X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=9f56206ec912dd9fef4bb9c7f375f3148cb3024a;hb=5019d046ada4f11d4273f8e826961a90b4405947;hp=9e096beb7d1f7a0efc9f1902b48ab3d7ed498a7d;hpb=64238c060481db2d63a9f6d3e013bcca1693eba5;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 9e096be..9f56206 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,33 +1,62 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
import jalview.util.MessageManager;
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JColorChooser;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.Scrollable;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
/**
* AnnotationPanel displays visible portion of annotation rows below unwrapped
* alignment
@@ -39,20 +68,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
MouseListener, MouseWheelListener, MouseMotionListener,
ActionListener, AdjustmentListener, Scrollable
{
- final String HELIX = "Helix";
+ String HELIX = MessageManager.getString("label.helix");
- final String SHEET = "Sheet";
+ String SHEET = MessageManager.getString("label.sheet");
/**
* For RNA secondary structure "stems" aka helices
*/
- final String STEM = "RNA Helix";
+ String STEM = MessageManager.getString("label.rna_helix");
- final String LABEL = "Label";
+ String LABEL = MessageManager.getString("label.label");
- final String REMOVE = "Remove Annotation";
+ String REMOVE = MessageManager.getString("label.remove_annotation");
- final String COLOUR = "Colour";
+ String COLOUR = MessageManager.getString("action.colour");
public final Color HELIX_COLOUR = Color.red.darker();
@@ -268,8 +297,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
else if (evt.getActionCommand().equals(LABEL))
{
String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
- String label = JOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"),
- exMesg);
+ String label = JOptionPane.showInputDialog(this,
+ MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
{
@@ -286,7 +315,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
@@ -304,14 +335,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
- "Choose foreground colour", Color.black);
+ MessageManager.getString("label.select_foreground_colour"), Color.black);
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
@@ -349,8 +382,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
aa[activeRow].hasIcons = true;
}
- String label = JOptionPane.showInputDialog(
- MessageManager.getString("label.enter_label_for_the_structure"), symbol);
+ String label = JOptionPane.showInputDialog(MessageManager
+ .getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
{
@@ -360,27 +393,35 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
+ if (evt.getActionCommand().equals(STEM))
+ {
+ aa[activeRow].showAllColLabels = true;
+ }
}
-
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
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;
+
+ anot[index].secondaryStructure = type != 'S' ? type : label
+ .length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
+
}
}
av.getAlignment().validateAnnotation(aa[activeRow]);
ap.alignmentChanged();
-
+
adjustPanelHeight();
repaint();
@@ -399,7 +440,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
int index = columnSelection.columnAt(i);
// always check for current display state - just in case
if (!viscols.isVisible(index))
+ {
continue;
+ }
String tlabel = null;
if (anot[index] != null)
{ // LML added stem code
@@ -483,7 +526,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
return;
}
- JPopupMenu pop = new JPopupMenu("Structure type");
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.structure_type"));
JMenuItem item;
/*
* Just display the needed structure options
@@ -665,7 +709,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
&& aa[row].annotations[res].description != null
&& aa[row].annotations[res].description.length() > 0)
{
- this.setToolTipText(aa[row].annotations[res].description);
+ this.setToolTipText(JvSwingUtils
+ .wrapTooltip(true, aa[row].annotations[res].description));
}
else
{
@@ -701,11 +746,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@Override
public void mouseClicked(MouseEvent evt)
{
-// if (activeRow != -1)
-// {
-// AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-// AlignmentAnnotation anot = aa[activeRow];
-// }
+ // if (activeRow != -1)
+ // {
+ // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ // AlignmentAnnotation anot = aa[activeRow];
+ // }
}
// TODO mouseClicked-content and drawCursor are quite experimental!
@@ -756,7 +801,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
if (imgWidth < 1)
+ {
return;
+ }
if (image == null || imgWidth != image.getWidth(this)
|| image.getHeight(this) != getHeight())
{
@@ -797,10 +844,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
+
/**
* set true to enable redraw timing debug output on stderr
*/
private final boolean debugRedraw = false;
+
/**
* non-Thread safe repaint
*
@@ -817,9 +866,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
repaint();
return;
}
- long stime=System.currentTimeMillis();
+ long stime = System.currentTimeMillis();
gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
- long mtime=System.currentTimeMillis();
+ long mtime = System.currentTimeMillis();
int sr = av.startRes;
int er = av.endRes + 1;
int transX = 0;
@@ -839,12 +888,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
drawComponent(gg, sr, er);
gg.translate(-transX, 0);
- long dtime=System.currentTimeMillis();
+ long dtime = System.currentTimeMillis();
fastPaint = true;
repaint();
- long rtime=System.currentTimeMillis();
- if (debugRedraw) {
- System.err.println("Scroll:\t"+horizontal+"\tCopyArea:\t"+(mtime-stime)+"\tDraw component:\t"+(dtime-mtime)+"\tRepaint call:\t"+(rtime-dtime));
+ long rtime = System.currentTimeMillis();
+ if (debugRedraw)
+ {
+ System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
+ + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
+ + "\tRepaint call:\t" + (rtime - dtime));
}
}
@@ -906,7 +958,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
fadedImage = null;
}
-
+
g.setColor(Color.white);
g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
@@ -924,7 +976,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
g.setColor(Color.black);
if (av.validCharWidth)
{
- g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15);
+ g.drawString(MessageManager
+ .getString("label.alignment_has_no_annotations"), 20, 15);
}
return;
@@ -954,16 +1007,23 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
return imgWidth;
}
+
private int[] bounds = new int[2];
+
@Override
public int[] getVisibleVRange()
{
- if (ap!=null && ap.alabels!=null)
+ if (ap != null && ap.alabels != null)
{
- int sOffset=-ap.alabels.scrollOffset;
- int visHeight = sOffset+ap.annotationSpaceFillerHolder.getHeight();
- bounds[0] = sOffset; bounds[1]=visHeight;
- return bounds;
- } else return null;
+ int sOffset = -ap.alabels.scrollOffset;
+ int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ {
+ return null;
+ }
}
}