Merge branch 'documentation/JAL-2751patch2102b2' into releases/Release_2_10_2b1_Branch

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index f7a45de..6c35ca1 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -37,9 +37,10 @@ public class ClustalFile extends AlignFile
   {
   }
 
-  public ClustalFile(String inFile, String type) throws IOException
+  public ClustalFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public ClustalFile(FileParse source) throws IOException
@@ -60,7 +61,8 @@ public class ClustalFile extends AlignFile
     boolean flag = false;
     boolean rna = false;
     boolean top = false;
-    StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
+    StringBuffer pssecstr = new StringBuffer(),
+            consstr = new StringBuffer();
     Vector headers = new Vector();
     Hashtable seqhash = new Hashtable();
     StringBuffer tempseq;
@@ -157,16 +159,15 @@ public class ClustalFile extends AlignFile
           }
 
           Sequence newSeq = parseId(headers.elementAt(i).toString());
-          newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
-                  .toString());
+          newSeq.setSequence(
+                  seqhash.get(headers.elementAt(i).toString()).toString());
 
           seqs.addElement(newSeq);
         }
         else
         {
-          System.err
-                  .println("Clustal File Reader: Can't find sequence for "
-                          + headers.elementAt(i));
+          System.err.println("Clustal File Reader: Can't find sequence for "
+                  + headers.elementAt(i));
         }
       }
       AlignmentAnnotation lastssa = null;
@@ -185,9 +186,8 @@ public class ClustalFile extends AlignFile
         AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
                 "secondary structure", consstr.toString());
         ssa.label = "Consensus Secondary Structure";
-        if (lastssa == null
-                || !lastssa.getRNAStruc().equals(
-                        ssa.getRNAStruc().replace('-', '.')))
+        if (lastssa == null || !lastssa.getRNAStruc()
+                .equals(ssa.getRNAStruc().replace('-', '.')))
         {
           annotations.addElement(ssa);
         }
@@ -196,13 +196,7 @@ public class ClustalFile extends AlignFile
   }
 
   @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-    // TODO: locaRNA style aln output
-  }
-
-  public String print(SequenceI[] s)
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
 
@@ -213,7 +207,7 @@ public class ClustalFile extends AlignFile
 
     while ((i < s.length) && (s[i] != null))
     {
-      String tmp = printId(s[i]);
+      String tmp = printId(s[i], jvsuffix);
 
       if (s[i].getSequence().length > max)
       {
@@ -244,7 +238,8 @@ public class ClustalFile extends AlignFile
 
       while ((j < s.length) && (s[j] != null))
       {
-        out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+        out.append(new Format("%-" + maxid + "s")
+                .form(printId(s[j], jvsuffix) + " "));
 
         int start = i * len;
         int end = start + len;