JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

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

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index d8890af..c698a31 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,26 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import java.io.*;
+import java.io.IOException;
 
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
 /**
  * DOCUMENT ME!
@@ -49,20 +55,31 @@ public class FastaFile extends AlignFile
    * 
    * @param inFile
    *          DOCUMENT ME!
-   * @param type
+   * @param sourceType
    *          DOCUMENT ME!
    * 
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public FastaFile(String inFile, String type) throws IOException
+  public FastaFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public FastaFile(FileParse source) throws IOException
   {
-    super(source);
+    this(source, true);
+  }
+
+  public FastaFile(FileParse source, boolean closeData) throws IOException
+  {
+    super(true, source, closeData);
+  }
+
+  public FastaFile(SequenceI[] seqs)
+  {
+    super(seqs);
   }
 
   /**
@@ -71,12 +88,13 @@ public class FastaFile extends AlignFile
    * @throws IOException
    *           DOCUMENT ME!
    */
+  @Override
   public void parse() throws IOException
   {
     StringBuffer sb = new StringBuffer();
     boolean firstLine = true;
 
-    String line,uline;
+    String line, uline;
     Sequence seq = null;
 
     boolean annotation = false;
@@ -138,23 +156,24 @@ public class FastaFile extends AlignFile
       seqs.addElement(seq);
     }
   }
+
   private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
   {
     Annotation[] anots = new Annotation[sb.length()];
     char cb;
-    for (int i=0;i<anots.length;i++)
+    for (int i = 0; i < anots.length; i++)
     {
       char cn = sb.charAt(i);
       if (cn != ' ')
       {
-        anots[i] = new Annotation(""+cn, null,
-              ' ', Float.NaN);
+        anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
       }
     }
-    AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
-            .substring(2), seq.getDescription(), anots);
+    AlignmentAnnotation aa = new AlignmentAnnotation(
+            seq.getName().substring(2), seq.getDescription(), anots);
     return aa;
   }
+
   /**
    * called by AppletFormatAdapter to generate an annotated alignment, rather
    * than bare sequences.
@@ -166,35 +185,21 @@ public class FastaFile extends AlignFile
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      AlignmentAnnotation aa = (AlignmentAnnotation) annotations
-              .elementAt(i);
+      AlignmentAnnotation aa = annotations.elementAt(i);
       aa.setPadGaps(true, al.getGapCharacter());
       al.addAnnotation(aa);
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param len
-   *          DOCUMENT ME!
-   * @param gaps
-   *          DOCUMENT ME!
-   * @param displayId
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     out = new StringBuffer();
     int i = 0;
 
     while ((i < s.length) && (s[i] != null))
     {
-      out.append(">" + printId(s[i]));
+      out.append(">" + printId(s[i], jvsuffix));
       if (s[i].getDescription() != null)
       {
         out.append(" " + s[i].getDescription());
@@ -202,7 +207,8 @@ public class FastaFile extends AlignFile
 
       out.append(newline);
 
-      int nochunks = (s[i].getLength() / len) + 1;
+      int nochunks = (s[i].getLength() / len)
+              + (s[i].getLength() % len > 0 ? 1 : 0);
 
       for (int j = 0; j < nochunks; j++)
       {
@@ -225,14 +231,4 @@ public class FastaFile extends AlignFile
 
     return out.toString();
   }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }