Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 5d58d42..c21b02c 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -61,7 +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;
@@ -158,16 +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;
@@ -186,9 +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);
         }
@@ -210,10 +209,7 @@ public class ClustalFile extends AlignFile
     {
       String tmp = printId(s[i], jvsuffix);
 
-      if (s[i].getSequence().length > max)
-      {
-        max = s[i].getSequence().length;
-      }
+      max = Math.max(max, s[i].getLength());
 
       if (tmp.length() > maxid)
       {
@@ -239,20 +235,20 @@ public class ClustalFile extends AlignFile
 
       while ((j < s.length) && (s[j] != null))
       {
-        out.append(new Format("%-" + maxid + "s").form(printId(s[j],
-                jvsuffix) + " "));
+        out.append(new Format("%-" + maxid + "s")
+                .form(printId(s[j], jvsuffix) + " "));
 
         int start = i * len;
         int end = start + len;
 
-        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].getSequenceAsString(start, end));
         }
         else
         {
-          if (start < s[j].getSequence().length)
+          if (start < length)
           {
             out.append(s[j].getSequenceAsString().substring(start));
           }