X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=c34a5c5556123df04f8b91fef1b99f8b251b5605;hb=dd81a4ab9d1ffc6168e7a041c7d488db37298cce;hp=501df8a23c5a8b071b0b06d7a5facdf2737e8308;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 501df8a..c34a5c5 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -47,8 +47,8 @@ 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.Vector;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -249,7 +249,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     {
       new AnnotationExporter().exportAnnotations(ap,
               new AlignmentAnnotation[]
-              { aa[selectedRow] }, null, null);
+      { aa[selectedRow] });
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
@@ -408,8 +408,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       Dimension d = ap.annotationScroller.getPreferredSize();
       int dif = evt.getY() - oldY;
 
-      dif /= ap.av.charHeight;
-      dif *= ap.av.charHeight;
+      dif /= ap.av.getCharHeight();
+      dif *= ap.av.getCharHeight();
 
       if ((d.height - dif) > 20)
       {
@@ -683,10 +683,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         pop.addSeparator();
         // av and sequencegroup need to implement same interface for
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-        		MessageManager.getString("label.ignore_gaps_consensus"),
+                        MessageManager.getString("label.ignore_gaps_consensus"),
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                         .getIgnoreGapsConsensus() : ap.av
-                        .getIgnoreGapsConsensus());
+                        .isIgnoreGapsConsensus());
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {
@@ -709,7 +709,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-        		  MessageManager.getString("label.show_group_histogram"),
+                          MessageManager.getString("label.show_group_histogram"),
                   aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
@@ -728,7 +728,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
-        		  MessageManager.getString("label.show_group_logo"),
+                          MessageManager.getString("label.show_group_logo"),
                   aa[selectedRow].groupRef.isShowSequenceLogo());
           cprofl.addActionListener(new ActionListener()
           {
@@ -747,7 +747,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprofl);
           final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
-        		  MessageManager.getString("label.normalise_group_logo"),
+                          MessageManager.getString("label.normalise_group_logo"),
                   aa[selectedRow].groupRef.isNormaliseSequenceLogo());
           cproflnorm.addActionListener(new ActionListener()
           {
@@ -772,7 +772,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         else
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-        		  MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+                          MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -791,7 +791,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-        		  MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+                          MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
           cprof.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -810,7 +810,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprof);
           final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
-        		  MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+                          MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
           cprofnorm.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -872,16 +872,13 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
-    Vector hiddenColumns = null;
+    ArrayList<int[]> hiddenColumns = null;
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = new Vector();
-      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      hiddenColumns = new ArrayList<int[]>();
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
-                .elementAt(i);
-
-        hiddenColumns.addElement(new int[]
+        hiddenColumns.add(new int[]
         { region[0], region[1] });
       }
     }
@@ -1125,7 +1122,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               dragEvent.getY() - getScrollOffset());
     }
 
-    if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+    if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
     {
       g.drawString(MessageManager.getString("label.right_click"), 2, 8);
       g.drawString(MessageManager.getString("label.to_add_annotation"), 2,