--- /dev/null
+Normalised logo feature todo
+
+* transfer and update calcs in applet
+* add flags for normalised logo display to AnnotationFile and Jalview Project
+* add parameter for applet
+* add preference for application
+* consider rationalising flag model for N types of consensus/logo calculation methods
+
}
;
jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 1;
+ rtnval[0] = 2;
+ rtnval[1]=0;
for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
{
if (((char[]) ca[c])[0] != '-')
{
rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
- rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ rtnval[rtnval[0]] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
+ rtnval[1]+=rtnval[rtnval[0]++];
}
}
return rtnval;
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
- int[] rtnval = new int[51]; // 2*(5*5)+1
+ int[] rtnval = new int[52]; // 2*(5*5)+2
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
}
jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 1;
+ rtnval[0] = 2;
+ rtnval[1] = 0;
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)
{
rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
- rtnval[rtnval[0]++] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ rtnval[rtnval[0]] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
+ rtnval[1]+=rtnval[rtnval[0]++];
}
}
* histogram.</li>
* <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
* logo.</li>
+ * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.</li>
* <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
* </li>
* consensus calculation property
*/
private boolean showSequenceLogo = false;
+ /**
+ * flag indicating if logo should be rendered normalised
+ */
+ private boolean normaliseSequenceLogo;
+
/**
* @return the includeAllConsSymbols
{
return showConsensusHistogram;
}
+
+ /**
+ * set flag indicating if logo should be normalised when rendered
+ * @param norm
+ */
+ public void setNormaliseSequenceLogo(boolean norm)
+ {
+ normaliseSequenceLogo=norm;
+ }
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
}
showGroupConservation.setSelected(av.showGroupConservation);
showConsensusHistogram.setSelected(av.showConsensusHistogram);
showSequenceLogo.setSelected(av.showSequenceLogo);
+ normaliseSequenceLogo.setSelected(av.normaliseSequenceLogo);
+
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
viewport.setShowSequenceLogo(showSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
-
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+ normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
// TODO: add menu option action that nulls or creates consensus object
// depending on if the user wants to see the annotation or not in a
* should consensus profile be rendered by default
*/
public boolean showSequenceLogo = false;
-
+ /**
+ * should consensus profile be rendered normalised to row height
+ */
+ public boolean normaliseSequenceLogo = false;
/**
* should consensus histograms be rendered by default
*/
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
+
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
}
boolean cons = av.isShowGroupConsensus();
boolean showprf = av.isShowSequenceLogo();
boolean showConsHist = av.isShowConsensusHistogram();
+ boolean normLogo = av.isNormaliseSequenceLogo();
boolean sortg = true;
// set defaults for this group's conservation/consensus
sg.setshowSequenceLogo(showprf);
sg.setShowConsensusHistogram(showConsHist);
+ sg.setNormaliseSequenceLogo(normLogo);
}
if (conv)
{
}
});
pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ "Normalise Group Logo",
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cproflnorm);
}
else
{
// can be
// updated.
av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
// can be
// updated.
av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ "Normalise Logo", av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofnorm);
}
final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
consclipbrd.addActionListener(this);
int column;
int aaMax = aa.annotations.length - 1;
- boolean renderHistogram = true, renderProfile = true;
- if (aa.autoCalculated && aa.label.startsWith("Consensus"))
+ boolean renderHistogram = true, renderProfile = true, normaliseProfile=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();
+ normaliseProfile= aa.groupRef.isNormaliseSequenceLogo();
}
else
{
renderHistogram = av.isShowConsensusHistogram();
renderProfile = av.isShowSequenceLogo();
+ normaliseProfile= av.isNormaliseSequenceLogo();
}
}
while (x < eRes - sRes)
if (profl != null)
{
- int ht = y1, htn = y2 - y1;// aa.graphHeight;
+ float ht = normaliseProfile ? y-aa.graphHeight : y1;
+ double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight;
float wdth;
double ht2 = 0;
char[] dc;
/**
- * profl.length == 51 indicates that the profile of a secondary
+ * profl.length == 52 indicates that the profile of a secondary
* structure conservation row was accesed.
* Therefore dc gets length 2, to have space for a basepair instead of
* just a single nucleotide
*/
- if (profl.length == 51)
+ if (profl.length == 52)
{
dc = new char[2];
}
{
dc = new char[1];
}
-
- LineMetrics lm;
- for (int c = 1; profl != null && c < profl[0];)
+ LineMetrics lm=g.getFontMetrics(ofont).getLineMetrics("Q", g);
+ double scale = 1f/(normaliseProfile ? profl[1] : 100f);
+ float ofontHeight = 1f/lm.getAscent();// magnify to fill box
+ double scl=0.0;
+ for (int c = 2; profl != null && c < profl[0];)
{
dc[0] = (char) profl[c++];
wdth = av.charWidth;
wdth /= (float) fm.charsWidth(dc, 0, dc.length);
-
- if (c > 2)
- {
- ht += (int) ht2;
- }
+
+ ht += scl;
{
// 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 {
+ scl=((double)htn)*scale* ((double) profl[c++]);
+ lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics().getFontRenderContext());
g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
- / av.charHeight)));
+ wdth, scl/lm.getAscent())));
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));
// System.out.println(dc[0]);
-
+ // Debug - render boxes around characters
+ // g.setColor(Color.red);
+ // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, (int)(scl));
+ // g.setColor(profcolour.findColour(dc[0]).darker());
+ g.setColor(profcolour.findColour(dc[0]));
+ // (av.globalColourScheme!=null)
g.drawChars(dc, 0, dc.length, x * av.charWidth,
- (int) (ht + lm.getHeight()));
-
+ (int) (ht + (scl-lm.getDescent()-lm.getBaselineOffsets()[lm.getBaselineIndex()])));
// ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
}
}
protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
private JMenuItem grpsFromSelection = new JMenuItem();
}
});
+ normaliseSequenceLogo.setText("Normalise Consensus Logo");
+ normaliseSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ normaliseSequenceLogo_actionPerformed(e);
+ }
+
+ });
applyAutoAnnotationSettings.setText("Apply to all groups");
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normaliseSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
//selectMenu.add(listenToViewSelections);
}
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
git://source.jalview.org / jalview.git / commitdiff