X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAMSAFile.java;h=e7e6d97bf3b1d74ab9cb982525f1112239e555cd;hb=49cc4c921eac8fd966dfe4fa4b86d00655ea2f67;hp=12a659db8145c4c9d08ada6da9da411f08c50598;hpb=68a0d4900885cec55096d1f266ee15ef6217f754;p=jalview.git

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 12a659d..e7e6d97 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,85 +1,100 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, 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 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.
-*
-* 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 - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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.
+ *
+ * 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
+ */
 package jalview.io;
 
 import jalview.datamodel.*;
 
-public class AMSAFile extends jalview.io.FastaFile
+public class AMSAFile
+    extends jalview.io.FastaFile
 {
 
-   AlignmentI al;
-    /**
-     * Creates a new AMSAFile object for output.
-     */
-    public AMSAFile(AlignmentI al)
-    {
-      this.al = al;
-    }
+  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());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String print()
+    AlignmentAnnotation aa;
+    if (al.getAlignmentAnnotation() != null)
     {
-      super.print(getSeqsAsArray());
 
-      AlignmentAnnotation aa;
-      if (al.getAlignmentAnnotation() != null)
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
-        for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+        aa = al.getAlignmentAnnotation()[i];
+
+
+        if (aa.autoCalculated || !aa.visible)
         {
-          aa = al.getAlignmentAnnotation()[i];
-          if (aa.autoCalculated)
-            continue;
+          continue;
+        }
 
-          out.append(">#_" + aa.label);
-          if (aa.description != null)
-            out.append(" " + aa.description);
+        out.append(">#_" + aa.label);
+        if (aa.description != null)
+        {
+          out.append(" " + aa.description);
+        }
 
-          out.append("\n");
+        out.append("\n");
 
-          int nochunks = (aa.annotations.length / len) + 1;
+        int nochunks = Math.min(aa.annotations.length, al.getWidth())
+                        / len + 1;
 
-          for (int j = 0; j < nochunks; j++)
+        for (int j = 0; j < nochunks; j++)
+        {
+          int start = j * len;
+          int end = start + len;
+          if (end > aa.annotations.length)
           {
-            int start = j * len;
-            int end = start + len;
-            if (end > aa.annotations.length)
-              end = aa.annotations.length;
+            end = aa.annotations.length;
+          }
 
-            String ch;
-            for (int k = start; k < end; k++)
+          String ch;
+          for (int k = start; k < end; k++)
+          {
+            if (aa.annotations[k] == null)
+            {
+              ch = " ";
+            }
+            else
             {
-              if (aa.annotations[k] == null)
-                ch = " ";
-              else
-                ch = aa.annotations[k].displayCharacter;
+              ch = aa.annotations[k].displayCharacter;
+            }
 
-              out.append(ch);
+            out.append(ch);
 
-            }
-            out.append("\n");
           }
+          out.append("\n");
         }
       }
-      return out.toString();
     }
+    return out.toString();
+  }
 }