From 7b2f004da1302ca4cb155c7470c0fe47f6bb2a49 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 17 Nov 2016 11:05:43 +0000
Subject: [PATCH] JAL-2327 disulfide bond abstracted to
 SequenceFeature.isContactFeature

---
 src/jalview/gui/AlignmentPanel.java                |   52 ++++++++++----------
 src/jalview/io/SequenceAnnotationReport.java       |    5 +-
 .../renderer/seqfeatures/FeatureRenderer.java      |    7 +--
 3 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 9f1162f..687361d 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1315,8 +1315,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (onscreen
             || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
     {
-      return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
-              : calculateIdWidth().width + 4);
+      int w = getIdPanel().getWidth();
+      return (w > 0 ? w : calculateIdWidth().width + 4);
     }
     return idwidth.intValue() + 4;
   }
@@ -1463,7 +1463,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
-    // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+    // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
     // ////////////////////////////////////////////
     int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
@@ -1477,7 +1477,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
                 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
-        StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
         out.println(jalview.io.HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName
@@ -1493,7 +1492,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
-            text = new StringBuffer();
+            StringBuilder text = new StringBuilder();
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
@@ -1517,18 +1516,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
             {
               if (text.length() < 1)
               {
-                text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.getCharWidth()) + "," + sy
-                        + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + "," + (av.getCharHeight() + sy) + "\""
-                        + " onMouseOver=\"toolTip('" + alIndex + " "
-                        + triplet);
+                text.append("<area shape=\"rect\" coords=\"")
+                        .append((idWidth + res * av.getCharWidth()))
+                        .append(",").append(sy).append(",")
+                        .append((idWidth + (res + 1) * av.getCharWidth()))
+                        .append(",").append((av.getCharHeight() + sy))
+                        .append("\"").append(" onMouseOver=\"toolTip('")
+                        .append(alIndex).append(" ").append(triplet);
               }
 
               if (groups[g].getStartRes() < res
                       && groups[g].getEndRes() > res)
               {
-                text.append("<br><em>" + groups[g].getName() + "</em>");
+                text.append("<br><em>").append(groups[g].getName())
+                        .append("</em>");
               }
             }
 
@@ -1536,12 +1537,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
             {
               if (text.length() < 1)
               {
-                text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.getCharWidth()) + "," + sy
-                        + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + "," + (av.getCharHeight() + sy) + "\""
-                        + " onMouseOver=\"toolTip('" + alIndex + " "
-                        + triplet);
+                text.append("<area shape=\"rect\" coords=\"")
+                        .append((idWidth + res * av.getCharWidth()))
+                        .append(",").append(sy).append(",")
+                        .append((idWidth + (res + 1) * av.getCharWidth()))
+                        .append(",").append((av.getCharHeight() + sy))
+                        .append("\"").append(" onMouseOver=\"toolTip('")
+                        .append(alIndex).append(" ").append(triplet);
               }
               fSize = features.length;
               for (f = 0; f < fSize; f++)
@@ -1550,15 +1552,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 if ((features[f].getBegin() <= seq.findPosition(res))
                         && (features[f].getEnd() >= seq.findPosition(res)))
                 {
-                  if (features[f].getType().equals("disulfide bond"))
+                  if (features[f].isContactFeature())
                   {
                     if (features[f].getBegin() == seq.findPosition(res)
                             || features[f].getEnd() == seq
                                     .findPosition(res))
                     {
-                      text.append("<br>disulfide bond "
-                              + features[f].getBegin() + ":"
-                              + features[f].getEnd());
+                      text.append("<br>").append(features[f].getType())
+                              .append(" ").append(features[f].getBegin())
+                              .append(":").append(features[f].getEnd());
                     }
                   }
                   else
@@ -1569,13 +1571,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
                             && !features[f].getType().equals(
                                     features[f].getDescription()))
                     {
-                      text.append(" " + features[f].getDescription());
+                      text.append(" ").append(features[f].getDescription());
                     }
 
                     if (features[f].getValue("status") != null)
                     {
-                      text.append(" (" + features[f].getValue("status")
-                              + ")");
+                      text.append(" (").append(features[f].getValue("status"))
+                              .append(")");
                     }
                   }
                 }
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 89f1068..702a107 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -79,7 +79,7 @@ public class SequenceAnnotationReport
   void appendFeature(final StringBuffer sb, int rpos,
           Map<String, float[][]> minmax, SequenceFeature feature)
   {
-    if ("disulfide bond".equals(feature.getType()))
+    if (feature.isContactFeature())
     {
       if (feature.getBegin() == rpos || feature.getEnd() == rpos)
       {
@@ -87,7 +87,8 @@ public class SequenceAnnotationReport
         {
           sb.append("<br>");
         }
-        sb.append("disulfide bond ").append(feature.getBegin()).append(":")
+        sb.append(feature.getType()).append(" ").append(feature.getBegin())
+                .append(":")
                 .append(feature.getEnd());
       }
     }
diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 07d97d0..1ccb673 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -365,7 +365,8 @@ public class FeatureRenderer extends FeatureRendererModel
         }
 
         Color featureColour = getColour(sequenceFeature);
-        boolean isDisulfideBond = "disulfide bond".equals(sequenceFeature.type);
+        boolean isContactFeature = sequenceFeature.isContactFeature();
+
         if (offscreenRender && offscreenImage == null)
         {
           /*
@@ -375,7 +376,7 @@ public class FeatureRenderer extends FeatureRendererModel
            */
           boolean featureIsAtPosition = sequenceFeature.begin <= start
                   && sequenceFeature.end >= start;
-          if (isDisulfideBond)
+          if (isContactFeature)
           {
             featureIsAtPosition = sequenceFeature.begin == start
                     || sequenceFeature.end == start;
@@ -392,7 +393,7 @@ public class FeatureRenderer extends FeatureRendererModel
 
           }
         }
-        else if (isDisulfideBond)
+        else if (isContactFeature)
         {
           renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
                   seq.findIndex(sequenceFeature.begin) - 1, featureColour,
-- 
1.7.10.2