From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 24 Jan 2007 17:27:44 +0000 (+0000)
Subject: Extension to fastaFile for myhits
X-Git-Tag: Release_2_3~452
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=68a0d4900885cec55096d1f266ee15ef6217f754;p=jalview.git

Extension to fastaFile for myhits
---

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
new file mode 100644
index 0000000..12a659d
--- /dev/null
+++ b/src/jalview/io/AMSAFile.java
@@ -0,0 +1,85 @@
+/*
+* 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
+*/
+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)
+            continue;
+
+          out.append(">#_" + aa.label);
+          if (aa.description != null)
+            out.append(" " + aa.description);
+
+          out.append("\n");
+
+          int nochunks = (aa.annotations.length / 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;
+
+              out.append(ch);
+
+            }
+            out.append("\n");
+          }
+        }
+      }
+      return out.toString();
+    }
+}