New implementation for holding search results

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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index ff4fe60..5f215ed 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -43,10 +43,11 @@ public class Finder extends GFinder
     AlignmentPanel ap;\r
     JInternalFrame frame;\r
     SuperGroup searchGroup;\r
-    Vector searchResults;\r
     int seqIndex = 0;\r
     int resIndex = 0;\r
 \r
+    SearchResults searchResults;\r
+\r
     /**\r
      * Creates a new Finder object.\r
      *\r
@@ -74,16 +75,6 @@ public class Finder extends GFinder
                             }\r
                         });\r
                 }\r
-\r
-                /**\r
-                 * DOCUMENT ME!\r
-                 *\r
-                 * @param evt DOCUMENT ME!\r
-                 */\r
-                public void internalFrameClosing(InternalFrameEvent evt)\r
-                {\r
-                    cancel_actionPerformed(null);\r
-                }\r
             });\r
     }\r
 \r
@@ -110,25 +101,6 @@ public class Finder extends GFinder
         doSearch(true);\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    public void cancel_actionPerformed(ActionEvent e)\r
-    {\r
-        try\r
-        {\r
-            // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
-            ap.highlightSearchResults(null);\r
-            ap.idPanel.highlightSearchResults(null);\r
-\r
-            // frame.setClosed(true);\r
-        }\r
-        catch (Exception ex)\r
-        {\r
-        }\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -149,16 +121,13 @@ public class Finder extends GFinder
 \r
         searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
 \r
-        for (int i = 0; i < searchResults.size(); i += 3)\r
+        for (int i = 0; i < searchResults.getSize(); i ++ )\r
         {\r
             // its possible edits may have occurred since search was performed\r
             // account for this here\r
-            SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(\r
-                        searchResults.elementAt(i).toString()));\r
-            int startRes = seq.findIndex(Integer.parseInt(\r
-                        searchResults.elementAt(i + 1).toString())) - 1;\r
-            int endRes = seq.findIndex(Integer.parseInt(\r
-                        searchResults.elementAt(i + 2).toString())) - 1;\r
+            SequenceI seq = searchResults.getResultSequence(i);\r
+            int startRes = seq.findIndex(searchResults.getResultStart(i)) - 1;\r
+            int endRes = seq.findIndex(searchResults.getResultEnd(i)) - 1;\r
 \r
             SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,\r
                     false, startRes, endRes);\r
@@ -186,9 +155,7 @@ public class Finder extends GFinder
 \r
         com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
 \r
-        searchResults = new Vector();\r
-\r
-        int[] allResults = null;\r
+        searchResults = new SearchResults();\r
 \r
         Sequence seq;\r
         String item = null;\r
@@ -208,9 +175,7 @@ public class Finder extends GFinder
               seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
             }\r
 \r
-            searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));\r
-            searchResults.add(res+"");\r
-            searchResults.add(res+"");\r
+            searchResults.addResult(seq, res, res);\r
         }\r
         catch (NumberFormatException ex)\r
         {\r
@@ -256,7 +221,7 @@ public class Finder extends GFinder
             item = seq.getSequence().toUpperCase();\r
 \r
             if ((selection != null) &&\r
-                    (selection.getEndRes() < av.alignment.getWidth()))\r
+                    (selection.getEndRes() < av.alignment.getWidth()-1))\r
             {\r
                 item = item.substring(0, selection.getEndRes() + 1);\r
             }\r
@@ -295,7 +260,6 @@ public class Finder extends GFinder
                         continue;\r
                     }\r
 \r
-                    searchResults.add(Integer.toString(seqIndex));\r
 \r
                     int sres = seq.findPosition(resIndex +\r
                             Integer.parseInt(spaces.elementAt(resIndex)\r
@@ -304,8 +268,7 @@ public class Finder extends GFinder
                             Integer.parseInt(spaces.elementAt(regex.matchedTo() -\r
                                     1).toString()));\r
 \r
-                    searchResults.addElement(sres + "");\r
-                    searchResults.addElement(eres + "");\r
+                    searchResults.addResult(seq, sres, eres);\r
 \r
                     if (!findAll)\r
                     {\r
@@ -341,23 +304,23 @@ public class Finder extends GFinder
             }\r
         }\r
 \r
-        if ((searchResults.size() == 0) && (idMatch.size() > 0))\r
+        if ((searchResults.getSize() == 0) && (idMatch.size() > 0))\r
         {\r
             ap.idPanel.highlightSearchResults(idMatch);\r
         }\r
 \r
-        if (searchResults.size() > 0)\r
-        {\r
-            allResults = new int[searchResults.size()];\r
 \r
-            for (int i = 0; i < searchResults.size(); i++)\r
-            {\r
-                allResults[i] = Integer.parseInt(searchResults.get(i).toString());\r
-            }\r
+        int resultSize = searchResults.getSize();\r
 \r
-            createNewGroup.setEnabled(true);\r
-        }\r
+        if (searchResults.getSize() > 0)\r
+          createNewGroup.setEnabled(true);\r
         else\r
+          searchResults = null;\r
+\r
+        // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
+        ap.highlightSearchResults(searchResults);\r
+\r
+        if(!findAll && resultSize==0)\r
         {\r
             JOptionPane.showInternalMessageDialog(this, "Finished searching",\r
                 null, JOptionPane.INFORMATION_MESSAGE);\r
@@ -365,14 +328,12 @@ public class Finder extends GFinder
             seqIndex = 0;\r
         }\r
 \r
-        // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
-        ap.highlightSearchResults(allResults);\r
-\r
         if (findAll)\r
         {\r
-            String message = (searchResults.size() / 3) + " matches found.";\r
-            JOptionPane.showInternalMessageDialog(this, message, null,\r
-                JOptionPane.INFORMATION_MESSAGE);\r
+          String message = resultSize + " matches found.";\r
+          JOptionPane.showInternalMessageDialog(this, message, null,\r
+                                                JOptionPane.INFORMATION_MESSAGE);\r
         }\r
+\r
     }\r
 }\r