apply version 2.7 copyright

[jalview.git] / src / jalview / io / AMSAFile.java

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 4f21875..64f8399 100644 (file)
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,85 +1,102 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, 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
-*\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
-*\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
-*/\r
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class AMSAFile extends jalview.io.FastaFile\r
-{\r
-\r
-   AlignmentI al;\r
-    /**\r
-     * Creates a new AMSAFile object for output.\r
-     */\r
-    public AMSAFile(AlignmentI al)\r
-    {\r
-      this.al = al;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String print()\r
-    {\r
-      super.print(getSeqsAsArray());\r
-\r
-      AlignmentAnnotation aa;\r
-      if (al.getAlignmentAnnotation() != null)\r
-      {\r
-        for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
-        {\r
-          aa = al.getAlignmentAnnotation()[i];\r
-          if (aa.autoCalculated || !aa.visible)\r
-            continue;\r
-\r
-          out.append(">#_" + aa.label);\r
-          if (aa.description != null)\r
-            out.append(" " + aa.description);\r
-\r
-          out.append("\n");\r
-\r
-          int nochunks = (aa.annotations.length / len) + 1;\r
-\r
-          for (int j = 0; j < nochunks; j++)\r
-          {\r
-            int start = j * len;\r
-            int end = start + len;\r
-            if (end > aa.annotations.length)\r
-              end = aa.annotations.length;\r
-\r
-            String ch;\r
-            for (int k = start; k < end; k++)\r
-            {\r
-              if (aa.annotations[k] == null)\r
-                ch = " ";\r
-              else\r
-                ch = aa.annotations[k].displayCharacter;\r
-\r
-              out.append(ch);\r
-\r
-            }\r
-            out.append("\n");\r
-          }\r
-        }\r
-      }\r
-      return out.toString();\r
-    }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * 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.
+ * 
+ * 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.io;
+
+import jalview.datamodel.*;
+
+public class AMSAFile extends jalview.io.FastaFile
+{
+
+  AlignmentI al;
+
+  /**
+   * Creates a new AMSAFile object for output.
+   */
+  public AMSAFile(AlignmentI al)
+  {
+    this.al = al;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    super.print(getSeqsAsArray());
+
+    AlignmentAnnotation aa;
+    if (al.getAlignmentAnnotation() != null)
+    {
+
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+      {
+        aa = al.getAlignmentAnnotation()[i];
+
+        if (aa.autoCalculated || !aa.visible)
+        {
+          continue;
+        }
+
+        out.append(">#_" + aa.label);
+        if (aa.description != null)
+        {
+          out.append(" " + aa.description);
+        }
+
+        out.append(newline);
+
+        int nochunks = Math.min(aa.annotations.length, al.getWidth()) / len
+                + 1;
+
+        for (int j = 0; j < nochunks; j++)
+        {
+          int start = j * len;
+          int end = start + len;
+          if (end > aa.annotations.length)
+          {
+            end = aa.annotations.length;
+          }
+
+          String ch;
+          for (int k = start; k < end; k++)
+          {
+            if (aa.annotations[k] == null)
+            {
+              ch = " ";
+            }
+            else
+            {
+              ch = aa.annotations[k].displayCharacter;
+            }
+            if (ch.length() > 1)
+            {
+              this.warningMessage = "Truncated column annotation to first letter.";
+              ch = ch.substring(0, 1);
+            }
+            out.append(ch);
+
+          }
+          out.append(newline);
+        }
+      }
+    }
+    return out.toString();
+  }
+}