Merge branch 'features/JAL-2446NCList' into features/JAL-2574findFeaturesByColumn

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 7f1ce31..72b1cc9 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -30,6 +30,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.HTMLOutput;
 import jalview.jbgui.GAlignmentPanel;
 import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
@@ -1439,32 +1440,32 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       try
       {
-        int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
-                .getAlignment().getWidth(), g, gSize, f, fSize, sy;
+        int sSize = av.getAlignment().getHeight();
+        int alwidth = av.getAlignment().getWidth();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
-        out.println(jalview.io.HTMLOutput.getImageMapHTML());
+        out.println(HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName
                 + "\" border=\"0\" usemap=\"#Map\" >"
                 + "<map name=\"Map\">");
 
-        for (s = 0; s < sSize; s++)
+        for (int s = 0; s < sSize; s++)
         {
-          sy = s * av.getCharHeight() + scaleHeight;
+          int sy = s * av.getCharHeight() + scaleHeight;
 
           SequenceI seq = av.getAlignment().getSequenceAt(s);
           SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
-          for (res = 0; res < alwidth; res++)
+          for (int column = 0; column < alwidth; column++)
           {
             StringBuilder text = new StringBuilder(512);
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
               triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(res) + "");
+                      .getCharAt(column) + "");
             }
             else
             {
-              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
                       + "");
             }
 
@@ -1473,23 +1474,23 @@ public class AlignmentPanel extends GAlignmentPanel implements
               continue;
             }
 
-            int seqPos = seq.findPosition(res);
-            gSize = groups.length;
-            for (g = 0; g < gSize; g++)
+            int seqPos = seq.findPosition(column);
+            int gSize = groups.length;
+            for (int g = 0; g < gSize; g++)
             {
               if (text.length() < 1)
               {
                 text.append("<area shape=\"rect\" coords=\"")
-                        .append((idWidth + res * av.getCharWidth()))
+                        .append((idWidth + column * av.getCharWidth()))
                         .append(",").append(sy).append(",")
-                        .append((idWidth + (res + 1) * av.getCharWidth()))
+                        .append((idWidth + (column + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
                         .append(seqPos).append(" ").append(triplet);
               }
 
-              if (groups[g].getStartRes() < res
-                      && groups[g].getEndRes() > res)
+              if (groups[g].getStartRes() < column
+                      && groups[g].getEndRes() > column)
               {
                 text.append("<br><em>").append(groups[g].getName())
                         .append("</em>");
@@ -1499,17 +1500,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
             if (text.length() < 1)
             {
               text.append("<area shape=\"rect\" coords=\"")
-                      .append((idWidth + res * av.getCharWidth()))
+                      .append((idWidth + column * av.getCharWidth()))
                       .append(",").append(sy).append(",")
-                      .append((idWidth + (res + 1) * av.getCharWidth()))
+                      .append((idWidth + (column + 1) * av.getCharWidth()))
                       .append(",").append((av.getCharHeight() + sy))
                       .append("\"").append(" onMouseOver=\"toolTip('")
                       .append(seqPos).append(" ").append(triplet);
             }
-            if (!Comparison.isGap(seq.getCharAt(res)))
+            if (!Comparison.isGap(seq.getCharAt(column)))
             {
-              List<SequenceFeature> features = seq.findFeatures(seqPos,
-                      seqPos);
+              List<SequenceFeature> features = seq.findFeatures(column, column);
               for (SequenceFeature sf : features)
               {
                 if (sf.isContactFeature())