X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=438e81b8b0e2ea101677afd7257c0960c661db0f;hb=6716ff86e500acc2800936b3f3c7132927a9246b;hp=398f57d0fcb9a1b975beea3a0fe41965878f4cd7;hpb=076e8c3064e29c735041c84abb792e60fa9522e5;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 398f57d..438e81b 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -23,11 +23,15 @@ package jalview.gui;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 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.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
@@ -48,10 +52,13 @@ import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.Scrollable;
@@ -66,7 +73,7 @@ import javax.swing.ToolTipManager;
  */
 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         MouseListener, MouseWheelListener, MouseMotionListener,
-        ActionListener, AdjustmentListener, Scrollable
+        ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
 {
   String HELIX = MessageManager.getString("label.helix");
 
@@ -119,8 +126,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   boolean mouseDragging = false;
 
-  boolean MAC = false;
-
   // for editing cursor
   int cursorX = 0;
 
@@ -138,9 +143,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public AnnotationPanel(AlignmentPanel ap)
   {
-
-    MAC = jalview.util.Platform.isAMac();
-
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -157,6 +159,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     // and then set our own listener to consume all mousewheel events
     ap.annotationScroller.addMouseWheelListener(this);
     renderer = new AnnotationRenderer();
+
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   public AnnotationPanel(AlignViewport av)
@@ -173,11 +177,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       e.consume();
       if (e.getWheelRotation() > 0)
       {
-        ap.scrollRight(true);
+        av.getRanges().scrollRight(true);
       }
       else
       {
-        ap.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
     }
     else
@@ -281,23 +285,28 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (anot.length < av.getColumnSelection().getMax())
     {
-      Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+      Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
+              + 2];
       System.arraycopy(anot, 0, temp, 0, anot.length);
       anot = temp;
       aa[activeRow].annotations = anot;
     }
 
-    if (evt.getActionCommand().equals(REMOVE))
+    String action = evt.getActionCommand();
+    if (action.equals(REMOVE))
     {
-      for (int sel : av.getColumnSelection().getSelected())
+      for (int index : av.getColumnSelection().getSelected())
       {
-        anot[sel] = null;
+        if (av.getAlignment().getHiddenColumns().isVisible(index))
+        {
+          anot[index] = null;
+        }
       }
     }
-    else if (evt.getActionCommand().equals(LABEL))
+    else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
-      String label = JOptionPane.showInputDialog(this,
+      String label = JvOptionPane.showInputDialog(this,
               MessageManager.getString("label.enter_label"), exMesg);
 
       if (label == null)
@@ -312,17 +321,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
 
         if (anot[index] == null)
         {
-          anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
-          // null exceptions
-          // aren't raised
-          // elsewhere.
+          anot[index] = new Annotation(label, "", ' ', 0);
         }
         else
         {
@@ -330,7 +336,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         }
       }
     }
-    else if (evt.getActionCommand().equals(COLOUR))
+    else if (action.equals(COLOUR))
     {
       Color col = JColorChooser.showDialog(this,
               MessageManager.getString("label.select_foreground_colour"),
@@ -338,7 +344,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -355,23 +361,24 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     // HELIX, SHEET or STEM
     {
       char type = 0;
-      String symbol = "\u03B1";
+      String symbol = "\u03B1"; // alpha
 
-      if (evt.getActionCommand().equals(HELIX))
+      if (action.equals(HELIX))
       {
         type = 'H';
       }
-      else if (evt.getActionCommand().equals(SHEET))
+      else if (action.equals(SHEET))
       {
         type = 'E';
-        symbol = "\u03B2";
+        symbol = "\u03B2"; // beta
       }
 
       // Added by LML to color stems
-      else if (evt.getActionCommand().equals(STEM))
+      else if (action.equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+        symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
       }
 
       if (!aa[activeRow].hasIcons)
@@ -379,7 +386,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         aa[activeRow].hasIcons = true;
       }
 
-      String label = JOptionPane.showInputDialog(MessageManager
+      String label = JvOptionPane.showInputDialog(MessageManager
               .getString("label.enter_label_for_the_structure"), symbol);
 
       if (label == null)
@@ -390,14 +397,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
-        if (evt.getActionCommand().equals(STEM))
+        if (action.equals(STEM))
         {
           aa[activeRow].showAllColLabels = true;
         }
       }
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -407,8 +414,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           anot[index] = new Annotation(label, "", type, 0);
         }
 
-        anot[index].secondaryStructure = type != 'S' ? type : label
-                .length() == 0 ? ' ' : label.charAt(0);
+        anot[index].secondaryStructure = type != 'S' ? type
+                : label.length() == 0 ? ' ' : label.charAt(0);
         anot[index].displayCharacter = label;
 
       }
@@ -423,36 +430,55 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     return;
   }
 
-  private String collectAnnotVals(Annotation[] anot, String label2)
+  /**
+   * Returns any existing annotation concatenated as a string. For each
+   * annotation, takes the description, if any, else the secondary structure
+   * character (if type is HELIX, SHEET or STEM), else the display character (if
+   * type is LABEL).
+   * 
+   * @param anots
+   * @param type
+   * @return
+   */
+  private String collectAnnotVals(Annotation[] anots, String type)
   {
-    String collatedInput = "";
+    // TODO is this method wanted? why? 'last' is not used
+
+    StringBuilder collatedInput = new StringBuilder(64);
     String last = "";
     ColumnSelection viscols = av.getColumnSelection();
-    // TODO: refactor and save av.getColumnSelection for efficiency
-    for (int index : viscols.getSelected())
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
+    /*
+     * the selection list (read-only view) is in selection order, not
+     * column order; make a copy so we can sort it
+     */
+    List<Integer> selected = new ArrayList<>(viscols.getSelected());
+    Collections.sort(selected);
+    for (int index : selected)
     {
       // always check for current display state - just in case
-      if (!viscols.isVisible(index))
+      if (!hidden.isVisible(index))
       {
         continue;
       }
       String tlabel = null;
-      if (anot[index] != null)
+      if (anots[index] != null)
       { // LML added stem code
-        if (label2.equals(HELIX) || label2.equals(SHEET)
-                || label2.equals(STEM) || label2.equals(LABEL))
+        if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+                || type.equals(LABEL))
         {
-          tlabel = anot[index].description;
+          tlabel = anots[index].description;
           if (tlabel == null || tlabel.length() < 1)
           {
-            if (label2.equals(HELIX) || label2.equals(SHEET)
-                    || label2.equals(STEM))
+            if (type.equals(HELIX) || type.equals(SHEET)
+                    || type.equals(STEM))
             {
-              tlabel = "" + anot[index].secondaryStructure;
+              tlabel = "" + anots[index].secondaryStructure;
             }
             else
             {
-              tlabel = "" + anot[index].displayCharacter;
+              tlabel = "" + anots[index].displayCharacter;
             }
           }
         }
@@ -460,13 +486,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           if (last.length() > 0)
           {
-            collatedInput += " ";
+            collatedInput.append(" ");
           }
-          collatedInput += tlabel;
+          collatedInput.append(tlabel);
         }
       }
     }
-    return collatedInput;
+    return collatedInput.toString();
   }
 
   /**
@@ -488,6 +514,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int height = 0;
     activeRow = -1;
 
+    final int y = evt.getY();
     for (int i = 0; i < aa.length; i++)
     {
       if (aa[i].visible)
@@ -495,7 +522,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         height += aa[i].height;
       }
 
-      if (evt.getY() < height)
+      if (y < height)
       {
         if (aa[i].editable)
         {
@@ -505,62 +532,71 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           // Stretch Graph
           graphStretch = i;
-          graphStretchY = evt.getY();
+          graphStretchY = y;
         }
 
         break;
       }
     }
 
+    /*
+     * isPopupTrigger fires in mousePressed on Mac,
+     * not until mouseRelease on Windows
+     */
     if (evt.isPopupTrigger() && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
-      {
-        return;
-      }
+      showPopupMenu(y, evt.getX());
+      return;
+    }
 
-      JPopupMenu pop = new JPopupMenu(
-              MessageManager.getString("label.structure_type"));
-      JMenuItem item;
-      /*
-       * Just display the needed structure options
-       */
-      if (av.getAlignment().isNucleotide() == true)
-      {
-        item = new JMenuItem(STEM);
-        item.addActionListener(this);
-        pop.add(item);
-      }
-      else
-      {
-        item = new JMenuItem(HELIX);
-        item.addActionListener(this);
-        pop.add(item);
-        item = new JMenuItem(SHEET);
-        item.addActionListener(this);
-        pop.add(item);
-      }
-      item = new JMenuItem(LABEL);
+    ap.getScalePanel().mousePressed(evt);
+  }
+
+  /**
+   * Construct and display a context menu at the right-click position
+   * 
+   * @param y
+   * @param x
+   */
+  void showPopupMenu(final int y, int x)
+  {
+    if (av.getColumnSelection() == null
+            || av.getColumnSelection().isEmpty())
+    {
+      return;
+    }
+
+    JPopupMenu pop = new JPopupMenu(
+            MessageManager.getString("label.structure_type"));
+    JMenuItem item;
+    /*
+     * Just display the needed structure options
+     */
+    if (av.getAlignment().isNucleotide())
+    {
+      item = new JMenuItem(STEM);
       item.addActionListener(this);
       pop.add(item);
-      item = new JMenuItem(COLOUR);
+    }
+    else
+    {
+      item = new JMenuItem(HELIX);
       item.addActionListener(this);
       pop.add(item);
-      item = new JMenuItem(REMOVE);
+      item = new JMenuItem(SHEET);
       item.addActionListener(this);
       pop.add(item);
-      pop.show(this, evt.getX(), evt.getY());
-
-      return;
     }
-
-    if (aa == null)
-    {
-      return;
-    }
-
-    ap.getScalePanel().mousePressed(evt);
-
+    item = new JMenuItem(LABEL);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(COLOUR);
+    item.addActionListener(this);
+    pop.add(item);
+    item = new JMenuItem(REMOVE);
+    item.addActionListener(this);
+    pop.add(item);
+    pop.show(this, x, y);
   }
 
   /**
@@ -576,6 +612,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     graphStretchY = -1;
     mouseDragging = false;
     ap.getScalePanel().mouseReleased(evt);
+
+    /*
+     * isPopupTrigger is set in mouseReleased on Windows
+     * (in mousePressed on Mac)
+     */
+    if (evt.isPopupTrigger() && activeRow != -1)
+    {
+      showPopupMenu(evt.getY(), evt.getX());
+    }
+
   }
 
   /**
@@ -613,15 +659,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   {
     if (graphStretch > -1)
     {
-      av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
-              - evt.getY();
-      if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+      av.getAlignment()
+              .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+                      - evt.getY();
+      if (av.getAlignment()
+              .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
       {
-        av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+        av.getAlignment()
+                .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
       }
       graphStretchY = evt.getY();
       adjustPanelHeight();
-      ap.paintAlignment(true);
+      ap.paintAlignment(false, false);
     }
     else
     {
@@ -669,11 +718,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int column = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
-      column = av.getColumnSelection().adjustForHiddenColumns(column);
+      column = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(column);
     }
 
     AlignmentAnnotation ann = aa[row];
@@ -773,16 +824,30 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       int seqIndex = av.getAlignment().findIndex(seqref);
       if (seqIndex != -1)
       {
-        text.append(", ")
-                .append(MessageManager.getString("label.sequence"))
-                .append(" ")
-                .append(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(residue).append(" (")
-                  .append(residuePos).append(")");
+          text.append(" (").append(residuePos).append(")");
         }
       }
     }
@@ -852,7 +917,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+            + 1) * av.getCharWidth();
     if (imgWidth < 1)
     {
       return;
@@ -862,8 +928,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       try
       {
-        image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
-                .getHeight(), BufferedImage.TYPE_INT_RGB);
+        image = new BufferedImage(imgWidth,
+                ap.getAnnotationPanel().getHeight(),
+                BufferedImage.TYPE_INT_RGB);
       } catch (OutOfMemoryError oom)
       {
         try
@@ -893,7 +960,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       imageFresh = true;
     }
 
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getRanges().getStartRes(),
+            av.getRanges().getEndRes() + 1);
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -919,13 +987,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       repaint();
       return;
     }
+
+    int sr = av.getRanges().getStartRes();
+    int er = av.getRanges().getEndRes() + 1;
+    int transX = 0;
+
     long stime = System.currentTimeMillis();
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
-    int sr = av.startRes;
-    int er = av.endRes + 1;
-    int transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -981,8 +1051,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       // and draw a faded image until the calculation
       // has completed
       if (lastImageGood
-              && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
-                      .getHeight() != image.getHeight()))
+              && (fadedImage == null || fadedImage.getWidth() != imgWidth
+                      || fadedImage.getHeight() != image.getHeight()))
       {
         // System.err.println("redraw faded image ("+(fadedImage==null ?
         // "null image" : "") + " lastGood="+lastImageGood+")");
@@ -994,8 +1064,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         fadedG.setColor(Color.white);
         fadedG.fillRect(0, 0, imgWidth, image.getHeight());
 
-        fadedG.setComposite(AlphaComposite.getInstance(
-                AlphaComposite.SRC_OVER, .3f));
+        fadedG.setComposite(
+                AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
         fadedG.drawImage(image, 0, 0, this);
 
       }
@@ -1036,8 +1106,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       return;
     }
-    lastImageGood = renderer.drawComponent(this, av, g, activeRow,
-            startRes, endRes);
+    lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
+            endRes);
     if (!lastImageGood && fadedImage == null)
     {
       fadedImage = oldFaded;
@@ -1080,4 +1150,49 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return null;
     }
   }
+
+  /**
+   * Try to ensure any references held are nulled
+   */
+  public void dispose()
+  {
+    av = null;
+    ap = null;
+    image = null;
+    fadedImage = null;
+    gg = null;
+    _mwl = null;
+
+    /*
+     * I created the renderer so I will dispose of it
+     */
+    if (renderer != null)
+    {
+      renderer.dispose();
+    }
+  }
+
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    // Respond to viewport range changes (e.g. alignment panel was scrolled)
+    // Both scrolling and resizing change viewport ranges: scrolling changes
+    // both start and end points, but resize only changes end values.
+    // Here we only want to fastpaint on a scroll, with resize using a normal
+    // paint, so scroll events are identified as changes to the horizontal or
+    // vertical start value.
+    if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
+    {
+      fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+    }
+    else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
+    {
+      fastPaint(((int[]) evt.getNewValue())[0]
+              - ((int[]) evt.getOldValue())[0]);
+    }
+    else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
+    {
+      repaint();
+    }
+  }
 }