JAL-2839 refactored analysis.Finder and tests

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

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index f44387f..286cd5f 100644 (file)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -68,21 +68,21 @@ public class Finder extends Panel implements ActionListener
   private SearchResultsI searchResults;
 
   /*
-   * sequence index and residue position of last match,
+   * sequence index and column position of last match,
    * for current search and per viewport
    */
   private int seqIndex = 0;
 
-  private int resIndex = -1;
+  private int colIndex = -1;
 
   Map<AlignViewportI, Integer> seqIndices;
 
-  Map<AlignViewportI, Integer> resIndices;
+  Map<AlignViewportI, Integer> colIndices;
 
   public Finder(final AlignmentPanel ap)
   {
     seqIndices = new HashMap<>();
-    resIndices = new HashMap<>();
+    colIndices = new HashMap<>();
 
     try
     {
@@ -126,7 +126,7 @@ public class Finder extends Panel implements ActionListener
 
     else if (evt.getSource() == findAll)
     {
-      resIndex = -1;
+      colIndex = -1;
       seqIndex = 0;
       doSearch(true);
     }
@@ -165,19 +165,19 @@ public class Finder extends Panel implements ActionListener
       ap = ap.av.applet.currentAlignFrame.alignPanel;
       av = ap.av;
       seqIndex = 0;
-      resIndex = -1;
+      colIndex = -1;
       if (seqIndices.containsKey(av))
       {
         seqIndex = seqIndices.get(av).intValue();
       }
-      if (resIndices.containsKey(av))
+      if (colIndices.containsKey(av))
       {
-        resIndex = resIndices.get(av).intValue();
+        colIndex = colIndices.get(av).intValue();
       }
     }
     createFeatures.setEnabled(false);
     jalview.analysis.Finder finder = new jalview.analysis.Finder(
-            av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+            av.getAlignment(), av.getSelectionGroup(), seqIndex, colIndex);
     finder.setCaseSensitive(caseSensitive.getState());
     finder.setIncludeDescription(searchDescription.getState());
     finder.setFindAll(doFindAll);
@@ -186,10 +186,10 @@ public class Finder extends Panel implements ActionListener
 
     finder.find(searchString);
 
-    seqIndex = finder.getSeqIndex();
-    resIndex = finder.getResIndex();
+    seqIndex = finder.getSequenceIndex();
+    colIndex = finder.getColumnIndex();
     seqIndices.put(av, seqIndex);
-    resIndices.put(av, resIndex);
+    colIndices.put(av, colIndex);
     searchResults = finder.getSearchResults();
 
     Vector<SequenceI> idMatch = finder.getIdMatch();
@@ -213,7 +213,7 @@ public class Finder extends Panel implements ActionListener
     {
       ap.alignFrame.statusBar.setText(
               MessageManager.getString("label.finished_searching"));
-      resIndex = -1;
+      colIndex = -1;
       seqIndex = 0;
     }
     else