From 2e9af306a6dc27274ea5eb047afd583b2caf2e69 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 1 Dec 2004 17:12:38 +0000
Subject: [PATCH] search function added

---
 src/jalview/gui/AlignmentPanel.java |   38 +++++++++++------------------------
 1 file changed, 12 insertions(+), 26 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2266462..4f56474 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -18,8 +18,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   ScalePanel scalePanel;
   ScorePanel scorePanel;
 
-  public boolean    groupEdit = false;
-
   public AlignmentPanel(AlignFrame af, AlignViewport av)
   {
     alignFrame = af;
@@ -38,7 +36,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
-    selectAll(false);
 
     addComponentListener(new ComponentAdapter()
    {
@@ -47,27 +44,19 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           RefreshPanels();
      }
    });
-
   }
 
-  public int countSelected()
-  {
-    return av.getSelection().size();
-  }
+ public void highlightSearchResults(int [] results)
+ {
+   seqPanel.seqCanvas.highlightSearchResults( results );
+
+   // do we need to scroll the panel?
+   if(av.getStartSeq()>results[0] || av.getEndSeq()<results[0]  || av.getStartRes()>results[1] || av.getEndRes()<results[2])
+       setScrollValues(results[1], results[0]);
+
+
+ }
 
-  public void selectAll(boolean flag) {
-    int i = 0;
-    if (flag) {
-      while (i < av.getAlignment().getHeight()) {
-        if (! av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
-          av.getSelection().addElement(av.getAlignment().getSequenceAt(i));
-        }
-        i++;
-      }
-    } else {
-      av.getSelection().clear();
-    }
-  }
 
  public OverviewPanel getOverviewPanel()
  {
@@ -89,14 +78,12 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setWrapAlignment(boolean wrap)
   {
-
       scalePanelHolder.setVisible(!wrap);
       scorePanelHolder.setVisible(!wrap);
 
       hscroll.setVisible(!wrap);
       idSpaceFillerPanel.setVisible(!wrap);
       idSpaceFillerPanel1.setVisible(!wrap);
-
   }
 
 
@@ -112,9 +99,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   {
     invalidate();
     validate();
+    seqPanel.seqCanvas.paintFlag = true;
     idPanel.idCanvas.paintFlag = true;
     idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
-    seqPanel.seqCanvas.paintFlag = true;
     setScrollValues(av.getStartRes(), av.getStartSeq());
     av.getConsensus(true);
     repaint();
@@ -146,7 +133,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
-    seqPanel.seqCanvas.paintFlag = true;
     repaint();
 
   }
@@ -173,7 +159,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     if(overviewPanel!=null)
       overviewPanel.setBoxPosition();
 
-
+    seqPanel.seqCanvas.paintFlag=true;
     repaint();
   }
 
-- 
1.7.10.2