/*
- * 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 2.5)
+ * 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.gui;
* Creates a new AnnotationPanel object.
*
* @param ap
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public AnnotationPanel(AlignmentPanel ap)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
}
/**
- * Calculates the height of the annotation displayed in the annotation panel.
- * Callers should normally call the ap.adjustAnnotationHeight method to ensure all
- * annotation associated components are updated correctly.
- *
+ * Calculates the height of the annotation displayed in the annotation panel.
+ * Callers should normally call the ap.adjustAnnotationHeight method to ensure
+ * all annotation associated components are updated correctly.
+ *
*/
public int adjustPanelHeight()
{
{
for (int i = 0; i < aa.length; i++)
{
- if (aa[i]==null)
+ if (aa[i] == null)
{
System.err.println("Null annotation row: ignoring.");
continue;
}
this.setPreferredSize(new Dimension(1, height));
- if (ap!=null)
+ if (ap != null)
{
// revalidate only when the alignment panel is fully constructed
ap.validate();
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
- // null exceptions
- // aren't raised
- // elsewhere.
+ // null exceptions
+ // aren't raised
+ // elsewhere.
}
else
{
|| label2.equals(LABEL))
{
tlabel = anot[index].description;
- if (tlabel == null || tlabel.length()<1)
+ if (tlabel == null || tlabel.length() < 1)
{
if (label2.equals(HELIX) || label2.equals(SHEET))
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
- if (row > -1 && aa[row].annotations != null
+ if (row > -1 && aa[row].annotations != null
&& res < (int) aa[row].annotations.length)
{
if (aa[row].graphGroup > -1)
}
}
else if (aa[row].annotations[res] != null
- && aa[row].annotations[res].description != null && aa[row].annotations[res].description.length()>0)
+ && aa[row].annotations[res].description != null
+ && aa[row].annotations[res].description.length() > 0)
{
this.setToolTipText(aa[row].annotations[res].description);
}
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
* non-Thread safe repaint
*
* @param horizontal
- * repaint with horizontal shift in alignment
+ * repaint with horizontal shift in alignment
*/
public void fastPaint(int horizontal)
{
* 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)
{
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
- boolean centreColLabels,centreColLabelsDef = av.getCentreColumnLabels();
- boolean scaleColLabel=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.
+ float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
+ // column.
Font ofont = g.getFont();
// \u03B2 \u03B1
for (int i = 0; i < aa.length; i++)
&& 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());
+ fmWidth = (float) fm.charsWidth(
+ row.annotations[column].displayCharacter.toCharArray(),
+ 0, row.annotations[column].displayCharacter.length());
- if ( scaleColLabel ) {
+ if (scaleColLabel)
+ {
// justify the label and scale to fit in column
- if (fmWidth > av.charWidth) {
+ if (fmWidth > av.charWidth)
+ {
// scale only if the current font isn't already small enough
fmScaling = av.charWidth;
fmScaling /= fmWidth;
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(fmScaling, 1.0)));
+ g.setFont(ofont.deriveFont(AffineTransform
+ .getScaleInstance(fmScaling, 1.0)));
// and update the label's width to reflect the scaling.
fmWidth = av.charWidth;
}
}
- } else {
+ }
+ else
+ {
fmWidth = (float) fm
- .charWidth(row.annotations[column].displayCharacter.charAt(0));
+ .charWidth(row.annotations[column].displayCharacter
+ .charAt(0));
}
- charOffset = (int) ((av.charWidth - fmWidth) / 2f);
-
+ charOffset = (int) ((av.charWidth - fmWidth) / 2f);
+
if (row.annotations[column].colour == null)
g.setColor(Color.black);
else
(x * av.charWidth) + charOffset, y + iconOffset);
}
else if (row.annotations[column - 1] == null
- || (labelAllCols||!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
int eRes, float min, float max, int y)
{
ColourSchemeI profcolour = av.getGlobalColourScheme();
- if (profcolour==null)
+ if (profcolour == null)
{
profcolour = new jalview.schemes.ZappoColourScheme();
}
int column;
int aaMax = aa.annotations.length - 1;
boolean renderHistogram = true, renderProfile = true;
- if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
- // TODO: generalise this to have render styles for consensus/profile data
- if (aa.groupRef!=null)
+ 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 {
+ }
+ else
+ {
renderHistogram = av.isShowConsensusHistogram();
renderProfile = av.isShowSequenceLogo();
}
- (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
if (renderHistogram)
- {
- 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);
- }
+ 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
- if (aa.annotations[column].value!=0 && renderProfile)
+ 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];)
+ 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)
{
- dc[0] = (char) profl[c++];
- wdth = av.charWidth;
- wdth/=(float) fm
- .charsWidth(dc,0,1);
-
- if (c>2)
- {
- ht+=(int)ht2;
- }
- {
- //if (aa.annotations[column].value==0) {
- // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, (ht2=(aa.graphHeight*0.1/av.charHeight)))));
- // ht = y2-(int)ht2;
- //} else {
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight)));
- lm = g.getFontMetrics().getLineMetrics(dc,0,1, g);
- //htn -=ht2;
- //}
- g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) ? );// try to get a colourscheme for the group(aa.groupRef.cs==null) ? av.textColour2 : cs.findColour(dc));
- g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight()));
- // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
- }
+ ht += (int) ht2;
}
- g.setFont(ofont);
+ {
+ // if (aa.annotations[column].value==0) {
+ // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
+ // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
+ // ht = y2-(int)ht2;
+ // } else {
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
+ / av.charHeight)));
+ lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
+ // htn -=ht2;
+ // }
+ g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null)
+ // ? );// try to get a
+ // colourscheme for the
+ // group(aa.groupRef.cs==null)
+ // ? av.textColour2 :
+ // cs.findColour(dc));
+ g.drawChars(dc, 0, 1, x * av.charWidth, (int) (ht + lm
+ .getHeight()));
+ // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
+ }
+ }
+ 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())
+ if (aa.autoCalculated && aa.label.startsWith("Consensus"))
{
- return AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
- }
+ 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;
}
git://source.jalview.org / jalview.git / blobdiff