X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=f8e1c5af7a3794d2a847cac4c951f37e0213e646;hb=ed3ef4a5d351592f978b6d7e793e70de6ad247ca;hp=c29b0e7218489f9c4a19a9da5394cba7767e471c;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index c29b0e7..f8e1c5a 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -21,29 +21,31 @@ package jalview.datamodel;
 public class SearchResults
 {
 
-  Match [] matches;
+  Match[] matches;
 
-    /**
-     * This method replaces the old search results which merely
-     * held an alignment index of search matches. This broke
-     * when sequences were moved around the alignment
-     * @param seq Sequence
-     * @param start int
-     * @param end int
-     */
+  /**
+   * This method replaces the old search results which merely
+   * held an alignment index of search matches. This broke
+   * when sequences were moved around the alignment
+   * @param seq Sequence
+   * @param start int
+   * @param end int
+   */
   public void addResult(SequenceI seq, int start, int end)
   {
-    if(matches == null)
+    if (matches == null)
     {
-      matches = new Match[]{new Match(seq, start, end)};
+      matches = new Match[]
+          {
+          new Match(seq, start, end)};
       return;
     }
 
     int mSize = matches.length;
 
-    Match [] tmp = new Match[mSize+1];
+    Match[] tmp = new Match[mSize + 1];
     int m;
-    for(m=0; m<mSize; m++)
+    for (m = 0; m < mSize; m++)
     {
       tmp[m] = matches[m];
     }
@@ -54,45 +56,54 @@ public class SearchResults
   }
 
   /**
-  * This Method returns the search matches which lie between the
-  * start and end points of the sequence in question. It is
-  * optimised for returning objects for drawing on SequenceCanvas
-  */
-  public int [] getResults(SequenceI sequence, int start, int end)
+   * This Method returns the search matches which lie between the
+   * start and end points of the sequence in question. It is
+   * optimised for returning objects for drawing on SequenceCanvas
+   */
+  public int[] getResults(SequenceI sequence, int start, int end)
   {
-    if(matches==null)
+    if (matches == null)
+    {
       return null;
+    }
 
-    int [] result = null;
-    int [] tmp = null;
+    int[] result = null;
+    int[] tmp = null;
     int resultLength;
 
-    for(int m=0; m<matches.length; m++)
+    for (int m = 0; m < matches.length; m++)
     {
-      if( matches[m].sequence == sequence )
+      if (matches[m].sequence == sequence)
       {
-        int matchStart = matches[m].sequence.findIndex( matches[m].start ) - 1;
-        int matchEnd = matches[m].sequence.findIndex( matches[m].end ) - 1;
+        int matchStart = matches[m].sequence.findIndex(matches[m].start) - 1;
+        int matchEnd = matches[m].sequence.findIndex(matches[m].end) - 1;
 
-        if(matchStart<=end && matchEnd>=start)
+        if (matchStart <= end && matchEnd >= start)
         {
-          if(matchStart<start)
+          if (matchStart < start)
+          {
             matchStart = start;
+          }
 
-          if(matchEnd>end)
+          if (matchEnd > end)
+          {
             matchEnd = end;
+          }
 
-
-          if(result==null)
-            result = new int[]{matchStart, matchEnd};
+          if (result == null)
+          {
+            result = new int[]
+                {
+                matchStart, matchEnd};
+          }
           else
           {
             resultLength = result.length;
-            tmp = new int[resultLength+2];
-            System.arraycopy(result,0,tmp,0,resultLength);
+            tmp = new int[resultLength + 2];
+            System.arraycopy(result, 0, tmp, 0, resultLength);
             result = tmp;
             result[resultLength] = matchStart;
-            result[resultLength+1] = matchEnd;
+            result[resultLength + 1] = matchEnd;
           }
         }
       }
@@ -102,17 +113,23 @@ public class SearchResults
 
   public int getSize()
   {
-    return matches==null ? 0 : matches.length;
+    return matches == null ? 0 : matches.length;
   }
 
   public SequenceI getResultSequence(int index)
-  {    return matches[index].sequence;  }
+  {
+    return matches[index].sequence;
+  }
 
   public int getResultStart(int index)
-  {    return matches[index].start;  }
+  {
+    return matches[index].start;
+  }
 
   public int getResultEnd(int index)
-  {    return matches[index].end;  }
+  {
+    return matches[index].end;
+  }
 
   class Match
   {
@@ -122,9 +139,9 @@ public class SearchResults
 
     public Match(SequenceI seq, int start, int end)
     {
-     sequence = seq;
-     this.start = start;
-     this.end = end;
+      sequence = seq;
+      this.start = start;
+      this.end = end;
     }
   }
 }