JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index fbe871b..498226b 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -214,7 +214,8 @@ public class FeaturesFile extends AlignFile
     {
       SequenceI seq = null;
       /**
-       * keep track of any sequences we try to create from the data if it is a GFF3 file
+       * keep track of any sequences we try to create from the data if it is a
+       * GFF3 file
        */
       ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
       String type, desc, token = null;
@@ -833,18 +834,19 @@ public class FeaturesFile extends AlignFile
    * @return true if sf was actually added to the sequence, false if it was
    *         processed in another way
    */
-  public boolean processOrAddSeqFeature(AlignmentI align, List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
+  public boolean processOrAddSeqFeature(AlignmentI align,
+          List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
           boolean gFFFile, boolean relaxedIdMatching)
   {
     String attr = (String) sf.getValue("ATTRIBUTES");
     boolean add = true;
     if (gFFFile && attr != null)
     {
-      int nattr=8;
+      int nattr = 8;
 
       for (String attset : attr.split("\t"))
       {
-        if (attset==null || attset.trim().length()==0)
+        if (attset == null || attset.trim().length() == 0)
         {
           continue;
         }
@@ -860,22 +862,25 @@ public class FeaturesFile extends AlignFile
             continue;
           }
 
-          // expect either space seperated (gff2) or '=' separated (gff3) 
+          // expect either space seperated (gff2) or '=' separated (gff3)
           // key/value pairs here
 
-          int eqpos = pair.indexOf('='),sppos = pair.indexOf(' ');
+          int eqpos = pair.indexOf('='), sppos = pair.indexOf(' ');
           String key = null, value = null;
 
           if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
           {
             key = pair.substring(0, sppos);
             value = pair.substring(sppos + 1);
-          } else {
+          }
+          else
+          {
             if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
             {
               key = pair.substring(0, eqpos);
               value = pair.substring(eqpos + 1);
-            } else
+            }
+            else
             {
               key = pair;
             }
@@ -898,8 +903,8 @@ public class FeaturesFile extends AlignFile
         {
           add &= processGffKey(set, nattr, seq, sf, align, newseqs,
                   relaxedIdMatching); // process decides if
-                                                     // feature is actually
-                                                     // added
+                                      // feature is actually
+                                      // added
         } catch (InvalidGFF3FieldException ivfe)
         {
           System.err.println(ivfe);
@@ -948,20 +953,20 @@ public class FeaturesFile extends AlignFile
     {
       int strand = sf.getStrand();
       // exonerate cdna/protein map
-      // look for fields 
+      // look for fields
       List<SequenceI> querySeq = findNames(align, newseqs,
-              relaxedIdMatching, set.get(attr="Query"));
-      if (querySeq==null || querySeq.size()!=1)
+              relaxedIdMatching, set.get(attr = "Query"));
+      if (querySeq == null || querySeq.size() != 1)
       {
-        throw new InvalidGFF3FieldException( attr, set,
+        throw new InvalidGFF3FieldException(attr, set,
                 "Expecting exactly one sequence in Query field (got "
                         + set.get(attr) + ")");
       }
-      if (set.containsKey(attr="Align"))
+      if (set.containsKey(attr = "Align"))
       {
         // process the align maps and create cdna/protein maps
         // ideally, the query sequences are in the alignment, but maybe not...
-        
+
         AlignedCodonFrame alco = new AlignedCodonFrame();
         MapList codonmapping = constructCodonMappingFromAlign(set, attr,
                 strand);
@@ -979,8 +984,8 @@ public class FeaturesFile extends AlignFile
   }
 
   private MapList constructCodonMappingFromAlign(
-          Map<String, List<String>> set,
-          String attr, int strand) throws InvalidGFF3FieldException
+          Map<String, List<String>> set, String attr, int strand)
+          throws InvalidGFF3FieldException
   {
     if (strand == 0)
     {
@@ -1134,21 +1139,21 @@ public class FeaturesFile extends AlignFile
           }
         }
       }
-      
+
     }
-    if (match==null && newseqs!=null)
+    if (match == null && newseqs != null)
     {
       match = new SequenceDummy(seqId);
       if (relaxedIdMatching)
       {
-        matcher.addAll(Arrays.asList(new SequenceI[]
-        { match }));
+        matcher.addAll(Arrays.asList(new SequenceI[] { match }));
       }
       // add dummy sequence to the newseqs list
       newseqs.add(match);
     }
     return match;
   }
+
   public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
   {
     if (sf.getDescription() == null)
@@ -1176,7 +1181,8 @@ public class FeaturesFile extends AlignFile
    *          hash of feature types and colours
    * @return features file contents
    */
-  public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
+  public String printJalviewFormat(SequenceI[] seqs,
+          Map<String, Object> visible)
   {
     return printJalviewFormat(seqs, visible, true, true);
   }
@@ -1424,13 +1430,13 @@ public class FeaturesFile extends AlignFile
    * @param visible
    * @return
    */
-  public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
+  public String printGFFFormat(SequenceI[] seqs, Map<String, Object> visible)
   {
     return printGFFFormat(seqs, visible, true, true);
   }
 
-  public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
-          boolean visOnly, boolean nonpos)
+  public String printGFFFormat(SequenceI[] seqs,
+          Map<String, Object> visible, boolean visOnly, boolean nonpos)
   {
     StringBuffer out = new StringBuffer();
     SequenceFeature[] next;