/*
- * 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 2.8.2b1)
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import java.awt.*;
import java.awt.event.*;
-import java.awt.font.LineMetrics;
-import java.awt.geom.AffineTransform;
-import jalview.analysis.AAFrequency;
import jalview.datamodel.*;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
-import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
-public class AnnotationPanel extends Panel implements AwtRenderPanelI, AdjustmentListener,
- ActionListener, MouseListener, MouseMotionListener
+public class AnnotationPanel extends Panel implements AwtRenderPanelI,
+ AdjustmentListener, ActionListener, MouseListener,
+ MouseMotionListener
{
AlignViewport av;
Vector activeRes;
- static String HELIX = "Helix";
+ final String HELIX = "Helix";
- static String SHEET = "Sheet";
+ final String SHEET = "Sheet";
- static String LABEL = "Label";
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ final String STEM = "RNA Helix";
- static String REMOVE = "Remove Annotation";
+ final String LABEL = "Label";
- static String COLOUR = "Colour";
+ final String REMOVE = "Remove Annotation";
- static Color HELIX_COLOUR = Color.red.darker();
+ final String COLOUR = "Colour";
- static Color SHEET_COLOUR = Color.green.darker().darker();
+ final Color HELIX_COLOUR = Color.red.darker();
+
+ final Color SHEET_COLOUR = Color.green.darker().darker();
Image image;
renderer = new AnnotationRenderer();
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
}
String label = "";
- if (av.colSel != null && av.colSel.size() > 0
- && anot[av.colSel.getMin()] != null)
+ if (av.getColumnSelection() != null
+ && av.getColumnSelection().size() > 0
+ && anot[av.getColumnSelection().getMin()] != null)
label = anot[av.getColumnSelection().getMin()].displayCharacter;
if (evt.getActionCommand().equals(REMOVE))
{
int index = av.getColumnSelection().columnAt(i);
- if (!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
continue;
if (anot[index] == null)
{
int index = av.getColumnSelection().columnAt(i);
- if (!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
continue;
if (anot[index] == null)
symbol = "\u03B2";
}
+ // Added by LML to color stems
+ else if (evt.getActionCommand().equals(STEM))
+ {
+ type = 'S';
+ symbol = "\u03C3";
+ }
+
if (!aa[activeRow].hasIcons)
{
aa[activeRow].hasIcons = true;
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.colSel.isVisible(index))
+ 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();
return null;
}
+ @Override
public void mousePressed(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
return;
}
- PopupMenu pop = new PopupMenu("Structure type");
- MenuItem item = new MenuItem(HELIX);
- item.addActionListener(this);
- pop.add(item);
- item = new MenuItem(SHEET);
- item.addActionListener(this);
- pop.add(item);
+ PopupMenu pop = new PopupMenu(
+ MessageManager.getString("label.structure_type"));
+ MenuItem item;
+ /*
+ * Just display the needed structure options
+ */
+ if (av.getAlignment().isNucleotide() == true)
+ {
+ item = new MenuItem(STEM);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ else
+ {
+ item = new MenuItem(HELIX);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new MenuItem(SHEET);
+ item.addActionListener(this);
+ pop.add(item);
+ }
item = new MenuItem(LABEL);
item.addActionListener(this);
pop.add(item);
ap.scalePanel.mousePressed(evt);
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
graphStretch = -1;
ap.scalePanel.mouseReleased(evt);
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
boolean needValidating = false;
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (graphStretch > -1)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
- evt.getY();
- if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
- calcPanelHeight();
+ av.calcPanelHeight();
needValidating = true;
ap.paintAlignment(true);
}
}
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
int res = evt.getX() / av.getCharWidth() + av.getStartRes();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
}
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
ap.scalePanel.mouseEntered(evt);
}
+ @Override
public void mouseExited(MouseEvent evt)
{
ap.scalePanel.mouseExited(evt);
public int adjustPanelHeight(boolean repaint)
{
- int height = calcPanelHeight();
+ int height = av.calcPanelHeight();
this.setSize(new Dimension(getSize().width, height));
if (repaint)
{
}
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.alignment.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)
{
if (activeRow == -1)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
activeRes.addElement(String.valueOf(i));
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
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();
public void fastPaint(int horizontal)
{
- if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null
- || av.alignment.getAlignmentAnnotation().length < 1)
+ if (horizontal == 0
+ || av.getAlignment().getAlignmentAnnotation() == null
+ || av.getAlignment().getAlignmentAnnotation().length < 1)
{
repaint();
return;
fm = g.getFontMetrics();
}
- if ((av.alignment.getAlignmentAnnotation() == null)
- || (av.alignment.getAlignmentAnnotation().length < 1))
+ if ((av.getAlignment().getAlignmentAnnotation() == null)
+ || (av.getAlignment().getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getSize().width, getSize().height);
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;
renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
g.translate(0, +scrollOffset);
}
-
+
int scrollOffset = 0;
- public void setScrollOffset(int value)
+ public void setScrollOffset(int value, boolean repaint)
{
scrollOffset = value;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
@Override
{
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff