can search ids

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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 2311a9f..5a2dfe9 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -13,7 +13,6 @@ public class Finder extends GFinder
   AlignViewport av;\r
   AlignmentPanel ap;\r
   JInternalFrame frame;\r
-  String searchString;\r
   SuperGroup searchGroup;\r
 \r
   int seqIndex = 0;\r
@@ -67,6 +66,7 @@ public class Finder extends GFinder
     try{\r
       // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
       ap.highlightSearchResults( null );\r
+      ap.idPanel.highlightSearchResults( null );\r
      // frame.setClosed(true);\r
     }catch(Exception ex){ }\r
   }\r
@@ -85,7 +85,10 @@ public class Finder extends GFinder
   void doSearch(boolean findAll)\r
   {\r
     createNewGroup.setEnabled(false);\r
-    searchString = textfield.getText().toUpperCase();\r
+\r
+    String searchString = textfield.getText().toUpperCase();\r
+\r
+    com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);\r
 \r
     ArrayList searchResults = new ArrayList();\r
     int [] allResults = null;\r
@@ -94,13 +97,13 @@ public class Finder extends GFinder
     String item=null;\r
     boolean found = false;\r
 \r
-    /// is the searchString a residue number?\r
+    ////// is the searchString a residue number?\r
     try{\r
       int res = Integer.parseInt(searchString);\r
       found = true;\r
 \r
-      if(av.getSelection().size()>0)\r
-        seq = (Sequence)(av.getSelection().sequenceAt(0));\r
+      if(av.getSelectionGroup().getSize()>0)\r
+        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));\r
       else\r
         seq = (Sequence)av.getAlignment().getSequenceAt(0);\r
 \r
@@ -109,6 +112,8 @@ public class Finder extends GFinder
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
 \r
     }catch(NumberFormatException ex){}\r
+    ///////////////////////////////////////////////\r
+\r
 \r
     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
     Color [] newColors = new Color[24];\r
@@ -121,30 +126,27 @@ public class Finder extends GFinder
 \r
     int end = av.alignment.getHeight();\r
 \r
-\r
-    SequenceGroup rubberband = av.getRubberbandGroup();\r
-    if(rubberband!=null)\r
-      end = rubberband.getEndRes();\r
-\r
-\r
+    SequenceGroup selection = av.getSelectionGroup();\r
+    if(selection!=null)\r
+     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))\r
+      selection = null;\r
 \r
     while( !found && seqIndex<end)\r
     {\r
-      seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);\r
+      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);\r
 \r
-      if(   av.getSelection().size()>0 && !av.getSelection().contains(seq)\r
-            || (rubberband!=null && !rubberband.sequences.contains(seq))  )\r
+\r
+      if(selection!=null && !selection.sequences.contains(seq))\r
       {\r
-        // if a selection has been made, only search within that selection\r
         seqIndex++;\r
         resIndex=0;\r
         continue;\r
       }\r
 \r
-      item = seq.getSequence();\r
+      item = seq.getSequence().toUpperCase();\r
 \r
-      if(rubberband!=null)\r
-        item = item.substring(0, rubberband.getEndRes()+1);\r
+      if(selection!=null && selection.getEndRes()<av.alignment.getWidth())\r
+          item = item.substring(0, selection.getEndRes()+1);\r
 \r
       ///Shall we ignore gaps????\r
       StringBuffer noGaps = new StringBuffer();\r
@@ -164,7 +166,6 @@ public class Finder extends GFinder
       }\r
 \r
 \r
-      com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);\r
 \r
       for(int r = resIndex; r<noGaps.length(); r++)\r
       {\r
@@ -172,9 +173,7 @@ public class Finder extends GFinder
        if( regex.searchFrom( noGaps.toString(), r ) )\r
        {\r
          resIndex = regex.matchedFrom();\r
-\r
-\r
-         if(rubberband!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<rubberband.getStartRes())\r
+         if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())\r
            continue;\r
 \r
          searchResults.add( Integer.toString( seqIndex) );\r
@@ -206,6 +205,18 @@ public class Finder extends GFinder
       }\r
     }\r
 \r
+\r
+    ArrayList idMatch = new ArrayList();\r
+    for(int id = 0; id<av.alignment.getHeight(); id++)\r
+    {\r
+      if(   regex.search( av.alignment.getSequenceAt(id).getName() ) )\r
+        idMatch.add( av.alignment.getSequenceAt(id) );\r
+    }\r
+\r
+    if(searchResults.size()==0 && idMatch.size()>0)\r
+      ap.idPanel.highlightSearchResults( idMatch );\r
+\r
+\r
     if(searchResults.size()>0)\r
     {\r
       allResults = new int[searchResults.size()];\r