+public class ArchiveReader {
+  /**
+   * tests VamsasArchiveReader archive reader on a vamsas jar file
+   * 
+   * @param args
+   */
+  public static void main(String args[]) {
+
+    try {
+      File av = new File(args[0]);
+      VamsasArchiveReader var = new VamsasArchiveReader(av);
+      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);
+    }
+  }
+}