import java.awt.*;
import java.awt.event.*;
-
import jalview.datamodel.*;
+import jalview.schemes.ColourSchemeI;
public class AnnotationPanel extends Panel implements AdjustmentListener,
ActionListener, MouseListener, MouseMotionListener
*/
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);
else
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
+ || (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)
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 (renderHistogram)
+ {
if (y1 - y2 > 0)
{
g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
{
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