JAL-2490 lookup features at each column position

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ccb3464..2f6e3e4 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -25,6 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -33,6 +34,7 @@ import jalview.jbgui.GAlignmentPanel;
 import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.ViewportRanges;
@@ -171,6 +173,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     av.alignmentChanged(this);
 
+    if (getCalculationDialog() != null)
+    {
+      getCalculationDialog().validateCalcTypes();
+    }
+
     alignFrame.updateEditMenuBar();
 
     paintAlignment(true);
@@ -397,11 +404,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       if (av.hasHiddenColumns())
       {
-        start = av.getColumnSelection().findColumnPosition(start);
-        end = av.getColumnSelection().findColumnPosition(end);
+        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+        start = hidden.findColumnPosition(start);
+        end = hidden.findColumnPosition(end);
         if (start == end)
         {
-          if (!av.getColumnSelection().isVisible(r[0]))
+          if (!hidden.isVisible(r[0]))
           {
             // don't scroll - position isn't visible
             return false;
@@ -706,7 +714,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       // reset the width to exclude hidden columns
-      width = av.getColumnSelection().findColumnPosition(width);
+      width = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(width);
     }
 
     hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@@ -919,7 +928,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
       if (av.hasHiddenColumns())
       {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
       }
 
       int canvasWidth = getSeqPanel().seqCanvas
@@ -1207,7 +1217,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
@@ -1401,7 +1412,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth);
     }
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
@@ -1484,11 +1496,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
           sy = s * av.getCharHeight() + scaleHeight;
 
           SequenceI seq = av.getAlignment().getSequenceAt(s);
-          SequenceFeature[] features = seq.getSequenceFeatures();
           SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
-            StringBuilder text = new StringBuilder();
+            StringBuilder text = new StringBuilder(512);
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
@@ -1506,7 +1517,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
               continue;
             }
 
-            int alIndex = seq.findPosition(res);
+            int seqPos = seq.findPosition(res);
             gSize = groups.length;
             for (g = 0; g < gSize; g++)
             {
@@ -1518,7 +1529,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                         .append((idWidth + (res + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
-                        .append(alIndex).append(" ").append(triplet);
+                        .append(seqPos).append(" ").append(triplet);
               }
 
               if (groups[g].getStartRes() < res
@@ -1529,61 +1540,51 @@ public class AlignmentPanel extends GAlignmentPanel implements
               }
             }
 
-            if (features != null)
+            if (text.length() < 1)
             {
-              if (text.length() < 1)
-              {
-                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++)
+              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(seqPos).append(" ").append(triplet);
+            }
+            if (!Comparison.isGap(seq.getCharAt(res)))
+            {
+              List<SequenceFeature> features = seq.getFeatures()
+                      .findFeatures(seqPos, seqPos);
+              for (SequenceFeature sf : features)
               {
-
-                if ((features[f].getBegin() <= seq.findPosition(res))
-                        && (features[f].getEnd() >= seq.findPosition(res)))
+                if (sf.isContactFeature())
                 {
-                  if (features[f].isContactFeature())
-                  {
-                    if (features[f].getBegin() == seq.findPosition(res)
-                            || features[f].getEnd() == seq
-                                    .findPosition(res))
-                    {
-                      text.append("<br>").append(features[f].getType())
-                              .append(" ").append(features[f].getBegin())
-                              .append(":").append(features[f].getEnd());
-                    }
-                  }
-                  else
+                  text.append("<br>").append(sf.getType()).append(" ")
+                          .append(sf.getBegin()).append(":")
+                          .append(sf.getEnd());
+                }
+                else
+                {
+                  text.append("<br>");
+                  text.append(sf.getType());
+                  String description = sf.getDescription();
+                  if (description != null
+                          && !sf.getType().equals(description))
                   {
-                    text.append("<br>");
-                    text.append(features[f].getType());
-                    if (features[f].getDescription() != null
-                            && !features[f].getType().equals(
-                                    features[f].getDescription()))
-                    {
-                      text.append(" ").append(features[f].getDescription());
-                    }
-
-                    if (features[f].getValue("status") != null)
-                    {
-                      text.append(" (").append(features[f].getValue("status"))
-                              .append(")");
-                    }
+                    description = description.replace("\"", "&quot;");
+                    text.append(" ").append(description);
                   }
                 }
-
+                String status = sf.getStatus();
+                if (status != null && !"".equals(status))
+                {
+                  text.append(" (").append(status).append(")");
+                }
+              }
+              if (text.length() > 1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
               }
-            }
-            if (text.length() > 1)
-            {
-              text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
-              out.println(text.toString());
             }
           }
         }
@@ -1631,7 +1632,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     int height = ((maxwidth / chunkWidth) + 1) * cHeight;