JAL-3438 spotless for 2.11.2.0

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

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 947d982..ede258e 100755 (executable)
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,20 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -33,10 +35,10 @@ package jalview.io;
  * found in Emboss (thanks David Martin!)
  * 
  */
-import java.io.*;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
 
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
 
 public class PileUpfile extends MSFfile
 {
@@ -52,16 +54,17 @@ public class PileUpfile extends MSFfile
    * Creates a new MSFfile object.
    * 
    * @param inFile
-   *                DOCUMENT ME!
-   * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
+   * @param sourceType
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
-  public PileUpfile(String inFile, String type) throws IOException
+  public PileUpfile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public PileUpfile(FileParse source) throws IOException
@@ -69,19 +72,12 @@ public class PileUpfile extends MSFfile
     super(source);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String print()
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
-    return print(getSeqsAsArray());
-  }
-
-  public String print(SequenceI[] s)
-  {
-    StringBuffer out = new StringBuffer("PileUp\n\n");
+    StringBuffer out = new StringBuffer("PileUp");
+    out.append(newline);
+    out.append(newline);
 
     int max = 0;
     int maxid = 0;
@@ -96,16 +92,20 @@ public class PileUpfile extends MSFfile
       i++;
     }
 
-    out.append("   MSF: " + s[0].getSequence().length
-            + "   Type: P    Check:  " + bigChecksum % 10000
-            + "   ..\n\n\n");
+    out.append("   MSF: " + s[0].getLength() + "   Type: P    Check:  "
+            + bigChecksum % 10000 + "   ..");
+    out.append(newline);
+    out.append(newline);
+    out.append(newline);
 
     i = 0;
     while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
-      out.append(" Name: " + printId(s[i]) + " oo  Len:  " + seq.length()
-              + "  Check:  " + checksums[i] + "  Weight:  1.00\n");
+      out.append(" Name: " + printId(s[i], jvsuffix) + " oo  Len:  "
+              + seq.length() + "  Check:  " + checksums[i]
+              + "  Weight:  1.00");
+      out.append(newline);
 
       if (seq.length() > max)
       {
@@ -126,16 +126,15 @@ public class PileUpfile extends MSFfile
     }
 
     maxid++;
-    out.append("\n\n//\n\n");
+    out.append(newline);
+    out.append(newline);
+    out.append("//");
+    out.append(newline);
+    out.append(newline);
 
     int len = 50;
 
-    int nochunks = (max / len) + 1;
-
-    if ((max % len) == 0)
-    {
-      nochunks--;
-    }
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {
@@ -143,7 +142,7 @@ public class PileUpfile extends MSFfile
 
       while ((j < s.length) && (s[j] != null))
       {
-        String name = printId(s[j]);
+        String name = printId(s[j], jvsuffix);
 
         out.append(new Format("%-" + maxid + "s").form(name + " "));
 
@@ -152,8 +151,8 @@ public class PileUpfile extends MSFfile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ((end < s[j].getSequence().length)
-                  && (start < s[j].getSequence().length))
+          int length = s[j].getLength();
+          if ((end < length) && (start < length))
           {
             out.append(s[j].getSequence(start, end));
 
@@ -163,21 +162,21 @@ public class PileUpfile extends MSFfile
             }
             else
             {
-              out.append("\n");
+              out.append(newline);
             }
           }
           else
           {
-            if (start < s[j].getSequence().length)
+            if (start < length)
             {
               out.append(s[j].getSequenceAsString().substring(start));
-              out.append("\n");
+              out.append(newline);
             }
             else
             {
               if (k == 0)
               {
-                out.append("\n");
+                out.append(newline);
               }
             }
           }
@@ -186,7 +185,7 @@ public class PileUpfile extends MSFfile
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();