X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=64d00ffef113a5396165b52f39ae19f7a55659f7;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=f5f37c435813d8a9f70485621423698cd7fccbba;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index f5f37c4..64d00ff 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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 General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -82,11 +81,11 @@ public class Jalview2XML_V1
    * DOCUMENT ME!
    * 
    * @param file
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
   {
-    final String file  = jprovider.getFilename();
+    final String file = jprovider.getFilename();
     jalview.gui.AlignFrame af = null;
 
     try
@@ -239,8 +238,8 @@ public class Jalview2XML_V1
         {
           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
-                  ae[aa].getSecondaryStructure().charAt(0), ae[aa]
-                          .getValue());
+                  ae[aa].getSecondaryStructure().charAt(0),
+                  ae[aa].getValue());
         }
 
         jalview.datamodel.AlignmentAnnotation jaa = null;
@@ -319,15 +318,13 @@ public class Jalview2XML_V1
                 groups[i].getDisplayText(), groups[i].getColourText(),
                 groups[i].getStart(), groups[i].getEnd());
 
-        sg
-                .setOutlineColour(new java.awt.Color(groups[i]
-                        .getOutlineColour()));
+        sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 
         if (groups[i].getConsThreshold() != 0)
         {
           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-                  "All", ResidueProperties.propHash, 3, sg
-                          .getSequences(null), 0, sg.getWidth() - 1);
+                  "All", ResidueProperties.propHash, 3,
+                  sg.getSequences(null), 0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);
@@ -337,8 +334,8 @@ public class Jalview2XML_V1
       }
     }
 
-    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
-            .getHeight());
+    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+            view.getHeight());
     af.viewport.setStartRes(view.getStartRes());
     af.viewport.setStartSeq(view.getStartSeq());
     af.viewport.setShowAnnotation(view.getShowAnnotation());
@@ -414,8 +411,8 @@ public class Jalview2XML_V1
 
     af.setMenusFromViewport(af.viewport);
 
-    Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
-            .getHeight());
+    Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+            view.getHeight());
 
     // LOAD TREES
     // /////////////////////////////////////
@@ -428,9 +425,10 @@ public class Jalview2XML_V1
 
           Tree tree = jms.getTree(t);
 
-          TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
-                  .getNewick()), tree.getTitle(), tree.getWidth(), tree
-                  .getHeight(), tree.getXpos(), tree.getYpos());
+          TreePanel tp = af.ShowNewickTree(
+                  new jalview.io.NewickFile(tree.getNewick()),
+                  tree.getTitle(), tree.getWidth(), tree.getHeight(),
+                  tree.getXpos(), tree.getYpos());
 
           tp.fitToWindow.setState(tree.getFitToWindow());
           tp.fitToWindow_actionPerformed(null);