X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=07c3e0af34527769886e942e9adf08384d1c4e9b;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=e383e9d15641d616ace5563299d5601950daea63;hpb=2e5393f81c78a3bb60a99f6e7eaa075d993c8eaa;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index e383e9d..07c3e0a 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,36 +1,73 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 java.awt.image.BufferedImage;
-
-import jalview.datamodel.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import jalview.util.ParseHtmlBodyAndLinks;
-public class AnnotationLabels extends Panel implements ActionListener,
- MouseListener, MouseMotionListener
+import java.awt.Checkbox;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+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.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Arrays;
+import java.util.Collections;
+
+public class AnnotationLabels extends Panel
+ implements ActionListener, MouseListener, MouseMotionListener
{
Image image;
+ /**
+ * width in pixels within which height adjuster arrows are shown and active
+ */
+ private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+
+ /**
+ * height in pixels for allowing height adjuster to be active
+ */
+ private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
boolean active = false;
AlignmentPanel ap;
@@ -66,23 +103,6 @@ public class AnnotationLabels extends Panel implements ActionListener,
this.ap = ap;
this.av = ap.av;
setLayout(null);
-
- /**
- * this retrieves the adjustable height glyph from resources. we don't use
- * it at the moment. java.net.URL url =
- * getClass().getResource("/images/idwidth.gif"); Image temp = null;
- *
- * if (url != null) { temp =
- * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
- *
- * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
- * mt.waitForID(0); } catch (Exception ex) { }
- *
- * BufferedImage bi = new BufferedImage(temp.getHeight(this),
- * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
- * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
- * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
- */
addMouseListener(this);
addMouseMotionListener(this);
}
@@ -92,10 +112,13 @@ public class AnnotationLabels extends Panel implements ActionListener,
this.av = av;
}
- public void setScrollOffset(int y)
+ public void setScrollOffset(int y, boolean repaint)
{
scrollOffset = y;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
/**
@@ -107,7 +130,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
int getSelectedRow(int y)
{
int row = -2;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (aa == null)
{
@@ -132,22 +156,23 @@ public class AnnotationLabels extends Panel implements ActionListener,
return row;
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
- new Annotation[ap.av.alignment.getWidth()]);
+ new Annotation[ap.av.getAlignment().getWidth()]);
if (!editLabelDescription(newAnnotation))
{
return;
}
- ap.av.alignment.addAnnotation(newAnnotation);
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
}
else if (evt.getActionCommand().equals(EDITNAME))
{
@@ -170,29 +195,42 @@ public class AnnotationLabels extends Panel implements ActionListener,
ap.alignFrame);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
- + " - " + aa[selectedRow].label, 500, 100);
+ jalview.bin.JalviewLite.addFrame(frame,
+ ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
+ 100);
cap.setText(aa[selectedRow].toString());
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
- SequenceI cons = av.getConsensusSeq();
+ SequenceGroup group = aa[selectedRow].groupRef;
+ SequenceI cons = group == null ? av.getConsensusSeq()
+ : group.getConsensusSeq();
if (cons != null)
{
copy_annotseqtoclipboard(cons);
}
}
+ refresh();
+ }
+
+ /**
+ * Adjust size and repaint
+ */
+ protected void refresh()
+ {
ap.annotationPanel.adjustPanelHeight();
setSize(getSize().width, ap.annotationPanel.getSize().height);
ap.validate();
- ap.paintAlignment(true);
+ // TODO: only paint if we needed to
+ ap.paintAlignment(true, true);
}
boolean editLabelDescription(AlignmentAnnotation annotation)
{
- Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
- + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+ Checkbox padGaps = new Checkbox(
+ "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
+ annotation.padGaps);
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Label",
@@ -215,20 +253,29 @@ public class AnnotationLabels extends Panel implements ActionListener,
return true;
}
else
+ {
return false;
+ }
}
boolean resizePanel = false;
+ @Override
public void mouseMoved(MouseEvent evt)
{
- resizePanel = evt.getY() < 10 && evt.getX() < 14;
+ resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+ && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+ setCursor(Cursor.getPredefinedCursor(
+ resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
int row = getSelectedRow(evt.getY() + scrollOffset);
if (row > -1)
{
- ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(av.alignment.getAlignmentAnnotation()[row].getDescription(true), true, "\n");
+ ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+ av.getAlignment().getAlignmentAnnotation()[row]
+ .getDescription(true),
+ true, "\n");
if (tooltip == null)
{
tooltip = new Tooltip(phb.getNonHtmlContent(), this);
@@ -263,6 +310,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
dragCancelled = true;
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (dragCancelled)
@@ -274,26 +322,28 @@ public class AnnotationLabels extends Panel implements ActionListener,
if (resizePanel)
{
- Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
- .getSize(), f = ap.seqPanelHolder.getSize();
+ Dimension d = ap.annotationPanelHolder.getSize(),
+ e = ap.annotationSpaceFillerHolder.getSize(),
+ f = ap.seqPanelHolder.getSize();
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 && (f.height + dif) > 20)
{
ap.annotationPanel.setSize(d.width, d.height - dif);
setSize(new Dimension(e.width, d.height - dif));
- ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
- d.height - dif));
- ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
- - dif));
+ ap.annotationSpaceFillerHolder
+ .setSize(new Dimension(e.width, d.height - dif));
+ ap.annotationPanelHolder
+ .setSize(new Dimension(d.width, d.height - dif));
ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
- ap.annotationPanel.calcPanelHeight());
+ av.calcPanelHeight());
f.height += dif;
ap.seqPanelHolder.setPreferredSize(f);
- ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+ ap.setScrollValues(av.getRanges().getStartRes(),
+ av.getRanges().getStartSeq());
ap.validate();
// ap.paintAlignment(true);
ap.addNotify();
@@ -322,10 +372,12 @@ public class AnnotationLabels extends Panel implements ActionListener,
}
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (!resizePanel && !dragCancelled)
@@ -334,29 +386,31 @@ public class AnnotationLabels extends Panel implements ActionListener,
int end = getSelectedRow(evt.getY() + scrollOffset);
- if (start>-1 && start != end)
+ if (start > -1 && start != end)
{
// Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment
+ AlignmentAnnotation startAA = ap.av.getAlignment()
.getAlignmentAnnotation()[start];
if (end == -1)
{
- end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
}
- AlignmentAnnotation endAA = ap.av.alignment
+ AlignmentAnnotation endAA = ap.av.getAlignment()
.getAlignmentAnnotation()[end];
- ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
}
}
resizePanel = false;
dragEvent = null;
dragCancelled = false;
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
repaint();
ap.annotationPanel.repaint();
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
if (evt.getY() < 10 && evt.getX() < 14)
@@ -364,8 +418,11 @@ public class AnnotationLabels extends Panel implements ActionListener,
resizePanel = true;
repaint();
}
+ setCursor(Cursor.getPredefinedCursor(
+ resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
}
+ @Override
public void mouseExited(MouseEvent evt)
{
dragCancelled = false;
@@ -384,6 +441,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
repaint();
}
+ @Override
public void mousePressed(MouseEvent evt)
{
oldY = evt.getY();
@@ -391,17 +449,20 @@ public class AnnotationLabels extends Panel implements ActionListener,
{
return;
}
- dragCancelled=false;
+ dragCancelled = false;
// todo: move below to mouseClicked ?
selectedRow = getSelectedRow(evt.getY() + scrollOffset);
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
{
- PopupMenu popup = new PopupMenu("Annotations");
+ PopupMenu popup = new PopupMenu(
+ MessageManager.getString("label.annotations"));
MenuItem item = new MenuItem(ADDNEW);
item.addActionListener(this);
@@ -426,6 +487,32 @@ public class AnnotationLabels extends Panel implements ActionListener,
item = new MenuItem(HIDE);
item.addActionListener(this);
popup.add(item);
+
+ /*
+ * Hide all