X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=b1a8aff6a863f3756989c1439747b8d3ef36ad01;hb=f0efe3029537bbbbe788e16eb85cb0af9c0fb81e;hp=dbf2ab120c4c3d20220077ae3d20980a14cd4dfd;hpb=4389a166735bf1203894abdf3cf7dd57c4856dbc;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index dbf2ab1..b1a8aff 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -25,6 +25,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -42,8 +43,6 @@ import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
-import java.awt.Image;
-import java.awt.MediaTracker;
 import java.awt.RenderingHints;
 import java.awt.Toolkit;
 import java.awt.datatransfer.StringSelection;
@@ -53,10 +52,9 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -74,9 +72,16 @@ import javax.swing.ToolTipManager;
 public class AnnotationLabels extends JPanel
         implements MouseListener, MouseMotionListener, ActionListener
 {
-  // width in pixels within which height adjuster arrows are shown and active
+  /**
+   * width in pixels within which height adjuster arrows are shown and active
+   */
   private static final int HEIGHT_ADJUSTER_WIDTH = 50;
 
+  /**
+   * height in pixels for allowing height adjuster to be active
+   */
+  private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
   private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
           .compile("<");
 
@@ -106,10 +111,6 @@ public class AnnotationLabels extends JPanel
   private static final String COPYCONS_SEQ = MessageManager
           .getString("label.copy_consensus_sequence");
 
-  private static Image adjusterImage;
-
-  private static int adjusterImageHeight;
-
   private final boolean debugRedraw = false;
 
   private AlignmentPanel ap;
@@ -139,11 +140,6 @@ public class AnnotationLabels extends JPanel
     av = ap.av;
     ToolTipManager.sharedInstance().registerComponent(this);
 
-    if (adjusterImage == null)
-    {
-      loadAdjusterImage();
-    }
-
     addMouseListener(this);
     addMouseMotionListener(this);
     addMouseWheelListener(ap.getAnnotationPanel());
@@ -155,37 +151,6 @@ public class AnnotationLabels extends JPanel
   }
 
   /**
-   * Loads the gif for the panel height adjustment
-   */
-  protected void loadAdjusterImage()
-  {
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-    Image temp = null;
-
-    if (url != null)
-    {
-      temp = Toolkit.getDefaultToolkit().createImage(url);
-    }
-
-    try
-    {
-      MediaTracker mt = new MediaTracker(this);
-      mt.addImage(temp, 0);
-      mt.waitForID(0);
-    } catch (Exception ex)
-    {
-    }
-
-    BufferedImage bi = new BufferedImage(temp.getHeight(this),
-            temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
-    Graphics2D g = (Graphics2D) bi.getGraphics();
-    g.rotate(Math.toRadians(90));
-    g.drawImage(temp, 0, -bi.getWidth(this), this);
-    adjusterImage = bi;
-    adjusterImageHeight = bi.getHeight();
-  }
-
-  /**
    * DOCUMENT ME!
    * 
    * @param y
@@ -492,13 +457,15 @@ public class AnnotationLabels extends JPanel
           if (!ann.groupRef.isUseInfoLetterHeight())
           {
             ann.groupRef.setIgnoreBelowBackground(cbmi.getState());
+            // todo and recompute group annotation
           }
         }
         else if (!ap.av.isInfoLetterHeight())
         {
           ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+          // todo and recompute annotation
         }
-        ap.alignmentChanged();
+        ap.alignmentChanged(); // todo not like this
       }
     });
     pop.add(cbmi);
@@ -515,11 +482,13 @@ public class AnnotationLabels extends JPanel
         {
           ann.groupRef.setInfoLetterHeight((letterHeight.getState()));
           ann.groupRef.setIgnoreBelowBackground(true);
+          // todo and recompute group annotation
         }
         else
         {
           ap.av.setInfoLetterHeight(letterHeight.getState(), ap);
           ap.av.setIgnoreBelowBackground(true, ap);
+          // todo and recompute annotation
         }
         ap.alignmentChanged();
       }
@@ -548,7 +517,7 @@ public class AnnotationLabels extends JPanel
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          ann.groupRef.setshowHMMSequenceLogo(cprofl.getState());
+          ann.groupRef.setShowHMMSequenceLogo(cprofl.getState());
           ap.repaint();
         }
       });
@@ -564,7 +533,7 @@ public class AnnotationLabels extends JPanel
           ann.groupRef
                   .setNormaliseHMMSequenceLogo(cproflnorm.getState());
           // automatically enable logo display if we're clicked
-          ann.groupRef.setshowHMMSequenceLogo(true);
+          ann.groupRef.setShowHMMSequenceLogo(true);
           ap.repaint();
         }
       });
@@ -593,7 +562,6 @@ public class AnnotationLabels extends JPanel
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          av.updateInformation(ap);
           av.setShowHMMSequenceLogo(cprof.getState());
           ap.repaint();
         }
@@ -936,7 +904,7 @@ public class AnnotationLabels extends JPanel
   protected void showOrHideAdjuster(MouseEvent evt)
   {
     boolean was = resizePanel;
-    resizePanel = evt.getY() < adjusterImageHeight && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+    resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
 
     if (resizePanel != was)
     {
@@ -1087,8 +1055,9 @@ public class AnnotationLabels extends JPanel
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getAlignment().getHiddenColumns()
-              .getVisibleSequenceStrings(0, sq.getLength(), seqs);
+      Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+              .getVisContigsIterator(0, sq.getLength(), false);
+      omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
@@ -1104,13 +1073,12 @@ public class AnnotationLabels extends JPanel
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
 
     if (av.hasHiddenColumns())
     {
-
-      hiddenColumns = av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy();
+      hiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
@@ -1343,11 +1311,7 @@ public class AnnotationLabels extends JPanel
       }
     }
 
-    if (resizePanel)
-    {
-      // g.drawImage(adjusterImage, 2, 0 - getScrollOffset(), this);
-    }
-    else if (dragEvent != null && aa != null)
+    if (!resizePanel && dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
       g.drawString(aa[selectedRow].label, dragEvent.getX(),