/*
- * 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
- * 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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
+ * 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/>.
*/
-
package jalview.appletgui;
import java.util.*;
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.schemes.ColourSchemeI;
-public class AnnotationPanel
- extends Panel
- implements AdjustmentListener, ActionListener, MouseListener, MouseMotionListener
+public class AnnotationPanel extends Panel implements AdjustmentListener,
+ ActionListener, MouseListener, MouseMotionListener
{
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();
-
+
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;
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 );
}
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- ap.alabels.setScrollOffset( -evt.getValue());
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
Annotation[] anot = aa[activeRow].annotations;
if (anot.length < av.getColumnSelection().getMax())
String label = "";
if (av.colSel != null && av.colSel.size() > 0
- && anot[av.colSel.getMin()] != null)
+ && anot[av.colSel.getMin()] != null)
label = anot[av.getColumnSelection().getMin()].displayCharacter;
-
if (evt.getActionCommand().equals(REMOVE))
{
for (int i = 0; i < av.getColumnSelection().size(); i++)
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.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();
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.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";
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
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;
public void mousePressed(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- if (aa == null)
- {
- return;
- }
-
- int height = 0;
- activeRow = -1;
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+ int height = -scrollOffset;
+ activeRow = -1;
- for (int i = 0; i < aa.length; i++)
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
{
- if (aa[i].visible)
- {
- height += aa[i].height;
- }
-
- if (evt.getY() < height)
- {
- if (aa[i].editable)
- {
- activeRow = i;
- }
-
- break;
- }
+ height += aa[i].height;
}
- if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
- InputEvent.BUTTON3_MASK && activeRow != -1)
+ if (evt.getY() < height)
{
- if (av.getColumnSelection() == null)
+ if (aa[i].editable)
{
- return;
+ activeRow = i;
+ }
+ else if (aa[i].graph > 0)
+ {
+ // Stretch Graph
+ graphStretch = i;
+ graphStretchY = evt.getY();
}
- 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);
- 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());
-
- return;
+ break;
}
+ }
- if (aa == null)
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+ && activeRow != -1)
+ {
+ if (av.getColumnSelection() == null)
{
return;
}
- ap.scalePanel.mousePressed(evt);
+ 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);
+ 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());
+
+ return;
+ }
+
+ if (aa == null)
+ {
+ return;
+ }
+
+ ap.scalePanel.mousePressed(evt);
}
public void mouseReleased(MouseEvent evt)
{
+ graphStretch = -1;
+ graphStretchY = -1;
+ mouseDragging = false;
+ if (needValidating)
+ {
+ ap.validate();
+ needValidating = false;
+ }
ap.scalePanel.mouseReleased(evt);
}
public void mouseClicked(MouseEvent evt)
- {}
+ {
+ }
+
+ boolean needValidating = false;
public void mouseDragged(MouseEvent evt)
{
- ap.scalePanel.mouseDragged(evt);
+ if (graphStretch > -1)
+ {
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
+ if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ {
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ }
+ graphStretchY = evt.getY();
+ calcPanelHeight();
+ needValidating = true;
+ ap.paintAlignment(true);
+ }
+ else
+ {
+ ap.scalePanel.mouseDragged(evt);
+ }
}
public void mouseMoved(MouseEvent evt)
}
int row = -1;
- int height = 0;
+ int height = -scrollOffset;
for (int i = 0; i < aa.length; i++)
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
- if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
+ if (row > -1 && res < aa[row].annotations.length
+ && aa[row].annotations[res] != null)
{
StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
if (aa[row].annotations[res].description != null)
ap.alignFrame.statusBar.setText(text.toString());
}
}
+
public void mouseEntered(MouseEvent evt)
{
ap.scalePanel.mouseEntered(evt);
}
+
public void mouseExited(MouseEvent evt)
{
ap.scalePanel.mouseExited(evt);
}
-
public int adjustPanelHeight()
{
+ return adjustPanelHeight(true);
+ }
+
+ public int adjustPanelHeight(boolean repaint)
+ {
+ int height = calcPanelHeight();
+ this.setSize(new Dimension(getSize().width, height));
+ if (repaint)
+ {
+ repaint();
+ }
+ return height;
+ }
+ /**
+ * 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;
height += aa[i].height;
}
}
- else
+ if (height == 0)
{
height = 20;
}
- this.setSize(getSize().width, height);
-
- repaint();
-
return height;
}
activeRes.addElement(String.valueOf(i));
}
-
public void update(Graphics g)
{
paint(g);
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();
public void fastPaint(int horizontal)
{
- if (horizontal == 0
- || av.alignment.getAlignmentAnnotation() == null
- || av.alignment.getAlignmentAnnotation().length < 1
- )
+ if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null
+ || av.alignment.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.charWidth, 0);
int sr = av.startRes, er = av.endRes + 1, transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
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);
fm = g.getFontMetrics();
}
- if ( (av.alignment.getAlignmentAnnotation() == null) ||
- (av.alignment.getAlignmentAnnotation().length < 1))
+ if ((av.alignment.getAlignmentAnnotation() == null)
+ || (av.alignment.getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getSize().width, getSize().height);
}
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
+ g.translate(0, -scrollOffset);
int x = 0;
int y = 0;
int column = 0;
int lastSSX;
int iconOffset = av.charHeight / 2;
boolean validRes = false;
-
+ boolean validEnd = false;
+ boolean labelAllCols = false;
+ boolean centreColLabels, centreColLabelsDef = av
+ .getCentreColumnLabels();
+ boolean scaleColLabel = false;
boolean[] graphGroupDrawn = new boolean[aa.length];
-
- //\u03B2 \u03B1
+ int charOffset = 0; // offset for a label
+ float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
+ // column.
+ // \u03B2 \u03B1
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
{
continue;
}
-
+ centreColLabels = row.centreColLabels || centreColLabelsDef;
+ labelAllCols = row.showAllColLabels;
+ scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
if (row.hasText)
{
+ iconOffset = av.charHeight - fm.getDescent();
y -= av.charHeight;
}
}
-
- if (row.hasText)
+ // TODO: else is the logic used in application, applet had no 'else'
+ else if (row.hasText)
{
- iconOffset = av.charHeight / 2;
+ iconOffset = av.charHeight - fm.getDescent();
+
}
else
{
{
if (av.hasHiddenColumns)
{
- column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+ column = av.getColumnSelection().adjustForHiddenColumns(
+ startRes + x);
if (column > row.annotations.length - 1)
{
break;
column = startRes + x;
}
- if ( (row.annotations.length <= column) ||
- (row.annotations[column] == null))
+ if ((row.annotations.length <= column)
+ || (row.annotations[column] == null))
{
validRes = false;
}
if (v == column)
{
- g.fillRect(x * av.charWidth, y,
- av.charWidth, av.charHeight);
+ g.fillRect(x * av.charWidth, y, av.charWidth, av.charHeight);
}
}
}
}
+ if (av.validCharWidth
+ && validRes
+ && (row.annotations[column].displayCharacter != null && row.annotations[column].displayCharacter
+ .length() > 0))
+ {
+ if (centreColLabels || scaleColLabel)
+ {
+ fmWidth = (float) fm.charsWidth(
+ row.annotations[column].displayCharacter.toCharArray(),
+ 0, row.annotations[column].displayCharacter.length());
- if (av.validCharWidth && validRes &&
- (row.annotations[column].displayCharacter!=null && row.annotations[column].displayCharacter.length() > 0))
- {
- int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth -
- fm.charsWidth(row.annotations[column].
- displayCharacter.toCharArray(),0,
- row.annotations[column].
- displayCharacter.length())) / 2)
- : (av.charWidth - fm.charWidth(row.annotations[column].
- displayCharacter.charAt(0))) / 2;
+ if (scaleColLabel)
+ {
+ // justify the label and scale to fit in column
+ if (fmWidth > av.charWidth)
+ {
+ // scale only if the current font isn't already small enough
+ fmScaling = av.charWidth;
+ fmScaling /= fmWidth;
+ // not 1.1 // g.setFont(new
+ // Font(ofont,AffineTransform.getScaleInstance(fmScaling,
+ // 1.0)));
+ // and update the label's width to reflect the scaling.
+ fmWidth = av.charWidth;
+ }
+ }
+ }
+ else
+ {
+ fmWidth = (float) fm
+ .charWidth(row.annotations[column].displayCharacter
+ .charAt(0));
+ }
+ charOffset = (int) ((av.charWidth - fmWidth) / 2f);
if (row.annotations[column].colour == null)
g.setColor(Color.black);
if (column == 0 || row.graph > 0)
{
g.drawString(row.annotations[column].displayCharacter,
- (x * av.charWidth) + charOffset,
- y + iconOffset + 3);
+ (x * av.charWidth) + charOffset, y + iconOffset + 3); // +
+ // 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 == ' ')))
+ else if (row.annotations[column - 1] == null
+ || (labelAllCols
+ || !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);
+ (x * av.charWidth) + charOffset, y + iconOffset + 3); // +3?
}
+ g.setFont(ofont);
}
if (row.hasIcons)
{
- if (!validRes ||
- (row.annotations[column].secondaryStructure != lastSS))
+ 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);
+ 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;
+ }
- 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);
+ int sCol = (lastSSX / av.charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * av.charWidth);
- break;
+ 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;
+ }
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
+ if (!validRes || 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;
+ }
- break;
+ 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)
if (column >= row.annotations.length)
{
column = row.annotations.length - 1;
+ validEnd = false;
+ }
+ else
+ {
+ validEnd = true;
}
- // x ++;
+ // 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;
- }
+ 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);
+ 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 (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;
- }
+ 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);
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
- break;
+ break;
- case 'E':
- g.setColor(SHEET_COLOUR);
+ 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;
+ if (!validEnd || 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);
- }
+ default:
+ g.setColor(Color.gray);
+ if (!av.wrapAlignment || endRes == av.endRes)
+ {
+ g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+ - lastSSX, 2);
+ }
- break;
+ break;
}
}
- if (row.graph > 0)
+ if (row.graph > 0 && row.graphHeight > 0)
{
if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
{
if (aa[gg].graphGroup == row.graphGroup)
{
- drawLineGraph(g, aa[gg], startRes, endRes, y,
- groupmin, groupmax,
- row.graphHeight);
+ drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
+ groupmax, row.graphHeight);
}
}
}
else
{
- drawLineGraph(g, row, startRes, endRes,
- y, row.graphMin, row.graphMax, row.graphHeight);
+ 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);
+ drawBarGraph(g, row, startRes, endRes, row.graphMin,
+ row.graphMax, y);
}
}
y += aa[i].height;
}
}
+ g.translate(0, +scrollOffset);
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- int y,
- float min, float max,
- int graphHeight)
+ public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+ int eRes, int y, float min, float max, int graphHeight)
{
if (sRes > aa.annotations.length)
{
int x = 0;
- //Adjustment for fastpaint to left
+ // Adjustment for fastpaint to left
if (eRes < av.endRes)
{
eRes++;
int y1 = y, y2 = y;
float range = max - min;
- ////Draw origin
+ // //Draw origin
if (min < 0)
{
- y2 = y - (int) ( (0 - min / range) * graphHeight);
+ y2 = y - (int) ((0 - min / range) * graphHeight);
}
g.setColor(Color.gray);
{
break;
}
-
- if (aa.annotations[column] == null) // || coaa.annotations[column - 1] == null)
+
+ if (aa.annotations[column] == null) // || coaa.annotations[column - 1] ==
+ // null)
{
x++;
continue;
g.setColor(Color.black);
else
g.setColor(aa.annotations[column].colour);
- if (column==0 || aa.annotations[column-1]==null)
+ 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].value - min) / range) * graphHeight);
- } else {
- y1 = y -
- (int) ( ( (aa.annotations[column-1].value - min) / range) * graphHeight);
+ y1 = y
+ - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
}
- y2 = y -
- (int) ( ( (aa.annotations[column].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);
+ g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth
+ + av.charWidth / 2, y2);
x++;
}
{
g.setColor(aa.threshold.colour);
- y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
+ y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- float min, float max,
- int y)
+ public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+ int eRes, float min, float max, int y)
{
+ ColourSchemeI profcolour = av.getGlobalColourScheme();
+ if (profcolour == null)
+ {
+ profcolour = new jalview.schemes.ZappoColourScheme();
+ }
if (sRes > aa.annotations.length)
{
return;
}
-
+ Font ofont = g.getFont();
eRes = Math.min(eRes, aa.annotations.length);
int x = 0, y1 = y, y2 = y;
if (min < 0)
{
- y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
+ y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
}
g.setColor(Color.gray);
int column;
int aaMax = aa.annotations.length - 1;
+ boolean renderHistogram = true, renderProfile = false;
+ if (aa.autoCalculated && aa.label.startsWith("Consensus"))
+ { // TODO: generalise this to have render styles for consensus/profile data
+ if (aa.groupRef != null)
+ {
+ renderHistogram = aa.groupRef.isShowConsensusHistogram();
+ renderProfile = aa.groupRef.isShowSequenceLogo();
+ }
+ else
+ {
+ renderHistogram = av.isShowConsensusHistogram();
+ renderProfile = av.isShowSequenceLogo();
+ }
+ }
while (x < eRes - sRes)
{
else
g.setColor(aa.annotations[column].colour);
- y1 = y -
- (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
+ y1 = y
+ - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
- if (y1 - y2 > 0)
+ if (renderHistogram)
{
- g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
+ 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);
+ }
}
- else
+ // draw profile if available
+ if (aa.annotations[column].value != 0 && renderProfile)
{
- g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
+ int profl[] = getProfileFor(aa, column);
+ int ht = y1, htn = y2 - y1;// aa.graphHeight;
+ float wdth;
+ double ht2 = 0;
+ char[] dc = new char[1];
+ LineMetrics lm;
+ for (int c = 1; profl != null && c < profl[0];)
+ {
+ dc[0] = (char) profl[c++];
+ wdth = av.charWidth;
+ wdth /= (float) fm.charsWidth(dc, 0, 1);
+
+ if (c > 2)
+ {
+ ht += (int) ht2;
+ }
+ { // not java 1.1 compatible: Bug # 0060064
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
+ / av.charHeight)));
+ lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
+ g.setColor(profcolour.findColour(dc[0]));
+ g.drawChars(dc, 0, 1, x * av.charWidth,
+ (int) (ht + lm.getHeight()));
+ }
+ }
+ g.setFont(ofont);
}
x++;
if (aa.threshold != null)
{
g.setColor(aa.threshold.colour);
- y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
+ y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
}
}
+ private int[] getProfileFor(AlignmentAnnotation aa, int column)
+ {
+ // if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
+ if (aa.groupRef != null && aa.groupRef.consensusData != null)
+ {
+ // && aa.groupRef.isShowSequenceLogo()) {
+ return AAFrequency.extractProfile(aa.groupRef.consensusData[column],
+ aa.groupRef.getIgnoreGapsConsensus());
+ }
+ // TODO extend annotation row to enable dynamic and static profile data to
+ // be stored
+ if (aa.groupRef == null && aa.sequenceRef == null)
+ // && av.isShowSequenceLogo())
+ {
+ return AAFrequency.extractProfile(av.hconsensus[column],
+ av.getIgnoreGapsConsensus());
+ }
+ // }
+ return null;
+ }
+
// used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,
- int sRes, int eRes)
+ 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);
else
g.setColor(aa.annotations[j].colour);
- height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+ height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
if (height > y)
{
height = y;
x += av.charWidth;
}
}
+
+ int scrollOffset = 0;
+
+ public void setScrollOffset(int value)
+ {
+ scrollOffset = value;
+ repaint();
+ }
}
git://source.jalview.org / jalview.git / blobdiff