X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=77700d036f2c92ba09196a50a6ec89f009213332;hb=479c44e27a46c7cbee33e293dbc38cbca4fd2e0b;hp=540a0e09eb6deaa77ad431c9eedf1d7d452665c9;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 540a0e0..77700d0 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,30 +1,48 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+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,
@@ -36,8 +54,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
int activeRow = -1;
- Vector activeRes;
-
final String HELIX = "Helix";
final String SHEET = "Sheet";
@@ -134,15 +150,20 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
String label = "";
if (av.getColumnSelection() != null
- && av.getColumnSelection().size() > 0
+ && !av.getColumnSelection().isEmpty()
&& anot[av.getColumnSelection().getMin()] != null)
+ {
label = anot[av.getColumnSelection().getMin()].displayCharacter;
+ }
if (evt.getActionCommand().equals(REMOVE))
{
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int sel : av.getColumnSelection().getSelected())
{
- anot[av.getColumnSelection().columnAt(i)] = null;
+ // TODO: JAL-2001 check if applet has faulty 'REMOVE' selected columns
+ // of
+ // annotation if selection includes hidden columns
+ anot[sel] = null;
}
}
else if (evt.getActionCommand().equals(LABEL))
@@ -159,12 +180,14 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
aa[activeRow].hasText = true;
}
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- int index = av.getColumnSelection().columnAt(i);
-
+ // TODO: JAL-2001 - provide a fast method to list visible selected
+ // columns
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
@@ -181,12 +204,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
Color col = udc.getColor();
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- int index = av.getColumnSelection().columnAt(i);
-
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
@@ -234,29 +257,34 @@ public class AnnotationPanel extends Panel 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++)
+ for (int index : av.getColumnSelection().getSelected())
{
- 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]);
- adjustPanelHeight();
ap.alignmentChanged();
+ adjustPanelHeight();
repaint();
return;
@@ -268,9 +296,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
ap.alignFrame, "Enter Label", 400, 200, true);
if (dialog.accept)
+ {
return dialog.getName();
+ }
else
+ {
return null;
+ }
}
@Override
@@ -317,7 +349,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
return;
}
- PopupMenu pop = new PopupMenu("Structure type");
+ PopupMenu pop = new PopupMenu(
+ MessageManager.getString("label.structure_type"));
MenuItem item;
/*
* Just display the needed structure options
@@ -352,11 +385,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
return;
}
- if (aa == null)
- {
- return;
- }
-
ap.scalePanel.mousePressed(evt);
}
@@ -502,15 +530,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
}
}
}
-
- if (activeRes == null)
- {
- activeRes = new Vector();
- activeRes.addElement(String.valueOf(i));
- return;
- }
-
- activeRes.addElement(String.valueOf(i));
}
@Override
@@ -563,13 +582,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
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)
@@ -603,7 +622,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
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)
{
@@ -618,7 +638,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
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;
@@ -630,10 +651,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
int scrollOffset = 0;
- public void setScrollOffset(int value)
+ public void setScrollOffset(int value, boolean repaint)
{
scrollOffset = value;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
@Override
@@ -653,4 +677,23 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
{
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;
+ }
+ }
}