From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 14 Mar 2018 09:25:04 +0000 (+0000)
Subject: JAL-2839 refactored out getNextVisibleSequenceRegion
X-Git-Tag: Release_2_11_0~17^2~67^2~2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=85b18307da5f85a9cb5c13bb6be97eaf2c7f7965

JAL-2839 refactored out getNextVisibleSequenceRegion
---

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index de57d69..adf7ff6 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -21,6 +21,7 @@
 package jalview.analysis;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Range;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -164,17 +165,55 @@ public class Finder
   }
 
   /**
-   * Answers the start-end column range of the visible region starting at or
-   * after the given column. if there are no hidden columns, this just returns
-   * the remaining width of the alignment. Answers null if there are no visible
-   * columns at or after <code>column</code>.
+   * Answers the start-end column range of the visible region of
+   * <code>sequence</code> starting at or after the given <code>column</code>.
+   * If there are no hidden columns, this just returns the remaining width of
+   * the sequence. The range is restricted to the current <code>selection</code>
+   * if there is one. Answers null if there are no visible columns at or after
+   * <code>column</code>.
    */
-  protected int[] getNextVisibleRegion(int column)
+  protected Range getNextVisibleSequenceRegion(SequenceI sequence,
+          int column)
   {
+    int seqColStart = column;
+    int seqColEnd = sequence.getLength() - 1;
+
+    /*
+     * restrict search to (next) visible column region, 
+     * in case there are hidden columns
+     */
     VisibleContigsIterator visibleRegions = alignment.getHiddenColumns()
             .getVisContigsIterator(column, alignment.getWidth(),
                     false);
-    return visibleRegions.hasNext() ? visibleRegions.next() : null;
+    int[] visible = visibleRegions.hasNext() ? visibleRegions.next() : null;
+    if (visible == null)
+    {
+      columnIndex = seqColEnd + 1;
+      return null;
+    }
+    seqColStart = Math.max(seqColStart, visible[0]);
+    seqColEnd = Math.min(seqColEnd, visible[1]);
+
+    /*
+     * restrict search to selected region if there is one
+     */
+    if (selection != null)
+    {
+      int selectionStart = selection.getStartRes();
+      int selectionEnd = selection.getEndRes();
+      if (selectionStart > seqColEnd || selectionEnd < seqColStart)
+      {
+        /*
+         * sequence region doesn't overlap selection region 
+         */
+        columnIndex = seqColEnd + 1;
+        return null;
+      }
+      seqColStart = Math.max(seqColStart, selectionStart);
+      seqColEnd = Math.min(seqColEnd, selectionEnd);
+    }
+
+    return new Range(seqColStart, seqColEnd);
   }
 
   /**
@@ -237,55 +276,17 @@ public class Finder
    */
   protected boolean searchNextVisibleRegion(SequenceI seq, Regex searchPattern)
   {
-    /*
-     * sequence columns to search (working in absolute column 
-     * positions, base 0, including any hidden columns)
-     */
-    int seqColStart = columnIndex;
-    int seqColEnd = seq.getLength() - 1;
-
-    /*
-     * restrict search to (next) visible column region, 
-     * in case there are hidden columns
-     */
-    int[] visible = getNextVisibleRegion(columnIndex);
-    if (visible != null)
-    {
-      seqColStart = Math.max(seqColStart, visible[0]);
-      seqColEnd = Math.min(seqColEnd, visible[1]);
-    }
-    else
+    Range visible = getNextVisibleSequenceRegion(seq, columnIndex);
+    if (visible == null)
     {
-      columnIndex = seqColEnd + 1;
       return false;
     }
-
-    /*
-     * restrict search to selected region if there is one
-     */
-    if (selection != null)
-    {
-      int selectionStart = selection.getStartRes();
-      int selectionEnd = selection.getEndRes();
-      if (selectionStart > seqColEnd || selectionEnd < seqColStart)
-      {
-        /*
-         * sequence region doesn't overlap selection region - 
-         * no match, advance to next visible region 
-         */
-        columnIndex = seqColEnd + 1;
-        return false;
-      }
-      seqColStart = Math.max(seqColStart, selectionStart);
-      seqColEnd = Math.min(seqColEnd, selectionEnd);
-    }
-
-    String seqString = seq.getSequenceAsString(seqColStart, seqColEnd + 1);
+    String seqString = seq.getSequenceAsString(visible.start, visible.end + 1);
     String noGaps = AlignSeq.extractGaps(Comparison.GapChars, seqString);
 
     if (searchPattern.search(noGaps))
     {
-      int sequenceStartPosition = seq.findPosition(seqColStart);
+      int sequenceStartPosition = seq.findPosition(visible.start);
       recordMatch(seq, searchPattern, sequenceStartPosition);
       return true;
     }
@@ -295,7 +296,7 @@ public class Finder
        * no match - advance columnIndex past this visible region
        * so the next visible region (if any) is searched next
        */
-      columnIndex = seqColEnd + 1;
+      columnIndex = visible.end + 1;
     }
 
     return false;