/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationPanel
- extends Panel
- implements AdjustmentListener, ActionListener, MouseListener, MouseMotionListener
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+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;
+import java.beans.PropertyChangeEvent;
+
+public class AnnotationPanel extends Panel
+ implements AwtRenderPanelI, AdjustmentListener, ActionListener,
+ MouseListener, MouseMotionListener, ViewportListenerI
{
AlignViewport av;
+
AlignmentPanel ap;
+
int activeRow = -1;
- Vector activeRes;
- static String HELIX = "Helix";
- static String SHEET = "Sheet";
- static String LABEL = "Label";
- static String REMOVE = "Remove Annotation";
- static String COLOUR = "Colour";
- static Color HELIX_COLOUR = Color.red.darker();
- static Color SHEET_COLOUR = Color.green.darker().darker();
+ final String HELIX = "Helix";
+
+ final String SHEET = "Sheet";
+
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ final String STEM = "RNA Helix";
+
+ final String LABEL = "Label";
+
+ final String REMOVE = "Remove Annotation";
+
+ final String COLOUR = "Colour";
+
+ final Color HELIX_COLOUR = Color.red.darker();
+
+ final Color SHEET_COLOUR = Color.green.darker().darker();
Image image;
+
Graphics gg;
+
FontMetrics fm;
+
int imgWidth = 0;
boolean fastPaint = false;
+ // Used For mouse Dragging and resizing graphs
+ int graphStretch = -1;
+
+ int graphStretchY = -1;
+
+ boolean mouseDragging = false;
+
public static int GRAPH_HEIGHT = 40;
- boolean MAC = false;
+ // boolean MAC = false;
+
+ public final AnnotationRenderer renderer;
public AnnotationPanel(AlignmentPanel ap)
{
- if (System.getProperty("os.name").startsWith("Mac"))
- {
- MAC = true;
- }
-
+ new jalview.util.Platform();
+ // MAC = Platform.isAMac();
this.ap = ap;
av = ap.av;
setLayout(null);
- adjustPanelHeight();
+ int height = adjustPanelHeight();
+ ap.apvscroll.setValues(0, getSize().height, 0, height);
addMouseMotionListener(this);
addMouseListener(this);
-
// ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
+ renderer = new AnnotationRenderer();
+
+ av.getRanges().addPropertyChangeListener(this);
}
public AnnotationPanel(AlignViewport av)
{
this.av = av;
+ renderer = new AnnotationRenderer();
+
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- ap.alabels.setScrollOffset( -evt.getValue());
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
Annotation[] anot = aa[activeRow].annotations;
if (anot.length < av.getColumnSelection().getMax())
{
- Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+ Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
+ + 2];
System.arraycopy(anot, 0, temp, 0, anot.length);
anot = temp;
aa[activeRow].annotations = anot;
}
String label = "";
- if (av.colSel != null && av.colSel.size() > 0
- && anot[av.colSel.getMin()] != null)
+ if (av.getColumnSelection() != null
+ && !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 index : av.getColumnSelection().getSelected())
{
- anot[av.getColumnSelection().columnAt(i)] = null;
+ if (av.getAlignment().getHiddenColumns().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
else if (evt.getActionCommand().equals(LABEL))
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
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);
-
- if(!av.colSel.isVisible(index))
+ // TODO: JAL-2001 - provide a fast method to list visible selected
+ // columns
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
}
else if (evt.getActionCommand().equals(COLOUR))
{
- UserDefinedColours udc = new UserDefinedColours(
- this,
- Color.black, ap.alignFrame);
+ UserDefinedColours udc = new UserDefinedColours(this, Color.black,
+ ap.alignFrame);
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.colSel.isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
anot[index].colour = col;
}
}
- else // HELIX OR SHEET
+ else
+ // HELIX OR SHEET
{
char type = 0;
String symbol = "\u03B1";
symbol = "\u03B2";
}
+ // Added by LML to color stems
+ else if (evt.getActionCommand().equals(STEM))
+ {
+ type = 'S';
+ int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+ symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
+ }
+
if (!aa[activeRow].hasIcons)
{
aa[activeRow].hasIcons = true;
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ 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.colSel.isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().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();
String enterLabel(String text, String label)
{
- EditNameDialog dialog = new EditNameDialog(text,null,label,null,
- ap.alignFrame,"Enter Label", 400,200, true);
+ EditNameDialog dialog = new EditNameDialog(text, null, label, null,
+ ap.alignFrame, "Enter Label", 400, 200, true);
- if(dialog.accept)
+ if (dialog.accept)
+ {
return dialog.getName();
+ }
else
+ {
return null;
+ }
}
+ @Override
public void mousePressed(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- if (aa == null)
- {
- return;
- }
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
- int height = 0;
- activeRow = -1;
+ int height = -scrollOffset;
+ activeRow = -1;
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
+ {
+ height += aa[i].height;
+ }
- for (int i = 0; i < aa.length; i++)
+ if (evt.getY() < height)
{
- if (aa[i].visible)
+ if (aa[i].editable)
{
- height += aa[i].height;
+ activeRow = i;
}
-
- if (evt.getY() < height)
+ else if (aa[i].graph != AlignmentAnnotation.NO_GRAPH)
{
- if (aa[i].editable)
- {
- activeRow = i;
- }
-
- break;
+ // Stretch Graph
+ graphStretch = i;
+ graphStretchY = evt.getY();
}
+
+ break;
}
+ }
- if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
- InputEvent.BUTTON3_MASK && activeRow != -1)
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK
+ && activeRow != -1)
+ {
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().isEmpty())
{
- if (av.getColumnSelection() == 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);
- item = new MenuItem(LABEL);
+ PopupMenu pop = new PopupMenu(
+ MessageManager.getString("label.structure_type"));
+ MenuItem item;
+
+ if (av.getAlignment().isNucleotide())
+ {
+ item = new MenuItem(STEM);
item.addActionListener(this);
pop.add(item);
- item = new MenuItem(COLOUR);
+ }
+ else
+ {
+ item = new MenuItem(HELIX);
item.addActionListener(this);
pop.add(item);
- item = new MenuItem(REMOVE);
+ item = new MenuItem(SHEET);
item.addActionListener(this);
pop.add(item);
- ap.alignFrame.add(pop);
- pop.show(this, evt.getX(), evt.getY());
-
- return;
}
+ item = new MenuItem(LABEL);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new MenuItem(COLOUR);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new MenuItem(REMOVE);
+ item.addActionListener(this);
+ pop.add(item);
+ ap.alignFrame.add(pop);
+ pop.show(this, evt.getX(), evt.getY());
- if (aa == null)
- {
- return;
- }
+ return;
+ }
- ap.scalePanel.mousePressed(evt);
+ ap.scalePanel.mousePressed(evt);
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
+ graphStretch = -1;
+ graphStretchY = -1;
+ mouseDragging = false;
+ if (needValidating)
+ {
+ ap.validate();
+ needValidating = false;
+ }
ap.scalePanel.mouseReleased(evt);
}
+ @Override
public void mouseClicked(MouseEvent evt)
- {}
+ {
+ }
+ boolean needValidating = false;
+
+ @Override
public void mouseDragged(MouseEvent evt)
{
- ap.scalePanel.mouseDragged(evt);
+ if (graphStretch > -1)
+ {
+ av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
+ if (av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ {
+ av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ }
+ graphStretchY = evt.getY();
+ av.calcPanelHeight();
+ needValidating = true;
+ // TODO: only update overview visible geometry
+ ap.paintAlignment(true, false);
+ }
+ else
+ {
+ ap.scalePanel.mouseDragged(evt);
+ }
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
}
int row = -1;
- int height = 0;
+ int height = -scrollOffset;
for (int i = 0; i < aa.length; i++)
{
}
}
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+ int column = evt.getX() / av.getCharWidth()
+ + av.getRanges().getStartRes();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(column);
}
- if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
+ if (row > -1 && column < aa[row].annotations.length
+ && aa[row].annotations[column] != null)
{
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
- if (aa[row].annotations[res].description != null)
+ StringBuilder text = new StringBuilder();
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+ String description = aa[row].annotations[column].description;
+ if (description != null && description.length() > 0)
+ {
+ text.append(" ").append(description);
+ }
+
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = aa[row].sequenceRef;
+ if (seqref != null)
{
- text.append(" " + aa[row].annotations[res].description);
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ").append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
+ {
+ text.append(" ");
+ String name;
+ if (av.getAlignment().isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName
+ .get(String.valueOf(residue));
+ text.append(" Nucleotide: ")
+ .append(name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X"
+ : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet
+ .get(String.valueOf(residue)));
+ text.append(" Residue: ")
+ .append(name != null ? name : residue);
+ }
+ int residuePos = seqref.findPosition(column);
+ text.append(" (").append(residuePos).append(")");
+ // int residuePos = seqref.findPosition(column);
+ // text.append(residue).append(" (")
+ // .append(residuePos).append(")");
+ }
+ }
}
+
ap.alignFrame.statusBar.setText(text.toString());
}
}
+
+ @Override
public void mouseEntered(MouseEvent evt)
{
ap.scalePanel.mouseEntered(evt);
}
+
+ @Override
public void mouseExited(MouseEvent evt)
{
ap.scalePanel.mouseExited(evt);
}
-
public int adjustPanelHeight()
{
- // 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;
- }
+ return adjustPanelHeight(true);
+ }
- height += aa[i].height;
- }
- }
- else
+ public int adjustPanelHeight(boolean repaint)
+ {
+ int height = av.calcPanelHeight();
+ this.setSize(new Dimension(getSize().width, height));
+ if (repaint)
{
- height = 20;
+ repaint();
}
-
- this.setSize(getSize().width, height);
-
- repaint();
-
return height;
-
}
+ /**
+ * calculate the height for visible annotation, revalidating bounds where
+ * necessary ABSTRACT GUI METHOD
+ *
+ * @return total height of annotation
+ */
+
public void addEditableColumn(int i)
{
if (activeRow == -1)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
}
}
}
-
- if (activeRes == null)
- {
- activeRes = new Vector();
- activeRes.addElement(String.valueOf(i));
- return;
- }
-
- activeRes.addElement(String.valueOf(i));
}
-
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
-
- imgWidth = getSize().width;
- //(av.endRes - av.startRes + 1) * av.charWidth;
-
- if (image == null || imgWidth != image.getWidth(this))
+ Dimension d = getSize();
+ imgWidth = d.width;
+ // (av.endRes - av.startRes + 1) * av.charWidth;
+ if (imgWidth < 1 || d.height < 1)
{
- image = createImage(imgWidth, ap.annotationPanel.getSize().height);
+ return;
+ }
+ if (image == null || imgWidth != image.getWidth(this)
+ || d.height != image.getHeight(this))
+ {
+ image = createImage(imgWidth, d.height);
gg = image.getGraphics();
gg.setFont(av.getFont());
fm = gg.getFontMetrics();
gg.setColor(Color.white);
gg.fillRect(0, 0, getSize().width, getSize().height);
- drawComponent(gg, av.startRes, av.endRes + 1);
+ drawComponent(gg, av.getRanges().getStartRes(),
+ av.getRanges().getEndRes() + 1);
g.drawImage(image, 0, 0, this);
}
public void fastPaint(int horizontal)
{
- if (horizontal == 0
- || av.alignment.getAlignmentAnnotation() == null
- || av.alignment.getAlignmentAnnotation().length < 1
- )
+ if (horizontal == 0 || gg == null
+ || av.getAlignment().getAlignmentAnnotation() == null
+ || av.getAlignment().getAlignmentAnnotation().length < 1)
{
repaint();
return;
}
- gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);
- int sr = av.startRes, er = av.endRes + 1, transX = 0;
+ gg.copyArea(0, 0, imgWidth, getSize().height,
+ -horizontal * av.getCharWidth(), 0);
+ int sr = av.getRanges().getStartRes(),
+ er = av.getRanges().getEndRes() + 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)
drawComponent(gg, sr, er);
- gg.translate( -transX, 0);
+ gg.translate(-transX, 0);
fastPaint = true;
repaint();
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startRes DOCUMENT ME!
- * @param endRes DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
- g.setFont(av.getFont());
+ Font ofont = av.getFont();
+ 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)
{
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;
}
+ g.translate(0, -scrollOffset);
+ renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
+ g.translate(0, +scrollOffset);
+ }
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- int x = 0;
- int y = 0;
- int column = 0;
- char lastSS;
- int lastSSX;
- int iconOffset = av.charHeight / 2;
- boolean validRes = false;
-
- boolean[] graphGroupDrawn = new boolean[aa.length];
+ int scrollOffset = 0;
- //\u03B2 \u03B1
- for (int i = 0; i < aa.length; i++)
+ public void setScrollOffset(int value, boolean repaint)
+ {
+ scrollOffset = value;
+ if (repaint)
{
- AlignmentAnnotation row = aa[i];
-
- if (!row.visible)
- {
- continue;
- }
-
- lastSS = ' ';
- lastSSX = 0;
-
- if (row.graph > 0)
- {
- if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
- {
- continue;
- }
-
- // this is so that we draw the characters below the graph
- y += row.height;
-
- if (row.hasText)
- {
- y -= av.charHeight;
- }
- }
-
- if (row.hasText)
- {
- iconOffset = av.charHeight / 2;
- }
- else
- {
- iconOffset = 0;
- }
-
- x = 0;
- while (x < endRes - startRes)
- {
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
- if (column > row.annotations.length - 1)
- {
- break;
- }
- }
- else
- {
- column = startRes + x;
- }
-
- if ( (row.annotations.length <= column) ||
- (row.annotations[column] == null))
- {
- validRes = false;
- }
- else
- {
- validRes = true;
- }
-
- if (activeRow == i)
- {
- g.setColor(Color.red);
-
- if (av.getColumnSelection() != null)
- {
- for (int n = 0; n < av.getColumnSelection().size(); n++)
- {
- int v = av.getColumnSelection().columnAt(n);
-
- if (v == column)
- {
- g.fillRect(x * av.charWidth, y,
- av.charWidth, av.charHeight);
- }
- }
- }
- }
-
-
-
- if (av.validCharWidth && validRes &&
- (row.annotations[column].displayCharacter.length() > 0))
- {
- int charOffset = (av.charWidth -
- fm.charWidth(row.annotations[column].
- displayCharacter.charAt(
- 0))) / 2;
-
- if (row.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(row.annotations[column].colour);
-
- if (column == 0 || row.graph > 0)
- {
- g.drawString(row.annotations[column].displayCharacter,
- (x * av.charWidth) + charOffset,
- y + iconOffset + 3);
- }
- else if (
- row.annotations[column - 1] == null
- || (!row.annotations[column].displayCharacter.equals(
- row.annotations[column - 1].displayCharacter)
- ||
- (row.annotations[column].displayCharacter.length() < 2 &&
- row.annotations[column].secondaryStructure == ' ')))
- {
- g.drawString(row.annotations[column].displayCharacter,
- (x * av.charWidth) + charOffset,
- y + iconOffset + 3);
- }
- }
-
- if (row.hasIcons)
- {
- if (!validRes ||
- (row.annotations[column].secondaryStructure != lastSS))
- {
- switch (lastSS)
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- if (MAC)
- {
- //Off by 1 offset when drawing rects and ovals
- //to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX, 7, 8, 8);
- break;
- }
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (sCol == 0 ||
- row.annotations[sCol - 1] == null ||
- row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
- 180);
- x1 += av.charWidth / 2;
- }
-
- if (row.annotations[column] == null ||
- row.annotations[column].secondaryStructure != 'H')
- {
- g.fillArc( (x * av.charWidth) - av.charWidth,
- y + 4 + iconOffset, av.charWidth, 8, 270, 180);
- x2 -= av.charWidth / 2;
- }
-
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
- break;
-
- case 'E':
- g.setColor(SHEET_COLOUR);
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * av.charWidth) - 4,
- (x * av.charWidth) - 4,
- (x * av.charWidth)},
- new int[]
- {
- y + iconOffset, y + 14 + iconOffset,
- y + 8 + iconOffset
- }, 3);
-
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
-
- break;
- }
-
- if (validRes)
- {
- lastSS = row.annotations[column].secondaryStructure;
- }
- else
- {
- lastSS = ' ';
- }
-
- lastSSX = (x * av.charWidth);
- }
- }
-
- column++;
- x++;
- }
-
- if (column >= row.annotations.length)
- {
- column = row.annotations.length - 1;
- }
-
- // x ++;
-
- if (row.hasIcons)
- {
- switch (lastSS)
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- if (MAC)
- {
- //Off by 1 offset when drawing rects and ovals
- //to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX, 7, 8, 8);
- break;
- }
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (sCol == 0 ||
- row.annotations[sCol - 1] == null ||
- row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
- x1 += av.charWidth / 2;
- }
-
- if (row.annotations[column] == null ||
- row.annotations[column].secondaryStructure != 'H')
- {
- g.fillArc( (x * av.charWidth) - av.charWidth,
- y + 4 + iconOffset, av.charWidth, 8, 270,
- 180);
- x2 -= av.charWidth / 2;
- }
-
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
-
- break;
-
- case 'E':
- g.setColor(SHEET_COLOUR);
-
- if (row.annotations[endRes] == null
- || row.annotations[endRes].secondaryStructure != 'E')
- {
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * av.charWidth) - 4,
- (x * av.charWidth) - 4,
- (x * av.charWidth)},
- new int[]
- {
- y + iconOffset, y + 14 + iconOffset,
- y + 7 + iconOffset
- }, 3);
- }
- else
- {
- g.fillRect(lastSSX, y + 4 + iconOffset,
- x * av.charWidth - lastSSX, 7);
- }
- break;
-
- default:
- g.setColor(Color.gray);
- if (!av.wrapAlignment || endRes == av.endRes)
- {
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
- }
-
- break;
- }
- }
-
- if (row.graph > 0)
- {
- if (row.graph == AlignmentAnnotation.LINE_GRAPH)
- {
- if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
- {
- float groupmax = -999999, groupmin = 9999999;
- for (int gg = 0; gg < aa.length; gg++)
- {
- if (aa[gg].graphGroup != row.graphGroup)
- {
- continue;
- }
-
- if (aa[gg] != row)
- {
- aa[gg].visible = false;
- }
-
- if (aa[gg].graphMax > groupmax)
- {
- groupmax = aa[gg].graphMax;
- }
- if (aa[gg].graphMin < groupmin)
- {
- groupmin = aa[gg].graphMin;
- }
- }
-
- for (int gg = 0; gg < aa.length; gg++)
- {
- if (aa[gg].graphGroup == row.graphGroup)
- {
- drawLineGraph(g, aa[gg], startRes, endRes, y,
- groupmin, groupmax,
- row.graphHeight);
- }
- }
-
- graphGroupDrawn[row.graphGroup] = true;
- }
- else
- {
- drawLineGraph(g, row, startRes, endRes,
- y, row.graphMin, row.graphMax, row.graphHeight);
- }
- }
- else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
- {
- drawBarGraph(g, row, startRes, endRes,
- row.graphMin, row.graphMax, y);
- }
- }
-
- if (row.graph > 0 && row.hasText)
- {
- y += av.charHeight;
- }
-
- if (row.graph == 0)
- {
- y += aa[i].height;
- }
+ repaint();
}
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- int y,
- float min, float max,
- int graphHeight)
+ @Override
+ public FontMetrics getFontMetrics()
{
- if (sRes > aa.annotations.length)
- {
- return;
- }
-
- int x = 0;
-
- //Adjustment for fastpaint to left
- if (eRes < av.endRes)
- {
- eRes++;
- }
-
- eRes = Math.min(eRes, aa.annotations.length);
-
- int y1 = y, y2 = y;
- float range = max - min;
-
- ////Draw origin
- if (min < 0)
- {
- y2 = y - (int) ( (0 - min / range) * graphHeight);
- }
+ return fm;
+ }
- g.setColor(Color.gray);
- g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2);
+ @Override
+ public Image getFadedImage()
+ {
+ return image;
+ }
- eRes = Math.min(eRes, aa.annotations.length);
+ @Override
+ public int getFadedImageWidth()
+ {
+ return imgWidth;
+ }
- int column;
- int aaMax = aa.annotations.length - 1;
+ private int[] bounds = new int[2];
- while (x < eRes - sRes)
+ @Override
+ public int[] getVisibleVRange()
+ {
+ if (ap != null && ap.alabels != null)
{
- column = sRes + x;
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(column);
- }
-
- if (column > aaMax)
- {
- break;
- }
-
- if (aa.annotations[column] == null) // || coaa.annotations[column - 1] == null)
- {
- x++;
- continue;
- }
-
- if (aa.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(aa.annotations[column].colour);
- if (column==0 || aa.annotations[column-1]==null)
- {
- y1 = y -
- (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
- } else {
- y1 = y -
- (int) ( ( (aa.annotations[column-1].value - min) / range) * graphHeight);
- }
- y2 = y -
- (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
-
- g.drawLine(x * av.charWidth - av.charWidth / 2, y1,
- x * av.charWidth + av.charWidth / 2, y2);
- x++;
+ int sOffset = -ap.alabels.scrollOffset;
+ int visHeight = sOffset + ap.annotationPanelHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
}
-
- if (aa.threshold != null)
+ else
{
- g.setColor(aa.threshold.colour);
-
- y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
+ return null;
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- float min, float max,
- int y)
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
{
- if (sRes > aa.annotations.length)
- {
- return;
- }
-
- eRes = Math.min(eRes, aa.annotations.length);
-
- int x = 0, y1 = y, y2 = y;
-
- float range = max - min;
-
- if (min < 0)
- {
- y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
- }
-
- g.setColor(Color.gray);
-
- g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);
-
- int column;
- int aaMax = aa.annotations.length - 1;
-
- while (x < eRes - sRes)
+ // Respond to viewport range changes (e.g. alignment panel was scrolled)
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
{
- column = sRes + x;
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(column);
- }
-
- if (column > aaMax)
- {
- break;
- }
-
- if (aa.annotations[column] == null)
- {
- x++;
- continue;
- }
-
- if (aa.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(aa.annotations[column].colour);
-
- y1 = y -
- (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
-
- if (y1 - y2 > 0)
- {
- g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
- }
- else
- {
- g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
- }
-
- x++;
-
+ fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
}
- if (aa.threshold != null)
+ else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
{
- g.setColor(aa.threshold.colour);
- y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
+ fastPaint(((int[]) evt.getNewValue())[0]
+ - ((int[]) evt.getOldValue())[0]);
}
- }
-
- // used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,
- int sRes, int eRes)
- {
- eRes = Math.min(eRes, aa.annotations.length);
- g.setColor(Color.white);
- g.fillRect(0, 0, width, y);
- g.setColor(new Color(0, 0, 180));
-
- int x = 0, height;
-
- for (int j = sRes; j < eRes; j++)
+ else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
{
- if (aa.annotations[j].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(aa.annotations[j].colour);
-
- height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
- if (height > y)
- {
- height = y;
- }
- g.fillRect(x, y - height, av.charWidth, height);
- x += av.charWidth;
+ repaint();
}
}
}
git://source.jalview.org / jalview.git / blobdiff