From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Feb 2006 11:46:41 +0000 (+0000)
Subject: Features now array
X-Git-Tag: Root_VamJalview_2_07b+~91
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=91d8c718e1e9d4f67e8840cfe402b46f79858d57;p=jalview.git

Features now array
---

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f81e471..0acf425 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -708,8 +708,7 @@ public class AlignmentPanel extends GAlignmentPanel
 
     // draw main sequence panel
     pg.translate(idWidth, 0);
-    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
-                                 startRes, startSeq, 0);
+    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
 
     if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
     {
@@ -940,7 +939,7 @@ public class AlignmentPanel extends GAlignmentPanel
           sy = s * av.charHeight + scaleHeight;
 
           SequenceI seq = av.alignment.getSequenceAt(s);
-          java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures();
+          SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
           SequenceGroup[] groups = av.alignment.findAllGroups(seq);
           for(res =0; res<alwidth; res++)
           {
@@ -987,33 +986,32 @@ public class AlignmentPanel extends GAlignmentPanel
                   + " onMouseOver=\"toolTip('"
                   + alIndex + " " + triplet );
               }
-                fSize = features.size();
+                fSize = features.length;
                 for (f = 0; f < fSize; f++)
                 {
-                  SequenceFeature sf = (SequenceFeature) features.elementAt(f);
 
-                  if ( (sf.getBegin() <= seq.findPosition(res)) &&
-                      (sf.getEnd() >= seq.findPosition(res)))
+                  if ( (features[f].getBegin() <= seq.findPosition(res)) &&
+                      (features[f].getEnd() >= seq.findPosition(res)))
                   {
-                    if (sf.getType().equals("disulfide bond"))
+                    if (features[f].getType().equals("disulfide bond"))
                     {
-                      if (sf.getBegin() == seq.findPosition(res)
-                          || sf.getEnd() == seq.findPosition(res))
+                      if (features[f].getBegin() == seq.findPosition(res)
+                          || features[f].getEnd() == seq.findPosition(res))
                       {
-                        text.append("<br>disulfide bond " + sf.getBegin() + ":" +
-                                       sf.getEnd());
+                        text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
+                                       features[f].getEnd());
                       }
                     }
                     else
                     {
                       text.append("<br>");
-                      text.append(sf.getType());
-                      if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))
-                        text.append(" " + sf.getDescription());
+                      text.append(features[f].getType());
+                      if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
+                        text.append(" " + features[f].getDescription());
 
-                      if (sf.getStatus() != null && sf.getStatus().length()>0)
+                      if (features[f].getStatus() != null && features[f].getStatus().length()>0)
                       {
-                        text.append(" (" + sf.getStatus() + ")");
+                        text.append(" (" + features[f].getStatus() + ")");
                       }
                     }
                   }