X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=6012c1ad5529d9caa8b5bcb80df00358dc000b52;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=13614300c5047464feded70ffee821d5db392d3e;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 1361430..6012c1a 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -20,15 +20,33 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+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;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
 
 public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         AdjustmentListener, ActionListener, MouseListener,
@@ -40,8 +58,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   int activeRow = -1;
 
-  Vector activeRes;
-
   final String HELIX = "Helix";
 
   final String SHEET = "Sheet";
@@ -86,7 +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);
@@ -138,15 +155,20 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     String label = "";
     if (av.getColumnSelection() != null
-            && av.getColumnSelection().size() > 0
+            && !av.getColumnSelection().isEmpty()
             && anot[av.getColumnSelection().getMin()] != null)
+    {
       label = anot[av.getColumnSelection().getMin()].displayCharacter;
+    }
 
     if (evt.getActionCommand().equals(REMOVE))
     {
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        anot[av.getColumnSelection().columnAt(i)] = null;
+        if (av.getColumnSelection().isVisible(index))
+        {
+          anot[index] = null;
+        }
       }
     }
     else if (evt.getActionCommand().equals(LABEL))
@@ -163,12 +185,14 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         aa[activeRow].hasText = true;
       }
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
+        // TODO: JAL-2001 - provide a fast method to list visible selected
+        // columns
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
@@ -185,12 +209,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
       Color col = udc.getColor();
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
@@ -220,7 +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)
@@ -244,19 +269,18 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         }
       }
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
           anot[index] = new Annotation(label, "", type, 0);
         }
 
-        
         anot[index].secondaryStructure = type != 'S' ? type : label
                 .length() == 0 ? ' ' : label.charAt(0);
         anot[index].displayCharacter = label;
@@ -278,9 +302,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
             ap.alignFrame, "Enter Label", 400, 200, true);
 
     if (dialog.accept)
+    {
       return dialog.getName();
+    }
     else
+    {
       return null;
+    }
   }
 
   @Override
@@ -322,7 +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;
       }
@@ -330,10 +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);
@@ -363,11 +390,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       return;
     }
 
-    if (aa == null)
-    {
-      return;
-    }
-
     ap.scalePanel.mousePressed(evt);
   }
 
@@ -440,21 +462,67 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int column = evt.getX() / av.getCharWidth() + av.getStartRes();
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      column = av.getColumnSelection().adjustForHiddenColumns(column);
     }
 
-    if (row > -1 && res < aa[row].annotations.length
-            && aa[row].annotations[res] != null)
+    if (row > -1 && column < aa[row].annotations.length
+            && aa[row].annotations[column] != null)
     {
-      StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
-      if (aa[row].annotations[res].description != null)
+      StringBuilder text = new StringBuilder();
+      text.append(MessageManager.getString("label.column")).append(" ")
+              .append(column + 1);
+      String description = aa[row].annotations[column].description;
+      if (description != null && description.length() > 0)
       {
-        text.append("  " + aa[row].annotations[res].description);
+        text.append("  ").append(description);
       }
+
+      /*
+       * if the annotation is sequence-specific, show the sequence number
+       * in the alignment, and (if not a gap) the residue and position
+       */
+      SequenceI seqref = aa[row].sequenceRef;
+      if (seqref != null)
+      {
+        int seqIndex = av.getAlignment().findIndex(seqref);
+        if (seqIndex != -1)
+        {
+          text.append(", ")
+                  .append(MessageManager.getString("label.sequence"))
+                  .append(" ").append(seqIndex + 1);
+          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(residuePos).append(")");
+            // int residuePos = seqref.findPosition(column);
+            // text.append(residue).append(" (")
+            // .append(residuePos).append(")");
+          }
+        }
+      }
+
       ap.alignFrame.statusBar.setText(text.toString());
     }
   }
@@ -513,15 +581,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         }
       }
     }
-
-    if (activeRes == null)
-    {
-      activeRes = new Vector();
-      activeRes.addElement(String.valueOf(i));
-      return;
-    }
-
-    activeRes.addElement(String.valueOf(i));
   }
 
   @Override
@@ -574,13 +633,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       return;
     }
 
-    gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal
-            * av.charWidth, 0);
+    gg.copyArea(0, 0, imgWidth, getSize().height,
+            -horizontal * av.getCharWidth(), 0);
     int sr = av.startRes, er = av.endRes + 1, transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
-      transX = (er - sr - horizontal) * av.charWidth;
+      transX = (er - sr - horizontal) * av.getCharWidth();
       sr = er - horizontal;
     }
     else if (horizontal < 0)
@@ -614,7 +673,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
     g.setFont(ofont);
 
     g.setColor(Color.white);
-    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
+    g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(),
+            getSize().height);
 
     if (fm == null)
     {
@@ -683,6 +743,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       return bounds;
     }
     else
+    {
       return null;
+    }
   }
 }