X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=a3a61247feb71cd293c13077e6c85b13dea4ce3b;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=e6fb5e6c16d35e8bc9439cf1f6fe69ba0407c58b;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index e6fb5e6..a3a6124 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,31 +1,34 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 
 package jalview.appletgui;
 
-import jalview.jbappletgui.GFinder;
-import jalview.datamodel.*;
-import java.awt.event.*;
 import java.util.*;
+
 import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
 
-public class Finder extends GFinder
+public class Finder
+    extends GFinder
 {
   AlignViewport av;
   AlignmentPanel ap;
@@ -41,12 +44,15 @@ public class Finder extends GFinder
     this.ap = ap;
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Find", 340,120);
+    jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
     frame.repaint();
     frame.addWindowListener(new WindowAdapter()
-        {public void windowClosing(WindowEvent evt)
-              { ap.highlightSearchResults( null ); }
-        });
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        ap.highlightSearchResults(null);
+      }
+    });
   }
 
   public void textfield_actionPerformed(ActionEvent e)
@@ -61,197 +67,229 @@ public class Finder extends GFinder
 
   public void findAll_actionPerformed(ActionEvent e)
   {
-    resIndex=0;
-    seqIndex=0;
+    resIndex = 0;
+    seqIndex = 0;
     doSearch(true);
   }
 
   public void cancel_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      ap.highlightSearchResults( null );
-      ap.idPanel.highlightSearchResults( null );
-     // frame.setClosed(true);
-    }catch(Exception ex){ }
+      ap.highlightSearchResults(null);
+      ap.idPanel.highlightSearchResults(null);
+      // frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {}
   }
 
-
   public void createNewGroup_actionPerformed(ActionEvent e)
   {
-   Color [] newColors = new Color[24];
-   for(int i=0; i<24; i++)
-     newColors[i] = new Color(60,160,115);
-
-   jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
-   String searchString = textfield.getText();
+    Color[] newColors = new Color[24];
+    for (int i = 0; i < 24; i++)
+    {
+      newColors[i] = new Color(60, 160, 115);
+    }
 
-   searchGroup = new SuperGroup(searchString, ucs , true, true, false);
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+        newColors);
+    String searchString = textfield.getText();
 
+    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
-    for(int i=0; i<searchResults.size(); i+=3)
+    for (int i = 0; i < searchResults.size(); i += 3)
     {
       // its possible edits may have occurred since search was performed
       // account for this here
 
-      SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );
-      int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;
-      int endRes = seq.findIndex(   Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;
+      SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(searchResults.
+          elementAt(i).toString()));
+      int startRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i +
+          1).toString())) - 1;
+      int endRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + 2).
+                                                  toString())) - 1;
 
-      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes  );
+      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
+                                           startRes, endRes);
       sg.addSequence(seq);
       av.alignment.addGroup(sg);
-      searchGroup.addGroup( sg );
+      searchGroup.addGroup(sg);
 
     }
 
     ap.av.alignment.addSuperGroup(searchGroup);
-    ap.highlightSearchResults( null );
+    ap.highlightSearchResults(null);
   }
 
-
   void doSearch(boolean findAll)
   {
     createNewGroup.setEnabled(false);
 
     String searchString = textfield.getText().toUpperCase();
 
-    com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);
+    com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
     searchResults = new Vector();
-    int [] allResults = null;
+    int[] allResults = null;
 
     Sequence seq;
-    String item=null;
+    String item = null;
     boolean found = false;
 
     ////// is the searchString a residue number?
-    try{
+    try
+    {
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if(av.getSelectionGroup().getSize()>0)
-        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
+      if (av.getSelectionGroup().getSize() > 0)
+      {
+        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+      }
       else
-        seq = (Sequence)av.getAlignment().getSequenceAt(0);
+      {
+        seq = (Sequence) av.getAlignment().getSequenceAt(0);
+      }
 
-      searchResults.addElement( Integer.toString( av.getAlignment().findIndex(seq) ) );
-      searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
-      searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
+      searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));
+      searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));
+      searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));
 
-    }catch(NumberFormatException ex){}
+    }
+    catch (NumberFormatException ex)
+    {}
     ///////////////////////////////////////////////
 
 
     int end = av.alignment.getHeight();
 
     SequenceGroup selection = av.getSelectionGroup();
-    if(selection!=null)
-     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
-      selection = null;
-
-    while( !found && seqIndex<end)
+    if (selection != null)
     {
-      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
+      if (selection.getSize() < 1 ||
+          (selection.getEndRes() - selection.getStartRes() < 2))
+      {
+        selection = null;
+      }
+    }
 
+    while (!found && seqIndex < end)
+    {
+      seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
-      if(selection!=null && !selection.sequences.contains(seq))
+      if (selection != null && !selection.sequences.contains(seq))
       {
         seqIndex++;
-        resIndex=0;
+        resIndex = 0;
         continue;
       }
 
       item = seq.getSequence().toUpperCase();
 
-      if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
-          item = item.substring(0, selection.getEndRes()+1);
+      if (selection != null && selection.getEndRes() < av.alignment.getWidth())
+      {
+        item = item.substring(0, selection.getEndRes() + 1);
+      }
 
       ///Shall we ignore gaps????
       StringBuffer noGaps = new StringBuffer();
-      int insertCount=0;
+      int insertCount = 0;
       Vector spaces = new Vector();
 
-      for (int j=0; j < item.length(); j++)
+      for (int j = 0; j < item.length(); j++)
       {
 
-        if(!jalview.util.Comparison.isGap(item.charAt(j)))
-         {
-           noGaps.append(item.charAt(j));
-           spaces.addElement(new Integer(insertCount));
-         }
+        if (!jalview.util.Comparison.isGap(item.charAt(j)))
+        {
+          noGaps.append(item.charAt(j));
+          spaces.addElement(new Integer(insertCount));
+        }
         else
-           insertCount++;
+        {
+          insertCount++;
+        }
       }
 
-
-
-      for(int r = resIndex; r<noGaps.length(); r++)
+      for (int r = resIndex; r < noGaps.length(); r++)
       {
 
-       if( regex.searchFrom( noGaps.toString(), r ) )
-       {
-         resIndex = regex.matchedFrom();
-         if(selection!=null && ( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) )<selection.getStartRes())
-           continue;
-
-         searchResults.addElement( Integer.toString( seqIndex) );
-         int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );
-         int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );
-          searchResults.addElement( sres+"" );
-          searchResults.addElement( eres+"" );
-
-
-         if(!findAll)
-         {
-           // thats enough, break and display the result
-           found = true;
-           resIndex++;
-           break;
-         }
-
-         r=resIndex;
-       }
+        if (regex.searchFrom(noGaps.toString(), r))
+        {
+          resIndex = regex.matchedFrom();
+          if (selection != null &&
+              (resIndex + Integer.parseInt(spaces.elementAt(resIndex).toString())) <
+              selection.getStartRes())
+          {
+            continue;
+          }
+
+          searchResults.addElement(Integer.toString(seqIndex));
+          int sres = seq.findPosition(resIndex +
+                                      Integer.parseInt(spaces.
+              elementAt(resIndex).toString()));
+          int eres = seq.findPosition(regex.matchedTo() - 1 +
+                                      Integer.parseInt(
+                                      spaces.elementAt(regex.matchedTo() - 1).
+                                      toString()));
+          searchResults.addElement(sres + "");
+          searchResults.addElement(eres + "");
+
+          if (!findAll)
+          {
+            // thats enough, break and display the result
+            found = true;
+            resIndex++;
+            break;
+          }
+
+          r = resIndex;
+        }
       }
-      if(!found)
+      if (!found)
       {
         seqIndex++;
         resIndex = 0;
       }
     }
 
-
     Vector idMatch = new Vector();
-    for(int id = 0; id<av.alignment.getHeight(); id++)
+    for (int id = 0; id < av.alignment.getHeight(); id++)
     {
-      if(   regex.search( av.alignment.getSequenceAt(id).getName() ) )
-        idMatch.addElement( av.alignment.getSequenceAt(id) );
+      if (regex.search(av.alignment.getSequenceAt(id).getName()))
+      {
+        idMatch.addElement(av.alignment.getSequenceAt(id));
+      }
     }
 
-    if(searchResults.size()==0 && idMatch.size()>0)
-      ap.idPanel.highlightSearchResults( idMatch );
-
+    if (searchResults.size() == 0 && idMatch.size() > 0)
+    {
+      ap.idPanel.highlightSearchResults(idMatch);
+    }
 
-    if(searchResults.size()>0)
+    if (searchResults.size() > 0)
     {
       allResults = new int[searchResults.size()];
-      for(int i=0; i<searchResults.size(); i++)
+      for (int i = 0; i < searchResults.size(); i++)
+      {
         allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());
+      }
 
       createNewGroup.setEnabled(true);
     }
     else
     {
-      resIndex=0;
-      seqIndex=0;
+      resIndex = 0;
+      seqIndex = 0;
     }
 
     // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-    ap.highlightSearchResults( allResults );
+    ap.highlightSearchResults(allResults);
 
     if (findAll)
     {
-      String message =  (searchResults.size()/3) + " matches found.";
+      String message = (searchResults.size() / 3) + " matches found.";
       System.out.println(message);
     }