/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 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 jalview.datamodel.*;
+import jalview.schemes.ColourSchemeI;
public class AnnotationPanel extends Panel implements AdjustmentListener,
ActionListener, MouseListener, MouseMotionListener
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;
* 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())
{
activeRow = i;
}
+ else if (aa[i].graph > 0)
+ {
+ // Stretch Graph
+ graphStretch = i;
+ graphStretchY = evt.getY();
+ }
break;
}
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();
+ adjustPanelHeight();
+ needValidating=true;
+ ap.paintAlignment(true);
+ }
+ else
+ {
+ ap.scalePanel.mouseDragged(evt);
+ }
}
public void mouseMoved(MouseEvent evt)
height += aa[i].height;
}
}
- else
+ if (height==0)
{
height = 20;
}
-
this.setSize(getSize().width, height);
-
repaint();
return height;
* 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);
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
{
&& (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 (row.graph > 0)
+ if (row.graph > 0 && row.graphHeight > 0)
{
if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
}
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;
+ /*
+ * Logos are disabled for 2.5 release : Bug # 0060064 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)
{
column = sRes + x;
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);
- }
- else
- {
- g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
+ 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);
+ }
}
-
+ // draw profile if available
+ // Disabled for 2.5 release: see bug #0060064
+ /**
+ * if (aa.annotations[column].value!=0 && renderProfile) { 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++;
}
}
}
+ /*
+ * Disabled for 2.5 release - see bug #0060064 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)
git://source.jalview.org / jalview.git / blobdiff