licencing and format applied (eclipse)

[jalview.git] / src / jalview / analysis / Finder.java

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 8bda592..756897c 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -28,16 +28,24 @@ public class Finder
    * Implements the search algorithms for the Find dialog box.
    */
   SearchResults searchResults;
+
   AlignmentI alignment;
+
   jalview.datamodel.SequenceGroup selection = null;
+
   Vector idMatch = null;
+
   boolean caseSensitive = false;
+
   boolean findAll = false;
+
   com.stevesoft.pat.Regex regex = null;
+
   /**
    * hold's last-searched position between calles to find(false)
    */
   int seqIndex = 0, resIndex = 0;
+
   public Finder(AlignmentI alignment, SequenceGroup selection)
   {
     this.alignment = alignment;
@@ -45,7 +53,7 @@ public class Finder
   }
 
   public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
-                int seqIndex, int resIndex)
+          int seqIndex, int resIndex)
   {
     this(alignment, selectionGroup);
     this.seqIndex = seqIndex;
@@ -66,7 +74,7 @@ public class Finder
     String item = null;
     boolean found = false;
 
-    ////// is the searchString a residue number?
+    // //// is the searchString a residue number?
     try
     {
       int res = Integer.parseInt(searchString);
@@ -82,19 +90,18 @@ public class Finder
 
       searchResults.addResult(seq, res, res);
       hasResults = true;
-    }
-    catch (NumberFormatException ex)
+    } catch (NumberFormatException ex)
     {
     }
 
-    ///////////////////////////////////////////////
+    // /////////////////////////////////////////////
 
     int end = alignment.getHeight();
 
     if (selection != null)
     {
-      if ( (selection.getSize() < 1) ||
-          ( (selection.getEndRes() - selection.getStartRes()) < 2))
+      if ((selection.getSize() < 1)
+              || ((selection.getEndRes() - selection.getStartRes()) < 2))
       {
         selection = null;
       }
@@ -104,7 +111,8 @@ public class Finder
     {
       seq = (Sequence) alignment.getSequenceAt(seqIndex);
 
-      if ( (selection != null) && !selection.getSequences(null).contains(seq))
+      if ((selection != null)
+              && !selection.getSequences(null).contains(seq))
       {
         seqIndex++;
         resIndex = 0;
@@ -113,16 +121,16 @@ public class Finder
       }
 
       item = seq.getSequenceAsString();
-      if(!caseSensitive)
+      if (!caseSensitive)
         item = item.toUpperCase();
 
-      if ( (selection != null) &&
-          (selection.getEndRes() < alignment.getWidth() - 1))
+      if ((selection != null)
+              && (selection.getEndRes() < alignment.getWidth() - 1))
       {
         item = item.substring(0, selection.getEndRes() + 1);
       }
 
-      ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
+      // /Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
       StringBuffer noGapsSB = new StringBuffer();
       int insertCount = 0;
       Vector spaces = new Vector();
@@ -149,22 +157,21 @@ public class Finder
         {
           resIndex = regex.matchedFrom();
 
-          if ( (selection != null) &&
-              ( (resIndex +
-                 Integer.parseInt(spaces.elementAt(resIndex).toString())) <
-               selection.getStartRes()))
+          if ((selection != null)
+                  && ((resIndex + Integer.parseInt(spaces.elementAt(
+                          resIndex).toString())) < selection.getStartRes()))
           {
             continue;
           }
 
-          int sres = seq.findPosition(resIndex +
-                                      Integer.parseInt(spaces.elementAt(
-              resIndex)
-              .toString()));
-          int eres = seq.findPosition(regex.matchedTo() - 1 +
-                                      Integer.parseInt(spaces.elementAt(regex.
-              matchedTo() -
-              1).toString()));
+          int sres = seq
+                  .findPosition(resIndex
+                          + Integer.parseInt(spaces.elementAt(resIndex)
+                                  .toString()));
+          int eres = seq.findPosition(regex.matchedTo()
+                  - 1
+                  + Integer.parseInt(spaces
+                          .elementAt(regex.matchedTo() - 1).toString()));
 
           searchResults.addResult(seq, sres, eres);
           hasResults = true;
@@ -212,7 +219,8 @@ public class Finder
   }
 
   /**
-   * @param alignment the alignment to set
+   * @param alignment
+   *                the alignment to set
    */
   public void setAlignment(AlignmentI alignment)
   {
@@ -228,7 +236,8 @@ public class Finder
   }
 
   /**
-   * @param caseSensitive the caseSensitive to set
+   * @param caseSensitive
+   *                the caseSensitive to set
    */
   public void setCaseSensitive(boolean caseSensitive)
   {
@@ -244,7 +253,8 @@ public class Finder
   }
 
   /**
-   * @param findAll the findAll to set
+   * @param findAll
+   *                the findAll to set
    */
   public void setFindAll(boolean findAll)
   {
@@ -260,7 +270,8 @@ public class Finder
   }
 
   /**
-   * @param selection the selection to set
+   * @param selection
+   *                the selection to set
    */
   public void setSelection(jalview.datamodel.SequenceGroup selection)
   {
@@ -300,7 +311,8 @@ public class Finder
   }
 
   /**
-   * @param resIndex the resIndex to set
+   * @param resIndex
+   *                the resIndex to set
    */
   public void setResIndex(int resIndex)
   {
@@ -316,7 +328,8 @@ public class Finder
   }
 
   /**
-   * @param seqIndex the seqIndex to set
+   * @param seqIndex
+   *                the seqIndex to set
    */
   public void setSeqIndex(int seqIndex)
   {