X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=f8cfcbfbb21501c2698be87bbcca3e3905dbb222;hb=05688ef13325c699644487ce1c08a53927f0eeb0;hp=d52e42a768a0e65db9a543e05031e5a5a164de6f;hpb=bf1fd68e2aea9ef1f5c0cbbae814b78d69f29e3a;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index d52e42a..f8cfcbf 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import jalview.api.AlignViewportI;
 import jalview.api.FinderI;
 import jalview.datamodel.AlignmentI;
@@ -121,7 +123,7 @@ public class Finder implements FinderI
   {
     doFind(theSearchString, matchCase, searchDescription, false,
             ignoreHidden);
-    
+
     if (searchResults.isEmpty() && idMatches.isEmpty())
     {
       /*
@@ -148,7 +150,7 @@ public class Finder implements FinderI
     idMatches = new ArrayList<>();
 
     String searchString = matchCase ? theSearchString
-            : theSearchString.toUpperCase();
+            : theSearchString.toUpperCase(Locale.ROOT);
     Regex searchPattern = new Regex(searchString);
     searchPattern.setIgnoreCase(!matchCase);
 
@@ -172,9 +174,9 @@ public class Finder implements FinderI
   }
 
   /**
-   * Calculates and saves the sequence string to search. The string is restricted
-   * to the current selection region if there is one, and is saved with all gaps
-   * removed.
+   * Calculates and saves the sequence string to search. The string is
+   * restricted to the current selection region if there is one, and is saved
+   * with all gaps removed.
    * <p>
    * If there are hidden columns, and option {@ignoreHidden} is selected, then
    * only visible positions of the sequence are included, and a mapping is also
@@ -246,13 +248,14 @@ public class Finder implements FinderI
   }
 
   /**
-   * Returns a string consisting of only the visible residues of {@code seq} from
-   * alignment column {@ fromColumn}, restricted to the current selection region
-   * if there is one.
+   * Returns a string consisting of only the visible residues of {@code seq}
+   * from alignment column {@ fromColumn}, restricted to the current selection
+   * region if there is one.
    * <p>
-   * As a side-effect, also computes the mapping from the true sequence positions
-   * to the positions (1, 2, ...) of the returned sequence. This is to allow
-   * search matches in the visible sequence to be converted to sequence positions.
+   * As a side-effect, also computes the mapping from the true sequence
+   * positions to the positions (1, 2, ...) of the returned sequence. This is to
+   * allow search matches in the visible sequence to be converted to sequence
+   * positions.
    * 
    * @param seq
    * @return
@@ -312,9 +315,9 @@ public class Finder implements FinderI
 
   /**
    * Advances the search to the next sequence in the alignment. Sequences not in
-   * the current selection group (if there is one) are skipped. The (sub-)sequence
-   * to be searched is extracted, gaps removed, and saved, or set to null if there
-   * are no more sequences to search.
+   * the current selection group (if there is one) are skipped. The
+   * (sub-)sequence to be searched is extracted, gaps removed, and saved, or set
+   * to null if there are no more sequences to search.
    * <p>
    * Returns true if a sequence could be found, false if end of alignment was
    * reached
@@ -346,9 +349,8 @@ public class Finder implements FinderI
    * @param ignoreHidden
    * @return
    */
-  protected boolean findNextMatch(String searchString,
-          Regex searchPattern, boolean matchDescription,
-          boolean ignoreHidden)
+  protected boolean findNextMatch(String searchString, Regex searchPattern,
+          boolean matchDescription, boolean ignoreHidden)
   {
     if (residueIndex < 0)
     {
@@ -356,8 +358,7 @@ public class Finder implements FinderI
        * at start of sequence; try find by residue number, in sequence id,
        * or (optionally) in sequence description
        */
-      if (doNonMotifSearches(searchString, searchPattern,
-              matchDescription))
+      if (doNonMotifSearches(searchString, searchPattern, matchDescription))
       {
         return true;
       }
@@ -410,14 +411,14 @@ public class Finder implements FinderI
      */
     int offset = searchPattern.matchedFrom();
     int matchStartPosition = this.searchedSequenceStartPosition + offset;
-    int matchEndPosition = matchStartPosition
-            + searchPattern.charsMatched() - 1;
+    int matchEndPosition = matchStartPosition + searchPattern.charsMatched()
+            - 1;
 
     /*
      * update residueIndex to next position after the start of the match
      * (findIndex returns a value base 1, columnIndex is held base 0)
      */
-    residueIndex = searchPattern.matchedFrom()+1;
+    residueIndex = searchPattern.matchedFrom() + 1;
 
     /*
      * return false if the match is entirely in a hidden region
@@ -445,9 +446,9 @@ public class Finder implements FinderI
   }
 
   /**
-   * Adds one match to the stored list. If hidden residues are being skipped, then
-   * the match may need to be split into contiguous positions of the sequence (so
-   * it does not include skipped residues).
+   * Adds one match to the stored list. If hidden residues are being skipped,
+   * then the match may need to be split into contiguous positions of the
+   * sequence (so it does not include skipped residues).
    * 
    * @param seq
    * @param matchStartPosition
@@ -550,10 +551,12 @@ public class Finder implements FinderI
    * @param searchPattern
    * @return
    */
-  protected boolean searchSequenceDescription(SequenceI seq, Regex searchPattern)
+  protected boolean searchSequenceDescription(SequenceI seq,
+          Regex searchPattern)
   {
     String desc = seq.getDescription();
-    if (desc != null && searchPattern.search(desc) && !idMatches.contains(seq))
+    if (desc != null && searchPattern.search(desc)
+            && !idMatches.contains(seq))
     {
       idMatches.add(seq);
       return true;
@@ -582,7 +585,8 @@ public class Finder implements FinderI
 
   /**
    * If the residue position is valid for the sequence, and in a visible column,
-   * adds the position to the search results and returns true, else answers false.
+   * adds the position to the search results and returns true, else answers
+   * false.
    * 
    * @param seq
    * @param resNo
@@ -615,7 +619,8 @@ public class Finder implements FinderI
       return true;
     }
     int col = seq.findIndex(res); // base 1
-    return viewport.getAlignment().getHiddenColumns().isVisible(col - 1); // base 0
+    return viewport.getAlignment().getHiddenColumns().isVisible(col - 1); // base
+                                                                          // 0
   }
 
   @Override