/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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 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.
*
- * 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 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.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
int imgWidth = 0;
boolean fastPaint = false;
- //Used For mouse Dragging and resizing graphs
+
+ // Used For mouse Dragging and resizing graphs
int graphStretch = -1;
int graphStretchY = -1;
-
- boolean mouseDragging=false;
-
+
+ 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);
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- ap.alabels.setScrollOffset(-evt.getValue());
}
/**
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * 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())
return;
}
- int height = 0;
+ int height = -scrollOffset;
activeRow = -1;
for (int i = 0; i < aa.length; i++)
{
activeRow = i;
}
- else if (aa[i].graph > 0)
+ else if (aa[i].graph > 0)
{
// Stretch Graph
graphStretch = i;
graphStretchY = evt.getY();
}
-
break;
}
graphStretch = -1;
graphStretchY = -1;
mouseDragging = false;
+ if (needValidating)
+ {
+ ap.validate();
+ needValidating = false;
+ }
ap.scalePanel.mouseReleased(evt);
}
{
}
+ boolean needValidating = false;
+
public void mouseDragged(MouseEvent evt)
{
if (graphStretch > -1)
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
- adjustPanelHeight();
+ calcPanelHeight();
+ needValidating = true;
ap.paintAlignment(true);
}
else
}
int row = -1;
- int height = 0;
+ int height = -scrollOffset;
for (int i = 0; i < aa.length; i++)
{
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;
}
public void paint(Graphics g)
{
-
- imgWidth = getSize().width;
+ Dimension d = getSize();
+ imgWidth = d.width;
// (av.endRes - av.startRes + 1) * av.charWidth;
-
- if (image == null || imgWidth != image.getWidth(this))
+ 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();
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startRes
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endRes
- * DOCUMENT ME!
+ * 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);
}
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
+ g.translate(0, -scrollOffset);
int x = 0;
int y = 0;
int column = 0;
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];
-
+ 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++)
{
{
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 (v == column)
{
- g
- .fillRect(x * av.charWidth, y, av.charWidth,
- av.charHeight);
+ g.fillRect(x * av.charWidth, y, av.charWidth, av.charHeight);
}
}
}
&& (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 (centreColLabels || scaleColLabel)
+ {
+ fmWidth = (float) fm.charsWidth(
+ row.annotations[column].displayCharacter.toCharArray(),
+ 0, row.annotations[column].displayCharacter.length());
+
+ 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
+ || (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)
x1 += av.charWidth / 2;
}
- if (row.annotations[column] == null
+ if (!validRes || row.annotations[column] == null
|| row.annotations[column].secondaryStructure != 'H')
{
g.fillArc((x * av.charWidth) - av.charWidth, y + 4
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);
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
x1 += av.charWidth / 2;
}
}
}
- if (row.graph > 0)
+ if (row.graph > 0 && row.graphHeight > 0)
{
if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
y += aa[i].height;
}
}
+ g.translate(0, +scrollOffset);
}
public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
}
if (aa.annotations[column] == null) // || coaa.annotations[column - 1] ==
- // null)
+ // null)
{
x++;
continue;
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;
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)
{
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++;
}
}
+ 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)
x += av.charWidth;
}
}
+
+ int scrollOffset = 0;
+
+ public void setScrollOffset(int value)
+ {
+ scrollOffset = value;
+ repaint();
+ }
}
git://source.jalview.org / jalview.git / blobdiff