X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=2dfa480b9b357fde120e7815035134ec0aa45008;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=7e6e3a153c89569cb34ed5690c3cdecafb5346ef;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 7e6e3a1..2dfa480 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,34 +1,52 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * 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
+ * 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.
+ *
+ * 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.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.BufferedImage;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
-
-public class AnnotationPanel extends Panel implements AwtRenderPanelI, AdjustmentListener,
- ActionListener, MouseListener, MouseMotionListener
+import jalview.util.MessageManager;
+
+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,
+ MouseMotionListener
{
AlignViewport av;
@@ -36,8 +54,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
int activeRow = -1;
- Vector activeRes;
-
final String HELIX = "Helix";
final String SHEET = "Sheet";
@@ -110,7 +126,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
@@ -133,9 +149,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
}
String label = "";
- if (av.getColumnSelection() != null && av.getColumnSelection().size() > 0
+ if (av.getColumnSelection() != null
+ && av.getColumnSelection().size() > 0
&& anot[av.getColumnSelection().getMin()] != null)
+ {
label = anot[av.getColumnSelection().getMin()].displayCharacter;
+ }
if (evt.getActionCommand().equals(REMOVE))
{
@@ -163,7 +182,9 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
@@ -185,7 +206,9 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
@@ -233,6 +256,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
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++)
@@ -240,20 +267,24 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
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;
}
}
- aa[activeRow].validateRangeAndDisplay();
+ av.getAlignment().validateAnnotation(aa[activeRow]);
+ ap.alignmentChanged();
adjustPanelHeight();
repaint();
@@ -266,9 +297,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
ap.alignFrame, "Enter Label", 400, 200, true);
if (dialog.accept)
+ {
return dialog.getName();
+ }
else
+ {
return null;
+ }
}
@Override
@@ -315,7 +350,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
return;
}
- PopupMenu pop = new PopupMenu("Structure type");
+ PopupMenu pop = new PopupMenu(
+ MessageManager.getString("label.structure_type"));
MenuItem item;
/*
* Just display the needed structure options
@@ -325,7 +361,9 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
item = new MenuItem(STEM);
item.addActionListener(this);
pop.add(item);
- } else {
+ }
+ else
+ {
item = new MenuItem(HELIX);
item.addActionListener(this);
pop.add(item);
@@ -348,11 +386,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
return;
}
- if (aa == null)
- {
- return;
- }
-
ap.scalePanel.mousePressed(evt);
}
@@ -389,7 +422,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
- calcPanelHeight();
+ av.calcPanelHeight();
needValidating = true;
ap.paintAlignment(true);
}
@@ -463,7 +496,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
public int adjustPanelHeight(boolean repaint)
{
- int height = calcPanelHeight();
+ int height = av.calcPanelHeight();
this.setSize(new Dimension(getSize().width, height));
if (repaint)
{
@@ -471,59 +504,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
}
return height;
}
+
/**
- * calculate the height for visible annotation, revalidating bounds where necessary
- * ABSTRACT GUI METHOD
+ * calculate the height for visible annotation, revalidating bounds where
+ * necessary ABSTRACT GUI METHOD
+ *
* @return total height of annotation
*/
- public int calcPanelHeight()
- {
- // setHeight of panels
- AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- int height = 0;
-
- if (aa != null)
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- continue;
- }
-
- aa[i].height = 0;
-
- if (aa[i].hasText)
- {
- aa[i].height += av.charHeight;
- }
-
- if (aa[i].hasIcons)
- {
- aa[i].height += 16;
- }
-
- if (aa[i].graph > 0)
- {
- aa[i].height += aa[i].graphHeight;
- }
-
- if (aa[i].height == 0)
- {
- aa[i].height = 20;
- }
-
- height += aa[i].height;
- }
- }
- if (height == 0)
- {
- height = 20;
- }
-
- return height;
-
- }
public void addEditableColumn(int i)
{
@@ -544,15 +531,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
}
}
}
-
- if (activeRes == null)
- {
- activeRes = new Vector();
- activeRes.addElement(String.valueOf(i));
- return;
- }
-
- activeRes.addElement(String.valueOf(i));
}
@Override
@@ -567,11 +545,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
Dimension d = getSize();
imgWidth = d.width;
// (av.endRes - av.startRes + 1) * av.charWidth;
- if (imgWidth<1 || d.height<1)
+ if (imgWidth < 1 || d.height < 1)
{
return;
}
- if (image == null || imgWidth != image.getWidth(this) || d.height != image.getHeight(this))
+ if (image == null || imgWidth != image.getWidth(this)
+ || d.height != image.getHeight(this))
{
image = createImage(imgWidth, d.height);
gg = image.getGraphics();
@@ -596,20 +575,21 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
public void fastPaint(int horizontal)
{
- if (horizontal == 0 || av.getAlignment().getAlignmentAnnotation() == null
+ if (horizontal == 0
+ || av.getAlignment().getAlignmentAnnotation() == null
|| av.getAlignment().getAlignmentAnnotation().length < 1)
{
repaint();
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)
@@ -629,7 +609,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
* @param startRes
@@ -643,7 +623,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
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)
{
@@ -658,7 +639,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
g.setColor(Color.black);
if (av.validCharWidth)
{
- g.drawString("Alignment has no annotations", 20, 15);
+ g.drawString(MessageManager
+ .getString("label.alignment_has_no_annotations"), 20, 15);
}
return;
@@ -670,10 +652,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
int scrollOffset = 0;
- public void setScrollOffset(int value)
+ public void setScrollOffset(int value, boolean repaint)
{
scrollOffset = value;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
@Override
@@ -693,4 +678,23 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
{
return imgWidth;
}
+
+ private int[] bounds = new int[2];
+
+ @Override
+ public int[] getVisibleVRange()
+ {
+ if (ap != null && ap.alabels != null)
+ {
+ int sOffset = -ap.alabels.scrollOffset;
+ int visHeight = sOffset + ap.annotationPanelHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ {
+ return null;
+ }
+ }
}