X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=0ec7adfc10eb0788c0e144f96fcf157955c45f66;hb=76c239505d13a123cc83621623aaca16e47ddb12;hp=dd652b1be7bdbf58d4f22ff9eedcab20c131458b;hpb=076e8c3064e29c735041c84abb792e60fa9522e5;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index dd652b1..0ec7adf 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -25,8 +25,10 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -100,7 +102,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   public AnnotationPanel(AlignmentPanel ap)
   {
-    MAC = new jalview.util.Platform().isAMac();
+    new jalview.util.Platform();
+    MAC = Platform.isAMac();
     this.ap = ap;
     av = ap.av;
     setLayout(null);
@@ -160,12 +163,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     if (evt.getActionCommand().equals(REMOVE))
     {
-      for (int sel : av.getColumnSelection().getSelected())
+      for (int index : av.getColumnSelection().getSelected())
       {
-        // TODO: JAL-2001 check if applet has faulty 'REMOVE' selected columns
-        // of
-        // annotation if selection includes hidden columns
-        anot[sel] = null;
+        if (av.getColumnSelection().isVisible(index))
+        {
+          anot[index] = null;
+        }
       }
     }
     else if (evt.getActionCommand().equals(LABEL))
@@ -241,7 +244,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       else if (evt.getActionCommand().equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+        symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
       }
 
       if (!aa[activeRow].hasIcons)
@@ -346,7 +350,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
             && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
+      if (av.getColumnSelection() == null
+              || av.getColumnSelection().isEmpty())
       {
         return;
       }
@@ -354,10 +359,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       PopupMenu pop = new PopupMenu(
               MessageManager.getString("label.structure_type"));
       MenuItem item;
-      /*
-       * Just display the needed structure options
-       */
-      if (av.getAlignment().isNucleotide() == true)
+
+      if (av.getAlignment().isNucleotide())
       {
         item = new MenuItem(STEM);
         item.addActionListener(this);
@@ -459,7 +462,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    int column = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int column = evt.getX() / av.getCharWidth()
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
@@ -472,9 +476,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       StringBuilder text = new StringBuilder();
       text.append(MessageManager.getString("label.column")).append(" ")
               .append(column + 1);
-      if (aa[row].annotations[column].description != null)
+      String description = aa[row].annotations[column].description;
+      if (description != null && description.length() > 0)
       {
-        text.append("  ").append(aa[row].annotations[column].description);
+        text.append("  ").append(description);
       }
 
       /*
@@ -493,9 +498,28 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
           char residue = seqref.getCharAt(column);
           if (!Comparison.isGap(residue))
           {
+            text.append(" ");
+            String name;
+            if (av.getAlignment().isNucleotide())
+            {
+              name = ResidueProperties.nucleotideName.get(String
+                      .valueOf(residue));
+              text.append(" Nucleotide: ").append(
+                      name != null ? name : residue);
+            }
+            else
+            {
+              name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+                      : ResidueProperties.aa2Triplet.get(String
+                              .valueOf(residue)));
+              text.append(" Residue: ").append(
+                      name != null ? name : residue);
+            }
             int residuePos = seqref.findPosition(column);
-            text.append(": ").append(residue).append(" (")
-                    .append(residuePos).append(")");
+            text.append(" (").append(residuePos).append(")");
+            // int residuePos = seqref.findPosition(column);
+            // text.append(residue).append(" (")
+            // .append(residuePos).append(")");
           }
         }
       }
@@ -595,7 +619,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+            .getEndRes() + 1);
 
     g.drawImage(image, 0, 0, this);
   }
@@ -612,7 +637,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.copyArea(0, 0, imgWidth, getSize().height,
             -horizontal * av.getCharWidth(), 0);
-    int sr = av.startRes, er = av.endRes + 1, transX = 0;
+    int sr = av.getRanges().getStartRes(), er = av.getRanges().getEndRes() + 1, transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {