Modified output on stdout for similarity matrix.

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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 7483a0a..ef28ebe 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -13,8 +13,8 @@ public class Finder extends GFinder
   AlignViewport av;\r
   AlignmentPanel ap;\r
   JInternalFrame frame;\r
-  String searchString;\r
   SuperGroup searchGroup;\r
+  Vector searchResults;\r
 \r
   int seqIndex = 0;\r
   int resIndex = 0;\r
@@ -67,6 +67,7 @@ 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
@@ -74,8 +75,32 @@ public class Finder extends GFinder
 \r
   public void createNewGroup_actionPerformed(ActionEvent e)\r
   {\r
-    for(int i=0; i<searchGroup.getSize(); i++)\r
-      av.alignment.addGroup( searchGroup.getGroupeAt(i));\r
+\r
+   Color [] newColors = new Color[24];\r
+   for(int i=0; i<24; i++)\r
+     newColors[i] = new Color(60,160,115);\r
+\r
+   jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
+   String searchString = textfield.getText();\r
+\r
+   searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+\r
+\r
+    for(int i=0; i<searchResults.size(); i+=3)\r
+    {\r
+      // its possible edits may have occurred since search was performed\r
+      // account for this here\r
+\r
+      SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );\r
+      int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;\r
+      int endRes = seq.findIndex(   Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;\r
+\r
+      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes  );\r
+      sg.addSequence(seq);\r
+      av.alignment.addGroup(sg);\r
+      searchGroup.addGroup( sg );\r
+\r
+    }\r
 \r
     ap.av.alignment.addSuperGroup(searchGroup);\r
     ap.highlightSearchResults( null );\r
@@ -85,9 +110,12 @@ public class Finder extends GFinder
   void doSearch(boolean findAll)\r
   {\r
     createNewGroup.setEnabled(false);\r
-    searchString = textfield.getText().toUpperCase();\r
 \r
-    ArrayList searchResults = new ArrayList();\r
+    String searchString = textfield.getText().toUpperCase();\r
+\r
+    com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);\r
+\r
+    searchResults = new Vector();\r
     int [] allResults = null;\r
 \r
     Sequence seq;\r
@@ -112,12 +140,12 @@ public class Finder extends GFinder
     ///////////////////////////////////////////////\r
 \r
 \r
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
+\r
     Color [] newColors = new Color[24];\r
     for(int i=0; i<24; i++)\r
       newColors[i] = new Color(60,160,115);\r
 \r
-    ucs.setColourScheme(newColors);\r
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
 \r
     searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
 \r
@@ -148,7 +176,7 @@ public class Finder extends GFinder
       ///Shall we ignore gaps????\r
       StringBuffer noGaps = new StringBuffer();\r
       int insertCount=0;\r
-      ArrayList spaces = new ArrayList();\r
+      Vector spaces = new Vector();\r
 \r
       for (int j=0; j < item.length(); j++)\r
       {\r
@@ -163,7 +191,6 @@ 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
@@ -175,15 +202,12 @@ public class Finder extends GFinder
            continue;\r
 \r
          searchResults.add( Integer.toString( seqIndex) );\r
-         searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );\r
-         searchResults.add( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString()) ) );\r
 \r
-         SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
-                                             resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,\r
-                                      regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())\r
-            );\r
-         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));\r
-         searchGroup.addGroup( sg );\r
+         int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );\r
+         int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );\r
+\r
+          searchResults.addElement( sres+"" );\r
+          searchResults.addElement( eres+"" );\r
 \r
          if(!findAll)\r
          {\r
@@ -203,6 +227,18 @@ public class Finder extends GFinder
       }\r
     }\r
 \r
+\r
+    Vector idMatch = new Vector();\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