apply version 2.7 copyright

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 7bcea33..c8ac01c 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,20 +1,19 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
  * \r
- * This program 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 General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.gui;\r
 \r
@@ -82,11 +81,11 @@ public class Jalview2XML_V1
    * DOCUMENT ME!\r
    * \r
    * @param file\r
-   *                DOCUMENT ME!\r
+   *          DOCUMENT ME!\r
    */\r
   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)\r
   {\r
-    final String file  = jprovider.getFilename();\r
+    final String file = jprovider.getFilename();\r
     jalview.gui.AlignFrame af = null;\r
 \r
     try\r
@@ -239,8 +238,8 @@ public class Jalview2XML_V1
         {\r
           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(\r
                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),\r
-                  ae[aa].getSecondaryStructure().charAt(0), ae[aa]\r
-                          .getValue());\r
+                  ae[aa].getSecondaryStructure().charAt(0),\r
+                  ae[aa].getValue());\r
         }\r
 \r
         jalview.datamodel.AlignmentAnnotation jaa = null;\r
@@ -319,15 +318,13 @@ public class Jalview2XML_V1
                 groups[i].getDisplayText(), groups[i].getColourText(),\r
                 groups[i].getStart(), groups[i].getEnd());\r
 \r
-        sg\r
-                .setOutlineColour(new java.awt.Color(groups[i]\r
-                        .getOutlineColour()));\r
+        sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));\r
 \r
         if (groups[i].getConsThreshold() != 0)\r
         {\r
           jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
-                  "All", ResidueProperties.propHash, 3, sg\r
-                          .getSequences(null), 0, sg.getWidth() - 1);\r
+                  "All", ResidueProperties.propHash, 3,\r
+                  sg.getSequences(null), 0, sg.getWidth() - 1);\r
           c.calculate();\r
           c.verdict(false, 25);\r
           sg.cs.setConservation(c);\r
@@ -337,8 +334,8 @@ public class Jalview2XML_V1
       }\r
     }\r
 \r
-    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view\r
-            .getHeight());\r
+    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
+            view.getHeight());\r
     af.viewport.setStartRes(view.getStartRes());\r
     af.viewport.setStartSeq(view.getStartSeq());\r
     af.viewport.setShowAnnotation(view.getShowAnnotation());\r
@@ -414,8 +411,8 @@ public class Jalview2XML_V1
 \r
     af.setMenusFromViewport(af.viewport);\r
 \r
-    Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view\r
-            .getHeight());\r
+    Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),\r
+            view.getHeight());\r
 \r
     // LOAD TREES\r
     // /////////////////////////////////////\r
@@ -428,9 +425,10 @@ public class Jalview2XML_V1
 \r
           Tree tree = jms.getTree(t);\r
 \r
-          TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree\r
-                  .getNewick()), tree.getTitle(), tree.getWidth(), tree\r
-                  .getHeight(), tree.getXpos(), tree.getYpos());\r
+          TreePanel tp = af.ShowNewickTree(\r
+                  new jalview.io.NewickFile(tree.getNewick()),\r
+                  tree.getTitle(), tree.getWidth(), tree.getHeight(),\r
+                  tree.getXpos(), tree.getYpos());\r
 \r
           tp.fitToWindow.setState(tree.getFitToWindow());\r
           tp.fitToWindow_actionPerformed(null);\r